Citrus Sinensis ID: 041190

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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-
Protein Sequence
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTATARLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHccccccccccccccccccccccccHHHHHHHHHHHccccccccccEEEEEEEccccccHHHHHHHHHccHHHHccccccEEEEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHccccEEEEEEccccccccccHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccccHHccccccccccccccccEccccEEcccHHHHHHHHHHHccccccccccEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccEEEEEEEccccccHHHHHHHHcHccc
Coil and Loop (DISEMBL)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDdaeekqitkplTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTATARLRygrvqerplstpslvdeeevygrekdKEVIVGLLlgddlnsgpgfsvipitgmgglgkTTLAQLVFNDAGVKKYFSFRACayvsedfdavGVTKVILQAAagsadvndLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTnlckpfka
Flexible Loop (DISEMBL)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVlddaeekqitkpltkkwlgKLQNLAYDAEDMLDEFATEAFRRKLLLleqadrqptatarlrygrvqerplstpslvdeeevygreKDKEVIVGLLLgddlnsgpGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA
Low Complexity Region (SEG)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTATARLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDlnllqlqlenqlknkkfllVLDDMWSENYDVWTNLCKPFKA
Disordered region (IsUnstruct)
*****EAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQ********************************Y***KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCK****
Disordered Region (DISOPRED)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKL***************************TPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG*****DLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA
Disordered Region (DISEMBL)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTATARLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA
Disordered Region (DISPRO)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQAD**********************SLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADxxxxxxxxxxxxxxxxxxxxxQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTATARLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA
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	261	2.2.26 [Sep-21-2011]
Q9LRR4	1054	Putative disease resistan	yes	no	0.988	0.244	0.350	4e-39
Q7XBQ9	970	Disease resistance protei	N/A	no	0.942	0.253	0.347	1e-35
Q7XA40	992	Putative disease resistan	N/A	no	0.938	0.246	0.336	2e-32
Q7XA42	979	Putative disease resistan	N/A	no	0.938	0.250	0.333	7e-31
Q7XA39	988	Putative disease resistan	N/A	no	0.942	0.248	0.317	7e-31
Q9LRR5	1424	Putative disease resistan	no	no	0.957	0.175	0.308	4e-26
Q9XIF0	906	Putative disease resistan	no	no	0.846	0.243	0.284	4e-15
Q9SX38	857	Putative disease resistan	no	no	0.934	0.284	0.28	5e-15
Q38834	852	Disease resistance RPP13-	no	no	0.919	0.281	0.253	2e-14
A7XGN8	910	Disease susceptibility pr	no	no	0.892	0.256	0.261	6e-14

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 106/302 (35%), Positives = 163/302 (53%), Gaps = 44/302 (14%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQ-LFARQEQIEADLKKWEELLVIIKVVLDDAEEKQ 59
           M+  GE  L   ++ L + L  E  +  F R+E  E  L++    L+ I  VL DAEEKQ
Sbjct: 1   MTGIGEMFLAAFLQALFQTLVSEPFRSFFKRRELNENLLERLSTALLTITAVLIDAEEKQ 60

Query: 60  ITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFR-------------RKLL---------- 96
           IT P+ +KW+ +L+++ Y AED LD+ ATEA R             R+L           
Sbjct: 61  ITNPVVEKWVNELRDVVYHAEDALDDIATEALRLNIGAESSSSNRLRQLRGRMSLGDFLD 120

Query: 97  -----LLEQADRQPTATARLRYGR-----------VQERPLSTPSLVDEEEVYGREKDKE 140
                L  + ++      RL   R           + ++ L T SLVDE EV+GR+ DK+
Sbjct: 121 GNSEHLETRLEKVTIRLERLASQRNILGLKELTAMIPKQRLPTTSLVDESEVFGRDDDKD 180

Query: 141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD 200
            I+  L+ ++     G +V+ I G+GG+GKTTL+QL++ND  V+ YF  +  A+VSE+FD
Sbjct: 181 EIMRFLIPEN-GKDNGITVVAIVGIGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFD 239

Query: 201 AVGVTKVILQAAAGS-ADVNDLNLLQLQLENQLKNK--KFLLVLDDMWSENYDVWTNLCK 257
              +TK + ++      +  DL++LQ++L+ +L      FLLVLDD+W+EN+  W  L +
Sbjct: 240 VFKITKKVYESVTSRPCEFTDLDVLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQ 299

Query: 258 PF 259
           PF
Sbjct: 300 PF 301

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 =  149 bits (377), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 97/279 (34%), Positives = 157/279 (56%), Gaps = 33/279 (11%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
            EA + V ++ L   L  E++ LF  Q++ +    +   +   I+ VL+DA+EKQ+    
Sbjct: 2   AEAFIQVLLDNLTSFLKGELVLLFGFQDEFQ----RLSSMFSTIQAVLEDAQEKQLNNKP 57

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEA-----------------FRRKL-LLLEQADRQPT 106
            + WL KL    Y+ +D+LDE+ T+A                 FR K+   ++Q  ++  
Sbjct: 58  LENWLQKLNAATYEVDDILDEYKTKATRFSQSEYGRYHPKVIPFRHKVGKRMDQVMKKLK 117

Query: 107 ATARLR-----YGRVQERPL---STPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFS 158
           A A  R     + ++ ER      T S++ E +VYGR+K+K+ IV +L+ ++++     S
Sbjct: 118 AIAEERKNFHLHEKIVERQAVRRETGSVLTEPQVYGRDKEKDEIVKILI-NNVSDAQHLS 176

Query: 159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADV 218
           V+PI GMGGLGKTTLAQ+VFND  V ++F  +    VSEDFD   + K I+++  G   +
Sbjct: 177 VLPILGMGGLGKTTLAQMVFNDQRVTEHFHSKIWICVSEDFDEKRLIKAIVESIEGRPLL 236

Query: 219 NDLNL--LQLQLENQLKNKKFLLVLDDMWSENYDVWTNL 255
            +++L  LQ +L+  L  K++LLVLDD+W+E+   W NL
Sbjct: 237 GEMDLAPLQKKLQELLNGKRYLLVLDDVWNEDQQKWANL 275

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 =  139 bits (349), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 94/279 (33%), Positives = 151/279 (54%), Gaps = 34/279 (12%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
            EA L V ++ L   +  E+  +F      E + KK   +  +I+ VL+DA+EKQ+    
Sbjct: 2   AEAFLQVLLDNLTFFIQGELGLVFG----FEKEFKKLSSMFSMIQAVLEDAQEKQLKYKA 57

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLL-------------------EQADRQP 105
            K WL KL   AY+ +D+LD+  TEA R K  +L                   E  ++  
Sbjct: 58  IKNWLQKLNVAAYEVDDILDDCKTEAARFKQAVLGRYHPRTITFCYKVGKRMKEMMEKLD 117

Query: 106 TATARLRYGRVQERPL-------STPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFS 158
                 R   + ER +        T  ++ E +VYGREK+++ IV +L+ ++++      
Sbjct: 118 AIAEERRNFHLDERIIERQAARRQTGFVLTEPKVYGREKEEDEIVKILI-NNVSYSEEVP 176

Query: 159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADV 218
           V+PI GMGGLGKTTLAQ+VFND  + ++F+ +    VS+DFD   + K I+++  G + +
Sbjct: 177 VLPILGMGGLGKTTLAQMVFNDQRITEHFNLKIWVCVSDDFDEKRLIKAIVESIEGKS-L 235

Query: 219 NDLNL--LQLQLENQLKNKKFLLVLDDMWSENYDVWTNL 255
            D++L  LQ +L+  L  K++ LVLDD+W+E+ + W NL
Sbjct: 236 GDMDLAPLQKKLQELLNGKRYFLVLDDVWNEDQEKWDNL 274

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 =  134 bits (337), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 93/279 (33%), Positives = 155/279 (55%), Gaps = 34/279 (12%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
            EA + V ++ L   L  E++ LF  Q++ +    +   +   I+ VL+DA+EKQ+    
Sbjct: 2   AEAFIQVVLDNLTSFLKGELVLLFGFQDEFQ----RLSSMFSTIQAVLEDAQEKQLNDKP 57

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEA-----------------FRRKL-LLLEQADRQPT 106
            + WL KL    Y+ +D+LDE+ T+A                 FR K+   ++Q  ++  
Sbjct: 58  LENWLQKLNAATYEVDDILDEYKTKATRFLQSEYGRYHPKVIPFRHKVGKRMDQVMKKLN 117

Query: 107 ATARLRYG-RVQERPLS-------TPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFS 158
           A A  R    +QE+ +        T S++ E +VYGR+K+K+ IV +L+ +  +     S
Sbjct: 118 AIAEERKKFHLQEKIIERQAATRETGSVLTEPQVYGRDKEKDEIVKILI-NTASDAQKLS 176

Query: 159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADV 218
           V+PI GMGGLGKTTL+Q+VFND  V + F  +    +S+DF+   + K I+++  G + +
Sbjct: 177 VLPILGMGGLGKTTLSQMVFNDQRVTERFYPKIWICISDDFNEKRLIKAIVESIEGKS-L 235

Query: 219 NDLNL--LQLQLENQLKNKKFLLVLDDMWSENYDVWTNL 255
           +D++L  LQ +L+  L  K++ LVLDD+W+E+   W NL
Sbjct: 236 SDMDLAPLQKKLQELLNGKRYFLVLDDVWNEDQHKWANL 274

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 =  134 bits (337), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 89/280 (31%), Positives = 145/280 (51%), Gaps = 34/280 (12%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
            EA L V +E L   +  +++ +F  +++ E    K   +   I+ VL DA+EKQ+    
Sbjct: 2   AEAFLQVLLENLTSFIGDKLVLIFGFEKECE----KLSSVFSTIQAVLQDAQEKQLKDKA 57

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEAFR----------------------RKLLLLEQAD 102
            + WL KL + AY+ +D+L E   EA R                      R   ++E+ D
Sbjct: 58  IENWLQKLNSAAYEVDDILGECKNEAIRFEQSRLGFYHPGIINFRHKIGRRMKEIMEKLD 117

Query: 103 RQPTATARLRY-GRVQERPLSTPS-----LVDEEEVYGREKDKEVIVGLLLGDDLNSGPG 156
                  +  +  ++ ER  +  +     ++ E +VYGR+K+++ IV +L+ +++N    
Sbjct: 118 AISEERRKFHFLEKITERQAAAATRETGFVLTEPKVYGRDKEEDEIVKILI-NNVNVAEE 176

Query: 157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL-QAAAGS 215
             V PI GMGGLGKTTLAQ++FND  V K+F+ +    VS+DFD   + K I+      S
Sbjct: 177 LPVFPIIGMGGLGKTTLAQMIFNDERVTKHFNPKIWVCVSDDFDEKRLIKTIIGNIERSS 236

Query: 216 ADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNL 255
             V DL   Q +L+  L  K++LLVLDD+W+++ + W  L
Sbjct: 237 PHVEDLASFQKKLQELLNGKRYLLVLDDVWNDDLEKWAKL 276

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 =  118 bits (296), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 90/292 (30%), Positives = 138/292 (47%), Gaps = 42/292 (14%)

Query: 9   LTVTVEMLVEKL--ALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTK 66
           L+    ++VE++  + E+++L  + +   A LK+ +  LV    VL DA+++       K
Sbjct: 6   LSSCANVMVERINTSQELVEL-CKGKSSSALLKRLKVALVTANPVLADADQRAEHVREVK 64

Query: 67  KWLGKLQNLAYDAEDMLDEFATEAFRRKLL------------------------------ 96
            WL  +++  + AED+LDE  TEA RR+++                              
Sbjct: 65  HWLTGIKDAFFQAEDILDELQTEALRRRVVAEAGGLGGLFQNLMAGREAIQKKIEPKMEK 124

Query: 97  ---LLEQADRQPTATARLRYGRVQE-----RPLSTPSLVDEEEVYGREKDKEVIVGLLLG 148
              LLE   +         Y   +E        S P  + +  + GR +DK  +V LLL 
Sbjct: 125 VVRLLEHHVKHIEVIGLKEYSETREPQWRQASRSRPDDLPQGRLVGRVEDKLALVNLLLS 184

Query: 149 DDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVI 208
           DD  S    +VI + GM G+GKTTL ++VFND  V ++F  +       +F+   VTK +
Sbjct: 185 DDEISIGKPAVISVVGMPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTVTKAV 244

Query: 209 LQAAAGSA-DVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF 259
           LQ    SA +  DL  LQ+QL+  L  K+FLLVLDD WSE+   W +    F
Sbjct: 245 LQDITSSAVNTEDLPSLQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAF 296

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 82.0 bits (201), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 125/264 (47%), Gaps = 43/264 (16%)

Query: 17  VEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLA 76
           VEKL   + Q + R + +E  + +  + L ++   L DA+ K+ T+ L +  L +++ + 
Sbjct: 15  VEKLWKLLSQEYERFQGVEEQITELRDDLKMLMAFLSDADAKKQTRALARNCLEEIKEIT 74

Query: 77  YDAEDMLDEFATEAF------------RRKLLLLEQADRQPTAT---------------- 108
           YDAED+++ F  +              RR++ L   +  +  +                 
Sbjct: 75  YDAEDIIEIFLLKGSVNMRSLACFPGGRREIALQITSISKRISKVIQVMQNLGIKSDIMD 134

Query: 109 -----ARLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPIT 163
                A+L   R      S+ S   E  + G EK+ E +V  L+G+D + G     + IT
Sbjct: 135 GVDSHAQLERKRELRHTFSSES---ESNLVGLEKNVEKLVEELVGNDSSHG-----VSIT 186

Query: 164 GMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDL-- 221
           G+GGLGKTTLA+ +F+   VK +F   A   VS++F    V K IL   +     +DL  
Sbjct: 187 GLGGLGKTTLARQIFDHDKVKSHFDGLAWVCVSQEFTRKDVWKTILGNLSPKYKDSDLPE 246

Query: 222 NLLQLQLENQLKNKKFLLVLDDMW 245
           + +Q +L   L+ KK L+V DD+W
Sbjct: 247 DDIQKKLFQLLETKKALIVFDDLW 270

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SX38|DRL4_ARATH Putative disease resistance protein At1g50180 OS=Arabidopsis thaliana GN=At1g50180 PE=3 SV=2

 Score = 81.6 bits (200), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 84/300 (28%), Positives = 134/300 (44%), Gaps = 56/300 (18%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
            EAI++VTV+    KL   +++       I   +K+ ++ L  +   L DA+EKQ     
Sbjct: 2   AEAIVSVTVQ----KLGQLLLEEPLFLFGIGDQVKQLQDELKRLNCFLKDADEKQHESER 57

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEA-----------FRRKLLLLEQADRQPTATARLR- 112
            + W+  ++  +YDAED+L+ F  +A            RR   +L +A    +  + +R 
Sbjct: 58  VRNWVAGIREASYDAEDILEAFFLKAESRKQKGMKRVLRRLACILNEAVSLHSVGSEIRE 117

Query: 113 --------------------YGR--------VQERPLSTPSLVDEEEVYGREKDKEVIVG 144
                                GR        ++E+  S P +V E  + G E+  E +V 
Sbjct: 118 ITSRLSKIAASMLDFGIKESMGREGLSLSDSLREQRQSFPYVV-EHNLVGLEQSLEKLVN 176

Query: 145 LLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGV 204
               D ++ G    V  I GMGGLGKTTLA+ +F+   V+++F   A  YVS+D     V
Sbjct: 177 ----DLVSGGEKLRVTSICGMGGLGKTTLAKQIFHHHKVRRHFDRFAWVYVSQDCRRRHV 232

Query: 205 TK-VILQAAAGSADVNDLNLLQLQLENQ----LKNKKFLLVLDDMWSENYDVWTNLCKPF 259
            + + L  +    +   L+L   QL  +    LK  K L+VLDD+W +  D W  L   F
Sbjct: 233 WQDIFLNLSYKDENQRILSLRDEQLGEELHRFLKRNKCLIVLDDIWGK--DAWDCLKHVF 290

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 = 79.7 bits (195), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 73/288 (25%), Positives = 130/288 (45%), Gaps = 48/288 (16%)

Query: 6   EAILTVTVEM---LVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITK 62
           +A++TV +E    ++E+    V     + E ++++LK  +  L        DAE ++ T 
Sbjct: 3   DAVVTVFLEKTLNILEEKGRTVSDYRKQLEDLQSELKYMQSFL-------KDAERQKRTN 55

Query: 63  PLTKKWLGKLQNLAYDAEDML------------DEFATEAFRRKL------LLLEQADRQ 104
              +  +  L+ L Y+AED+L            ++ ++ A+  +L      L  +++ R 
Sbjct: 56  ETLRTLVADLRELVYEAEDILVDCQLADGDDGNEQRSSNAWLSRLHPARVPLQYKKSKRL 115

Query: 105 PTATARLRYGRVQERP---LSTPSLV--------------DEEEVYGREKDKEVIVGLLL 147
                R+   + Q  P     TPS V              D  +V G E DK  I   L 
Sbjct: 116 QEINERITKIKSQVEPYFEFITPSNVGRDNGTDRWSSPVYDHTQVVGLEGDKRKIKEWLF 175

Query: 148 GDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV 207
             + +      ++   GMGGLGKTT+AQ VFND  ++  F  R    VS+ F    + + 
Sbjct: 176 RSNDSQ---LLIMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRS 232

Query: 208 ILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNL 255
           IL+    ++  +D+  L  +++  L  K++L+V+DD+W +N   W  +
Sbjct: 233 ILRNLGDASVGDDIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKI 280

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|A7XGN8|LOV1B_ARATH Disease susceptibility protein LOV1 OS=Arabidopsis thaliana GN=LOV1 PE=1 SV=1

 Score = 78.2 bits (191), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 126/287 (43%), Gaps = 54/287 (18%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
            E ++   V  L E L  E  +L    EQ++   ++   L  ++K    DA+ K+     
Sbjct: 2   AEGVVLFGVHKLWELLNRESARLNGIGEQVDGLKRQLGRLQSLLK----DADAKKHESER 57

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEAFRRK------------------------------ 94
            + +L  ++++ YDAED+++ F    FR K                              
Sbjct: 58  VRNFLEDVRDIVYDAEDIIESFLLNEFRTKEKGIKKHARRLACFLVDRRKFASDIKGITK 117

Query: 95  -----------LLLLEQADRQPTATARLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIV 143
                      L + E  D   + + + R  R Q+    T +   E ++ G E+  E + 
Sbjct: 118 KISEVIGGMKSLGIQEIIDGASSMSLQERQ-REQKEIRQTFANSSESDLVGVEQSVEALA 176

Query: 144 GLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVG 203
           G L+ +D        V+ I+GMGG+GKTTLA+ VF+   V+++F   A  +VS+ F    
Sbjct: 177 GHLVEND-----NIQVVSISGMGGIGKTTLARQVFHHDMVQRHFDGFAWVFVSQQFTQKH 231

Query: 204 VTKVI---LQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE 247
           V + I   LQ   G     D ++LQ +L   L+  ++L+VLDD+W E
Sbjct: 232 VWQRIWQELQPQNGDISHMDEHILQGKLFKLLETGRYLVVLDDVWKE 278

Confers susceptibility to the fungus Cochliobolus victoriae by conditioning victorin-dependent (victorin is a toxin synthesized by C.victoriae) induction of defense-associated proteins.

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	261
297742675	906	unnamed protein product [Vitis vinifera]	0.988	0.284	0.485	9e-64
359487182	2283	PREDICTED: putative disease resistance p	0.980	0.112	0.472	8e-63
147862409	1466	hypothetical protein VITISV_042289 [Viti	0.980	0.174	0.469	9e-63
147860511	1406	hypothetical protein VITISV_014536 [Viti	0.988	0.183	0.442	2e-62
359495024	1390	PREDICTED: putative disease resistance p	0.988	0.185	0.442	2e-62
359495026	2204	PREDICTED: uncharacterized protein LOC10	0.988	0.117	0.445	5e-62
359487176	1308	PREDICTED: putative disease resistance R	0.988	0.197	0.442	9e-62
147787628	1420	hypothetical protein VITISV_019639 [Viti	0.984	0.180	0.448	9e-60
359487180	1629	PREDICTED: putative disease resistance R	0.984	0.157	0.448	1e-59
255556671	1318	Disease resistance protein RPS2, putativ	0.988	0.195	0.442	1e-58

>gi|297742675|emb|CBI35128.3| unnamed protein product [Vitis vinifera]

 Score =  249 bits (636), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 134/276 (48%), Positives = 180/276 (65%), Gaps = 18/276 (6%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           M+  GEA L+ +++ LV+ LA   ++ FAR+EQ+ A+LKKWE +L+ I  VL DAEEKQ+
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTATA----------- 109
           T    + WL +L++LAYD ED+LD+FATEA RRKL+     D QP+ +            
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRKLI---TDDPQPSTSTISTQKGDLDLR 117

Query: 110 ---RLRYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMG 166
                R  R ++R   T  LV E  VYGRE DKE I+ +LL D+L       VIPI GMG
Sbjct: 118 ENVEGRSNRKRKRVPETTCLVVESRVYGRETDKEAILEVLLRDELVHDNEVCVIPIVGMG 177

Query: 167 GLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSA-DVNDLNLLQ 225
           G+GKTTLAQL ++D  VK +F  RA   VS+DFD + + K +LQ+ A  A ++NDLNLLQ
Sbjct: 178 GVGKTTLAQLAYHDDRVKNHFDLRAWVCVSDDFDVLRIAKTLLQSIASYAREINDLNLLQ 237

Query: 226 LQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA 261
           ++L+ +L  KKFLLVLDD+W+ENYD W  LC P +A
Sbjct: 238 VKLKEKLSGKKFLLVLDDVWNENYDKWDRLCTPLRA 273

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 =  246 bits (627), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 147/311 (47%), Positives = 184/311 (59%), Gaps = 55/311 (17%)

Query: 1    MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
            M+  GEAIL+   E L  KLA   +  FARQEQ+ A+LKKWE++L+ I  VLDDAEEKQ+
Sbjct: 1012 MAFVGEAILSALFETLFFKLASSDLLKFARQEQVHAELKKWEKILLKIHAVLDDAEEKQM 1071

Query: 61   TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTAT------------ 108
            T  L K WL +L++LAYD ED+LDEF TEA RRKL+    A+ +P+ +            
Sbjct: 1072 TDRLVKIWLDELRDLAYDVEDILDEFGTEALRRKLM----AETEPSTSMVCSLIPSCCTS 1127

Query: 109  ---ARLRY------------GRVQE----------------------RPLSTPSLVDEEE 131
               + +R+             R+QE                        L T SLVDE  
Sbjct: 1128 FNPSTVRFNVKMGSKIEEITARLQEISGQKNDLHLRENAGGSSYTMKSRLPTTSLVDESR 1187

Query: 132  VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRA 191
            VYGRE DKE I+ LLL D+  S     VIPI GMGG+GKTTLAQL FND  VK +F  RA
Sbjct: 1188 VYGRETDKEAILNLLLKDE-PSDDEVCVIPIVGMGGIGKTTLAQLAFNDCKVKDHFDLRA 1246

Query: 192  CAYVSEDFDAVGVTKVILQAAA-GSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYD 250
               VS+DFD V VTK ILQ+ +  + DVNDLNLLQ+ L+ +L   KFLLVLDD+W+EN +
Sbjct: 1247 WVCVSDDFDVVRVTKTILQSVSLDTHDVNDLNLLQVMLKEKLSGNKFLLVLDDVWNENCE 1306

Query: 251  VWTNLCKPFKA 261
             W  LC P +A
Sbjct: 1307 EWDILCSPMRA 1317

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  246 bits (627), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 146/311 (46%), Positives = 184/311 (59%), Gaps = 55/311 (17%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           M+  GEAIL+   E L  KLA   +  FARQEQ+ A+LKKWE++L+ I  VLDDAEEKQ+
Sbjct: 1   MAFVGEAILSALFETLFFKLASSDLLKFARQEQVHAELKKWEKILLKIHAVLDDAEEKQM 60

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTAT------------ 108
           T  L K WL +L++LAYD ED+LDEF TEA RRKL+    A+ +P+ +            
Sbjct: 61  TDRLVKIWLDELRDLAYDVEDILDEFGTEALRRKLM----AETEPSTSMVCSLIPSCCTS 116

Query: 109 ---ARLRY------------GRVQE----------------------RPLSTPSLVDEEE 131
              + +R+             R+QE                        L T SLVDE  
Sbjct: 117 FNPSTVRFNVKMGSKIEEITARLQEISGQKNDLHLRENAGGSSYTMKSRLPTTSLVDESR 176

Query: 132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRA 191
           VYGRE DKE I+ LLL D+  S     VIPI GMGG+GKTTLAQL FND  V+ +F  RA
Sbjct: 177 VYGRETDKEAILNLLLKDE-PSDDEVCVIPIVGMGGIGKTTLAQLAFNDCKVEDHFDLRA 235

Query: 192 CAYVSEDFDAVGVTKVILQAAA-GSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYD 250
              VS+DFD V VTK ILQ+ +  + DVNDLNLLQ+ L+ +L   KFLLVLDD+W+EN +
Sbjct: 236 WVCVSDDFDVVRVTKTILQSVSLDTHDVNDLNLLQVMLKEKLSGNKFLLVLDDVWNENCE 295

Query: 251 VWTNLCKPFKA 261
            W  LC P +A
Sbjct: 296 EWDILCSPMRA 306

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 =  245 bits (625), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 138/312 (44%), Positives = 186/312 (59%), Gaps = 54/312 (17%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           M+  GEA L+ +++ LV+ LA   ++ FAR+EQ+ A+LKKWE +L+ I  VL DAEEKQ+
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTA------------- 107
           T    + WL +L++LAYD ED+LD+FATEA RR L+   + D QP+              
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRNLI---KDDPQPSTSTVRSLISSLSSR 117

Query: 108 -------------------TARL------------------RYGRVQERPLSTPSLVDEE 130
                              TARL                  R  R ++R   T SLV E 
Sbjct: 118 FNPNALVYNLNMGSKIEEITARLHEISTQKGDLDLRENVEGRSHRKRKRVPETASLVVES 177

Query: 131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFR 190
            VYGRE DKE I+ +LL D+L       VIPI GMGG+GKTTLAQL +ND  VK +F  R
Sbjct: 178 RVYGRETDKEAILEVLLRDELIHDNEVCVIPIVGMGGVGKTTLAQLAYNDDRVKNHFDLR 237

Query: 191 ACAYVSEDFDAVGVTKVILQAAAG-SADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY 249
           A   VS+DFD + +TK +LQ+ A  + ++NDLNLLQ++++ +L  KKFLLVLDD+W+ENY
Sbjct: 238 AWVCVSDDFDVLRITKTLLQSIASYTREINDLNLLQVKMKEKLSGKKFLLVLDDVWNENY 297

Query: 250 DVWTNLCKPFKA 261
           D W +LC P +A
Sbjct: 298 DKWDSLCTPLRA 309

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 =  245 bits (625), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 138/312 (44%), Positives = 186/312 (59%), Gaps = 54/312 (17%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           M+  GEA L+ +++ LV+ LA   ++ FAR+EQ+ A+LKKWE +L+ I  VL DAEEKQ+
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTA------------- 107
           T    + WL +L++LAYD ED+LD+FATEA RR L+   + D QP+              
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRNLI---KDDPQPSTSTVRSLISSLSSR 117

Query: 108 -------------------TARL------------------RYGRVQERPLSTPSLVDEE 130
                              TARL                  R  R ++R   T SLV E 
Sbjct: 118 FNPNALVYNLNMGSKIEEITARLHEISTQKGDLDLRENVEGRSHRKRKRVPETASLVVES 177

Query: 131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFR 190
            VYGRE DKE I+ +LL D+L       VIPI GMGG+GKTTLAQL +ND  VK +F  R
Sbjct: 178 RVYGRETDKEAILEVLLRDELIHDNEVCVIPIVGMGGVGKTTLAQLAYNDDRVKNHFDLR 237

Query: 191 ACAYVSEDFDAVGVTKVILQAAAG-SADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY 249
           A   VS+DFD + +TK +LQ+ A  + ++NDLNLLQ++++ +L  KKFLLVLDD+W+ENY
Sbjct: 238 AWVCVSDDFDVLRITKTLLQSIASYTREINDLNLLQVKMKEKLSGKKFLLVLDDVWNENY 297

Query: 250 DVWTNLCKPFKA 261
           D W +LC P +A
Sbjct: 298 DKWDSLCTPLRA 309

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 =  243 bits (621), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 139/312 (44%), Positives = 184/312 (58%), Gaps = 54/312 (17%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           M+  GEA L+ +++ LV+ LA   ++ FAR+EQ+ A+LKKWE +L+ I  VL DAEEKQ+
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTA------------- 107
           T    + WL +L++LAYD ED+LD+FATEA RRKL+     D QP+              
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRKLI---TDDPQPSTSTVRSIISSLSSR 117

Query: 108 -------------------TARL------------------RYGRVQERPLSTPSLVDEE 130
                              TARL                  R  R ++R   T SLV E 
Sbjct: 118 FNPNALVYNLNMGSKLEEITARLHEISTQKGDLDLRENVEERSNRKRKRVPETTSLVVES 177

Query: 131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFR 190
            VYGRE DKE I+ +LL D+        VIPI GMGG+GKTTLAQL ++D  VK +F  R
Sbjct: 178 RVYGRETDKEAILEVLLRDESIHDNEVCVIPIVGMGGVGKTTLAQLAYHDDRVKNHFDLR 237

Query: 191 ACAYVSEDFDAVGVTKVILQAAAGSA-DVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY 249
           A   VS+DFD + +TK +LQ+ A  A ++NDLNLLQ++L+ +L  KKFLLVLDD+W+ENY
Sbjct: 238 AWVCVSDDFDVLRITKTLLQSIASYAREINDLNLLQVKLKEKLSGKKFLLVLDDVWNENY 297

Query: 250 DVWTNLCKPFKA 261
           D W  LC P +A
Sbjct: 298 DKWDRLCTPLRA 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487176|ref|XP_003633526.1| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  242 bits (618), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 138/312 (44%), Positives = 183/312 (58%), Gaps = 54/312 (17%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           M+  GEA L+ +++ LV+ LA   ++ FAR+EQ+ A+LKKWE +L+ I  VL DAEEKQ+
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQADRQPTA------------- 107
           T    + WL +L++LAYD ED+LD+FATEA RRKL+     D QP+              
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRKLI---TDDPQPSTSTVRSLISSLSSR 117

Query: 108 -------------------TARL------------------RYGRVQERPLSTPSLVDEE 130
                              TARL                  R  R ++R   T  LV E 
Sbjct: 118 FNPNALVYNLNMGSKIEEITARLHEISTQKGDLDLRENVEGRSNRKRKRVPETTCLVVES 177

Query: 131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFR 190
            VYGRE DKE I+ +LL D+L       VIPI GMGG+GKTTLAQL ++D  VK +F  R
Sbjct: 178 RVYGRETDKEAILEVLLRDELVHDNEVCVIPIVGMGGVGKTTLAQLAYHDDRVKNHFDLR 237

Query: 191 ACAYVSEDFDAVGVTKVILQAAAGSA-DVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY 249
           A   VS+DFD + + K +LQ+ A  A ++NDLNLLQ++L+ +L  KKFLLVLDD+W+ENY
Sbjct: 238 AWVCVSDDFDVLRIAKTLLQSIASYAREINDLNLLQVKLKEKLSGKKFLLVLDDVWNENY 297

Query: 250 DVWTNLCKPFKA 261
           D W  LC P +A
Sbjct: 298 DKWDRLCTPLRA 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147787628|emb|CAN62744.1| hypothetical protein VITISV_019639 [Vitis vinifera]

 Score =  236 bits (601), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 136/303 (44%), Positives = 185/303 (61%), Gaps = 46/303 (15%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
           GEAIL+  ++ LV+ +    +  +AR+EQ++++LK+W+ +L+ I VVL+DAEEKQ+T PL
Sbjct: 6   GEAILSGFIQKLVDMVTSPELWKYARKEQVDSELKRWKNILIKIYVVLNDAEEKQMTNPL 65

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLE--QADRQ---------PTA------ 107
            K WL +L++LAYD ED+LD+FATEA R  L++ +  Q   +         P+A      
Sbjct: 66  VKIWLDELRDLAYDVEDILDDFATEALRSSLIMAQPQQGTSKVRGMLSSLIPSASTSNSS 125

Query: 108 --------TARLR--------------------YGRVQERPLSTPSLVDEEEVYGREKDK 139
                   TARL+                      R + + L T SLV E +VYGRE DK
Sbjct: 126 MRSKIEEITARLKDISAQKNDLDLREIEGGWSDRKRKRAQILPTTSLVVESDVYGRETDK 185

Query: 140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF 199
             IV +LL  D +S    SVIPI GMGG+GKTTLAQLVFND  VK  F  RA   VS+ F
Sbjct: 186 AAIVDMLLKHDPSSDDEVSVIPIVGMGGIGKTTLAQLVFNDDEVKGRFDLRAWVCVSDYF 245

Query: 200 DAVGVTKVILQAA-AGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP 258
           D + +TK+ILQ+  + + DVNDLNLLQ++L+ +   KKFLLVLDD+W+EN   W  LC P
Sbjct: 246 DVLRITKIILQSVDSDTRDVNDLNLLQVKLKEKFSGKKFLLVLDDVWNENCHEWDTLCMP 305

Query: 259 FKA 261
            +A
Sbjct: 306 MRA 308

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487180|ref|XP_002268806.2| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 136/303 (44%), Positives = 185/303 (61%), Gaps = 46/303 (15%)

Query: 5   GEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPL 64
           GEAIL+  ++ LV+ +    +  +AR+EQ++++LK+W+ +L+ I VVL+DAEEKQ+T PL
Sbjct: 6   GEAILSGFIQKLVDMVTSPELWKYARKEQVDSELKRWKNILIKIYVVLNDAEEKQMTNPL 65

Query: 65  TKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLE--QADRQ---------PTA------ 107
            K WL +L++LAYD ED+LD+FATEA R  L++ +  Q   +         P+A      
Sbjct: 66  VKIWLDELRDLAYDVEDILDDFATEALRSSLIMAQPQQGTSKVRGMLSSLIPSASTSNSS 125

Query: 108 --------TARLR--------------------YGRVQERPLSTPSLVDEEEVYGREKDK 139
                   TARL+                      R + + L T SLV E +VYGRE DK
Sbjct: 126 MRSKIEEITARLKDISAQKNDLDLREIEGGWSDRKRKRAQILPTTSLVVESDVYGRETDK 185

Query: 140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF 199
             IV +LL  D +S    SVIPI GMGG+GKTTLAQLVFND  VK  F  RA   VS+ F
Sbjct: 186 AAIVDMLLKHDPSSDDEVSVIPIVGMGGIGKTTLAQLVFNDDEVKGRFDLRAWVCVSDYF 245

Query: 200 DAVGVTKVILQAA-AGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP 258
           D + +TK+ILQ+  + + DVNDLNLLQ++L+ +   KKFLLVLDD+W+EN   W  LC P
Sbjct: 246 DVLRITKIILQSVDSDTRDVNDLNLLQVKLKEKFSGKKFLLVLDDVWNENCHEWDTLCMP 305

Query: 259 FKA 261
            +A
Sbjct: 306 MRA 308

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556671|ref|XP_002519369.1| Disease resistance protein RPS2, putative [Ricinus communis] gi|223541436|gb|EEF42986.1| Disease resistance protein RPS2, putative [Ricinus communis]

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 134/303 (44%), Positives = 182/303 (60%), Gaps = 45/303 (14%)

Query: 1   MSITGEAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI 60
           MSI GEA+L+  +++L +KLA   +  FARQEQ+ AD+KKWE++L+ I  VLDDAEEKQ+
Sbjct: 22  MSIIGEAVLSAFLQVLFDKLASPELLKFARQEQVYADIKKWEKILLKIHAVLDDAEEKQL 81

Query: 61  TKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKLLLLEQAD------------------ 102
           T    K WL +L++LAYD ED+LDEFATEA  R L+   +A+                  
Sbjct: 82  TNQFVKIWLAELRDLAYDVEDILDEFATEAVHRGLIFESEANTSKLLKLIHTCNGLISSN 141

Query: 103 ---------RQPTATARLR-------YGRVQE----------RPLSTPSLVDEEEVYGRE 136
                    +    T RL+       Y  ++E          + L T SLV+E +V+GRE
Sbjct: 142 SVFRVRMISKMKGITTRLQAISNQKNYLNLRENLEGSSTKVRKRLPTTSLVNETQVFGRE 201

Query: 137 KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVS 196
           +DKE ++ LLL D  N      VI I GMGG+GKTTLAQLVFND  VK  F  +  A VS
Sbjct: 202 RDKEAVLELLLTDYANDSK-VCVIAIIGMGGVGKTTLAQLVFNDTKVKDSFDLKVWACVS 260

Query: 197 EDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC 256
           ++FD + +TK IL++    +  ++LNLLQ +L++ L  K+FLLVLDD+W+ENY  W  LC
Sbjct: 261 DEFDVLNITKSILESITNRSVGSNLNLLQGRLQDILTEKRFLLVLDDVWNENYQYWDALC 320

Query: 257 KPF 259
            PF
Sbjct: 321 SPF 323

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	261
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.911	0.225	0.291	6.5e-20
UNIPROTKB|O48647	1802	O48647 "XA1" [Oryza sativa (ta	0.559	0.081	0.331	1.6e-19
TAIR|locus:2011982	857	AT1G50180 [Arabidopsis thalian	0.325	0.099	0.348	6.2e-13
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.846	0.155	0.275	8.3e-13
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.314	0.090	0.413	8e-12
TAIR|locus:2037623	899	AT1G58410 [Arabidopsis thalian	0.467	0.135	0.325	1.4e-10
TAIR|locus:504956182	1049	AT1G58848 [Arabidopsis thalian	0.471	0.117	0.338	7.4e-10
TAIR|locus:2826978	1049	AT1G59218 [Arabidopsis thalian	0.471	0.117	0.338	7.4e-10
TAIR|locus:504956184	1017	AT1G58807 "AT1G58807" [Arabido	0.471	0.120	0.338	1.4e-09
TAIR|locus:2827038	1017	AT1G59124 "AT1G59124" [Arabido	0.471	0.120	0.338	1.4e-09

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

 Score = 249 (92.7 bits), Expect = 6.5e-20, P = 6.5e-20
 Identities = 75/257 (29%), Positives = 125/257 (48%)

Query:    20 LALEVIQLFARQEQIEADL-KKW-EELLVII---KVVLDD--AEEKQITKPLTKKWLGKL 72
             L +  + + A ++QI   + +KW  EL  ++   +  LDD   E  ++          +L
Sbjct:    47 LTITAVLIDAEEKQITNPVVEKWVNELRDVVYHAEDALDDIATEALRLNIGAESSSSNRL 106

Query:    73 QNLA--YDAEDMLD---EFATEAFRRKLLLLEQ-ADRQPTATARLRYGRVQERPLSTPSL 126
             + L       D LD   E       +  + LE+ A ++     +     + ++ L T SL
Sbjct:   107 RQLRGRMSLGDFLDGNSEHLETRLEKVTIRLERLASQRNILGLKELTAMIPKQRLPTTSL 166

Query:   127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKY 186
             VDE EV+GR+ DK+ I+  L+ ++     G +V+ I G+GG+GKTTL+QL++ND  V+ Y
Sbjct:   167 VDESEVFGRDDDKDEIMRFLIPEN-GKDNGITVVAIVGIGGVGKTTLSQLLYNDQHVRSY 225

Query:   187 FSFRACAYVSEDFDAVGVTKVILQAAAGS----ADVNDXXXXXXXXXXXXXXXXXXXVLD 242
             F  +  A+VSE+FD   +TK + ++         D+ D                   VLD
Sbjct:   226 FGTKVWAHVSEEFDVFKITKKVYESVTSRPCEFTDL-DVLQVKLKERLTGTGLPFLLVLD 284

Query:   243 DMWSENYDVWTNLCKPF 259
             D+W+EN+  W  L +PF
Sbjct:   285 DLWNENFADWDLLRQPF 301

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

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

 Score = 203 (76.5 bits), Expect = 1.6e-19, Sum P(2) = 1.6e-19
 Identities = 50/151 (33%), Positives = 72/151 (47%)

Query:   112 RYGRVQERPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKT 171
             R G       +T S + E  VYGR  + E I  L++ +  N   G +V+PI G GG+GKT
Sbjct:   277 RQGTPPATNATTSSYLPEPIVYGRAAEMETIKQLIMSNRSN---GITVLPIVGNGGIGKT 333

Query:   172 TLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSAD--VNDXXXXXXXXX 229
             TLAQLV  D  +K  F+ +   YVS+ FD V +T+ IL   +  +   +++         
Sbjct:   334 TLAQLVCKDLVIKSQFNVKIWVYVSDKFDVVKITRQILDHVSNQSHEGISNLDTLQQDLE 393

Query:   230 XXXXXXXXXXVLDDMWSENYDVWTNLCKPFK 260
                       VLDD+W    D W  L  P +
Sbjct:   394 EQMKSKKFLIVLDDVWEIRTDDWKKLLAPLR 424

GO:0006915 "apoptotic process" evidence=IGI

GO:0006952 "defense response" evidence=IGI

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

 Score = 122 (48.0 bits), Expect = 6.2e-13, Sum P(3) = 6.2e-13
 Identities = 31/89 (34%), Positives = 51/89 (57%)

Query:     6 EAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLT 65
             EAI++VTV+ L + L  E + LF   +Q+    K+ ++ L  +   L DA+EKQ      
Sbjct:     3 EAIVSVTVQKLGQLLLEEPLFLFGIGDQV----KQLQDELKRLNCFLKDADEKQHESERV 58

Query:    66 KKWLGKLQNLAYDAEDMLDEFATEAFRRK 94
             + W+  ++  +YDAED+L+ F  +A  RK
Sbjct:    59 RNWVAGIREASYDAEDILEAFFLKAESRK 87

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009506 "plasmodesma" evidence=IDA

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

 Score = 184 (69.8 bits), Expect = 8.3e-13, P = 8.3e-13
 Identities = 65/236 (27%), Positives = 104/236 (44%)

Query:    30 RQEQIEADLKKW----EELLVIIKVVLDDAEEKQITKPLTKK--WLGKL-QNLAYDAEDM 82
             R E +  ++K W    ++     + +LD+ + + + + +  +   LG L QNL    E +
Sbjct:    56 RAEHVR-EVKHWLTGIKDAFFQAEDILDELQTEALRRRVVAEAGGLGGLFQNLMAGREAI 114

Query:    83 LDEFATEAFRRKLLLLEQADRQPTATARLRYGRVQE---RPLST--PSLVDEEEVYGREK 137
               +   +   + + LLE   +         Y   +E   R  S   P  + +  + GR +
Sbjct:   115 QKKIEPK-MEKVVRLLEHHVKHIEVIGLKEYSETREPQWRQASRSRPDDLPQGRLVGRVE 173

Query:   138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE 197
             DK  +V LLL DD  S    +VI + GM G+GKTTL ++VFND  V ++F  +       
Sbjct:   174 DKLALVNLLLSDDEISIGKPAVISVVGMPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGI 233

Query:   198 DFDAVGVTKVILQAAAGSA-DVNDXXXXXXXXXXXXXXXXXXXVLDDMWSENYDVW 252
             +F+   VTK +LQ    SA +  D                   VLDD WSE+   W
Sbjct:   234 NFNVFTVTKAVLQDITSSAVNTEDLPSLQIQLKKTLSGKRFLLVLDDFWSESDSEW 289

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 = 136 (52.9 bits), Expect = 8.0e-12, Sum P(2) = 8.0e-12
 Identities = 36/87 (41%), Positives = 50/87 (57%)

Query:   123 TPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAG 182
             T S   E  + G EK+ E +V  L+G+D + G     + ITG+GGLGKTTLA+ +F+   
Sbjct:   151 TFSSESESNLVGLEKNVEKLVEELVGNDSSHG-----VSITGLGGLGKTTLARQIFDHDK 205

Query:   183 VKKYFSFRACAYVSEDFDAVGVTKVIL 209
             VK +F   A   VS++F    V K IL
Sbjct:   206 VKSHFDGLAWVCVSQEFTRKDVWKTIL 232

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 140 (54.3 bits), Expect = 1.4e-10, Sum P(2) = 1.4e-10
 Identities = 44/135 (32%), Positives = 62/135 (45%)

Query:   129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS 188
             E +  G E + + +VG L+  D      + ++ +TGMGGLGKTTLA+ VFN   VK  F 
Sbjct:   159 ENDFVGMEANVKKLVGYLVEKD-----DYQIVSLTGMGGLGKTTLARQVFNHDVVKDRFD 213

Query:   189 FRACAYVSEDFDAVGVTKVILQAAAGSADVNDXXXXXXXXXXXXX-----XXXXXXVLDD 243
               A   VS++F  + V + ILQ        ++                        VLDD
Sbjct:   214 GFAWVSVSQEFTRISVWQTILQNLTSKERKDEIQNMKEADLHDDLFRLLESSKTLIVLDD 273

Query:   244 MWSENYDVWTNLCKP 258
             +W E  D W +L KP
Sbjct:   274 IWKEE-D-W-DLIKP 285

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:504956182 AT1G58848 [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 7.4e-10, Sum P(2) = 7.4e-10
 Identities = 46/136 (33%), Positives = 62/136 (45%)

Query:   128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF 187
             D+ +  G E + + +VG L+ D+ N      V+ ITGMGGLGKTTLA+ VFN   VK  F
Sbjct:   159 DDSDFVGLEANVKKLVGYLV-DEAN----VQVVSITGMGGLGKTTLAKQVFNHEDVKHQF 213

Query:   188 SFRACAYVSEDFDAVGVTKVILQAAAGSADVNDXXXXXXXXXXXXX-----XXXXXXVLD 242
                +   VS+DF  + V + IL+      +                           VLD
Sbjct:   214 DGLSWVCVSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLD 273

Query:   243 DMWSENYDVWTNLCKP 258
             D+W E  D W  L KP
Sbjct:   274 DIW-EKED-W-ELIKP 286

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2826978 AT1G59218 [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 7.4e-10, Sum P(2) = 7.4e-10
 Identities = 46/136 (33%), Positives = 62/136 (45%)

Query:   128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF 187
             D+ +  G E + + +VG L+ D+ N      V+ ITGMGGLGKTTLA+ VFN   VK  F
Sbjct:   159 DDSDFVGLEANVKKLVGYLV-DEAN----VQVVSITGMGGLGKTTLAKQVFNHEDVKHQF 213

Query:   188 SFRACAYVSEDFDAVGVTKVILQAAAGSADVNDXXXXXXXXXXXXX-----XXXXXXVLD 242
                +   VS+DF  + V + IL+      +                           VLD
Sbjct:   214 DGLSWVCVSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLD 273

Query:   243 DMWSENYDVWTNLCKP 258
             D+W E  D W  L KP
Sbjct:   274 DIW-EKED-W-ELIKP 286

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:504956184 AT1G58807 "AT1G58807" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 1.4e-09, Sum P(2) = 1.4e-09
 Identities = 46/136 (33%), Positives = 62/136 (45%)

Query:   128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF 187
             D+ +  G E + + +VG L+ D+ N      V+ ITGMGGLGKTTLA+ VFN   VK  F
Sbjct:   159 DDSDFVGLEANVKKLVGYLV-DEAN----VQVVSITGMGGLGKTTLAKQVFNHEDVKHQF 213

Query:   188 SFRACAYVSEDFDAVGVTKVILQAAAGSADVNDXXXXXXXXXXXXX-----XXXXXXVLD 242
                +   VS+DF  + V + IL+      +                           VLD
Sbjct:   214 DGLSWVCVSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLD 273

Query:   243 DMWSENYDVWTNLCKP 258
             D+W E  D W  L KP
Sbjct:   274 DIW-EKED-W-ELIKP 286

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2827038 AT1G59124 "AT1G59124" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 1.4e-09, Sum P(2) = 1.4e-09
 Identities = 46/136 (33%), Positives = 62/136 (45%)

Query:   128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF 187
             D+ +  G E + + +VG L+ D+ N      V+ ITGMGGLGKTTLA+ VFN   VK  F
Sbjct:   159 DDSDFVGLEANVKKLVGYLV-DEAN----VQVVSITGMGGLGKTTLAKQVFNHEDVKHQF 213

Query:   188 SFRACAYVSEDFDAVGVTKVILQAAAGSADVNDXXXXXXXXXXXXX-----XXXXXXVLD 242
                +   VS+DF  + V + IL+      +                           VLD
Sbjct:   214 DGLSWVCVSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLD 273

Query:   243 DMWSENYDVWTNLCKP 258
             D+W E  D W  L KP
Sbjct:   274 DIW-EKED-W-ELIKP 286

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	261
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-21
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.001

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

 Score = 90.1 bits (224), Expect = 2e-21
 Identities = 45/130 (34%), Positives = 66/130 (50%), Gaps = 9/130 (6%)

Query: 135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAY 194
           RE   E ++  LL    N G    V+ I GMGG+GKTTLA+ ++ND  V  +F   A   
Sbjct: 1   REDMIEALIEKLLEMSDNLG----VVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVV 56

Query: 195 VSEDFDAVGVTKVILQ---AAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDV 251
           VS+ +    + K ILQ            + + L ++++  L  K+FLLVLDD+W +N   
Sbjct: 57  VSKTYTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKN--D 114

Query: 252 WTNLCKPFKA 261
           W  +  PF  
Sbjct: 115 WDKIGVPFPD 124

Length = 285

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

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 33/131 (25%), Positives = 53/131 (40%), Gaps = 20/131 (15%)

Query: 131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFR 190
            + GRE++ E ++  L      SG   SV+ +TG  G GKT+L + +     V      +
Sbjct: 1   RLVGREEELERLLDAL--RRARSGGPPSVL-LTGPSGTGKTSLLRELLEGLLVAAGKCDQ 57

Query: 191 ACAYVSEDF----------------DAVGVTKVILQAAAGSADVNDLNLLQLQLENQL-K 233
           A       F                  + + +  L AA G+  +  L  L   LE  L +
Sbjct: 58  AERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLAR 117

Query: 234 NKKFLLVLDDM 244
            +  +LVLDD+
Sbjct: 118 ARPLVLVLDDL 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	261
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	99.97
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.84
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.52
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.15
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.15
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.96
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.96
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.88
cd01128	249	rho_factor Transcription termination factor rho is	98.81
PRK09376	416	rho transcription termination factor Rho; Provisio	98.77
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.77
PTZ00202	550	tuzin; Provisional	98.67
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.63
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.62
TIGR00767	415	rho transcription termination factor Rho. Members	98.58
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.52
PRK13342	413	recombination factor protein RarA; Reviewed	98.4
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.39
PF05729	166	NACHT: NACHT domain	98.39
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.25
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.24
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.24
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.2
PRK04195	482	replication factor C large subunit; Provisional	98.18
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.17
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.17
PF13173	128	AAA_14: AAA domain	98.16
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.12
KOG2028	554	consensus ATPase related to the helicase subunit o	98.1
smart00382	148	AAA ATPases associated with a variety of cellular	98.05
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.02
PRK12402	337	replication factor C small subunit 2; Reviewed	98.01
PRK13341	725	recombination factor protein RarA/unknown domain f	98.0
PRK08118	167	topology modulation protein; Reviewed	97.98
PLN03025	319	replication factor C subunit; Provisional	97.94
PF00004	132	AAA: ATPase family associated with various cellula	97.91
PRK04841	903	transcriptional regulator MalT; Provisional	97.9
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.88
PRK06893	229	DNA replication initiation factor; Validated	97.88
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.87
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.87
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.85
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.81
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.81
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.8
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.79
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.79
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.78
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.78
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.76
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.76
PRK07261	171	topology modulation protein; Provisional	97.75
PRK08116	268	hypothetical protein; Validated	97.74
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.73
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.72
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.71
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.71
PHA02544	316	44 clamp loader, small subunit; Provisional	97.71
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.7
PRK12608	380	transcription termination factor Rho; Provisional	97.69
PRK12377	248	putative replication protein; Provisional	97.69
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.69
PRK08727	233	hypothetical protein; Validated	97.68
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.67
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.66
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.65
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.63
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.63
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.61
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.61
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.61
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.6
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.59
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.59
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.58
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.58
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.57
CHL00095	821	clpC Clp protease ATP binding subunit	97.54
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.53
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.53
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.52
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.52
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.48
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.48
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.47
PRK08939	306	primosomal protein DnaI; Reviewed	97.47
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.47
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.43
PRK07952	244	DNA replication protein DnaC; Validated	97.42
PRK08084	235	DNA replication initiation factor; Provisional	97.41
PRK05541	176	adenylylsulfate kinase; Provisional	97.41
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.41
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.4
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.4
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.39
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.39
PRK06696	223	uridine kinase; Validated	97.38
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.38
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.37
PRK08181	269	transposase; Validated	97.37
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.36
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.36
CHL00095	821	clpC Clp protease ATP binding subunit	97.36
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.36
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.35
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.35
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.35
PRK05642	234	DNA replication initiation factor; Validated	97.34
PRK10865	857	protein disaggregation chaperone; Provisional	97.34
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.34
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.33
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.33
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.32
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.32
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.32
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.32
CHL00181	287	cbbX CbbX; Provisional	97.31
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.3
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	97.29
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.29
PRK10865	857	protein disaggregation chaperone; Provisional	97.29
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.29
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.27
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.27
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.27
PRK10867	433	signal recognition particle protein; Provisional	97.26
TIGR00959	428	ffh signal recognition particle protein. This mode	97.26
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.24
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	97.23
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.23
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.23
PRK13531	498	regulatory ATPase RavA; Provisional	97.23
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.22
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.22
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.21
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.21
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.2
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.19
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.19
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.18
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.18
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.16
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.16
PRK06526	254	transposase; Provisional	97.14
PRK06921	266	hypothetical protein; Provisional	97.14
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.13
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.13
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.13
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.13
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.12
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.12
PRK07667	193	uridine kinase; Provisional	97.12
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.11
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.11
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.11
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.09
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	97.09
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.08
PRK12422	445	chromosomal replication initiation protein; Provis	97.07
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.07
PRK05480	209	uridine/cytidine kinase; Provisional	97.07
CHL00176	638	ftsH cell division protein; Validated	97.06
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.06
PRK09354	349	recA recombinase A; Provisional	97.05
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.05
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.05
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.04
PTZ00301	210	uridine kinase; Provisional	97.04
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.03
PRK09183	259	transposase/IS protein; Provisional	97.02
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	97.01
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.99
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.98
PRK08233	182	hypothetical protein; Provisional	96.98
KOG0736	953	consensus Peroxisome assembly factor 2 containing	96.97
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.97
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.97
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.96
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.95
PRK15455	644	PrkA family serine protein kinase; Provisional	96.95
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.94
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.94
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.93
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.93
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.91
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.91
PRK06835	329	DNA replication protein DnaC; Validated	96.9
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.89
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.89
PRK06762	166	hypothetical protein; Provisional	96.87
PRK00625	173	shikimate kinase; Provisional	96.86
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.86
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.85
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	96.85
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.83
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.82
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.82
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.82
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.82
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.8
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.79
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.79
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.79
PRK06067	234	flagellar accessory protein FlaH; Validated	96.77
PRK06547	172	hypothetical protein; Provisional	96.77
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.76
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.76
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.76
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.74
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.73
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.7
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.7
PRK14974	336	cell division protein FtsY; Provisional	96.7
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	96.69
PRK04328	249	hypothetical protein; Provisional	96.68
PRK05439	311	pantothenate kinase; Provisional	96.67
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.67
PRK04296	190	thymidine kinase; Provisional	96.66
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.66
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.65
PRK03839	180	putative kinase; Provisional	96.65
PRK00131	175	aroK shikimate kinase; Reviewed	96.65
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.64
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.64
PRK04040	188	adenylate kinase; Provisional	96.62
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.62
PF00154	322	RecA: recA bacterial DNA recombination protein; In	96.62
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.61
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.6
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.59
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.59
PTZ00035	337	Rad51 protein; Provisional	96.59
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.57
PRK00279	215	adk adenylate kinase; Reviewed	96.57
PTZ00088	229	adenylate kinase 1; Provisional	96.55
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.54
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	96.54
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.54
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.53
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.53
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	96.5
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.49
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.49
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.49
COG0714	329	MoxR-like ATPases [General function prediction onl	96.48
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.48
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.48
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	96.47
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.47
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.47
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.46
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	96.46
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	96.46
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	96.46
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.45
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	96.44
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	96.44
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	96.43
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.43
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	96.43
PRK00889	175	adenylylsulfate kinase; Provisional	96.42
PRK08149	428	ATP synthase SpaL; Validated	96.41
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.41
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.4
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.4
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.39
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	96.38
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.38
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	96.37
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.37
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.36
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.36
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.36
PF14516	331	AAA_35: AAA-like domain	96.35
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.34
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	96.34
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.34
PRK00300	205	gmk guanylate kinase; Provisional	96.33
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	96.32
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.32
PRK03846	198	adenylylsulfate kinase; Provisional	96.32
PRK06936	439	type III secretion system ATPase; Provisional	96.3
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.29
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.28
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	96.27
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.27
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.25
PRK06620	214	hypothetical protein; Validated	96.25
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.24
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.24
PHA00729	226	NTP-binding motif containing protein	96.24
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	96.23
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	96.23
PTZ00494	664	tuzin-like protein; Provisional	96.23
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.23
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.23
PF11868	192	DUF3388: Protein of unknown function (DUF3388); In	96.22
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	96.2
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	96.2
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	96.19
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	96.18
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	96.16
PRK07594	433	type III secretion system ATPase SsaN; Validated	96.16
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.16
PRK06217	183	hypothetical protein; Validated	96.16
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.15
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	96.15
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	96.14
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.14
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	96.14
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	96.13
PRK13949	169	shikimate kinase; Provisional	96.13
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.12
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	96.12
CHL00195	489	ycf46 Ycf46; Provisional	96.12
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	96.11
PRK05922	434	type III secretion system ATPase; Validated	96.11
PTZ00185	574	ATPase alpha subunit; Provisional	96.1
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	96.1
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.1
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	96.1
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.1
PRK14527	191	adenylate kinase; Provisional	96.1
PRK14738	206	gmk guanylate kinase; Provisional	96.08
PRK14530	215	adenylate kinase; Provisional	96.08
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.07
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	96.06
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	96.06
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.06
PRK10536	262	hypothetical protein; Provisional	96.06
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.04
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	96.04
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.03
PRK10416	318	signal recognition particle-docking protein FtsY;	96.03
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	96.03
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	96.02
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.01
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	96.01
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	96.0
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.0
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	96.0
PRK14737	186	gmk guanylate kinase; Provisional	96.0
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.99
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	95.99
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.99
PRK13947	171	shikimate kinase; Provisional	95.98
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	95.97
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.97
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.97
PRK13975	196	thymidylate kinase; Provisional	95.96
PRK09087	226	hypothetical protein; Validated	95.96
PLN02200	234	adenylate kinase family protein	95.95
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.95
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	95.93
PLN02348	395	phosphoribulokinase	95.93
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.93
PRK08356	195	hypothetical protein; Provisional	95.93
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	95.93
PRK12678	672	transcription termination factor Rho; Provisional	95.91
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.91
PRK05057	172	aroK shikimate kinase I; Reviewed	95.9
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.89
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	95.88
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.88
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.86
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.83
COG3899	849	Predicted ATPase [General function prediction only	95.83
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.82
PRK11823	446	DNA repair protein RadA; Provisional	95.82
PRK09825	176	idnK D-gluconate kinase; Provisional	95.81
PRK13695	174	putative NTPase; Provisional	95.81
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.79
PRK04182	180	cytidylate kinase; Provisional	95.79
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	95.78
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.76
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	95.76
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	95.76
PRK05022	509	anaerobic nitric oxide reductase transcription reg	95.76
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	95.76
PRK09099	441	type III secretion system ATPase; Provisional	95.74
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.73
PLN02796	347	D-glycerate 3-kinase	95.73
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	95.72
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.7
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	95.69
PLN02318	656	phosphoribulokinase/uridine kinase	95.68
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.67
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.66
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	95.66
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.66
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.66
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	95.65
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	95.65
PF07726	131	AAA_3: ATPase family associated with various cellu	95.65
PRK15453	290	phosphoribulokinase; Provisional	95.64
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	95.63
PRK06761	282	hypothetical protein; Provisional	95.63
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	95.62
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.62
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	95.61
PRK14532	188	adenylate kinase; Provisional	95.61
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.6
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	95.6
PRK06820	440	type III secretion system ATPase; Validated	95.6
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	95.59
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.59
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.58
PRK13948	182	shikimate kinase; Provisional	95.58
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	95.56
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.56
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	95.56
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	95.56
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	95.55
PHA02530	300	pseT polynucleotide kinase; Provisional	95.55
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	95.55
cd03116	159	MobB Molybdenum is an essential trace element in t	95.54
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.54
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.54
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	95.54
PRK13946	184	shikimate kinase; Provisional	95.53
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.52
PRK01184	184	hypothetical protein; Provisional	95.52
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	95.52
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	95.5
PLN02165	334	adenylate isopentenyltransferase	95.48
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	95.47
PF13245	76	AAA_19: Part of AAA domain	95.47
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	95.47
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	95.46
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.46
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	95.44
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.44
PRK03731	171	aroL shikimate kinase II; Reviewed	95.43
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.43
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	95.42
PRK14531	183	adenylate kinase; Provisional	95.42
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	95.4
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	95.4
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	95.39
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	95.36
COG4240	300	Predicted kinase [General function prediction only	95.36
CHL00059	485	atpA ATP synthase CF1 alpha subunit	95.35
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.35
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	95.35
COG1100	219	GTPase SAR1 and related small G proteins [General	95.34
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	95.34
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	95.34
cd03269	210	ABC_putative_ATPase This subfamily is involved in	95.34
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	95.33
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	95.33
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.33
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	95.33
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.33
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	95.32
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	95.32
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.31
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	95.29
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	95.29
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	95.29
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	95.29
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	95.28
PLN03046	460	D-glycerate 3-kinase; Provisional	95.28
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	95.26
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	95.26
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	95.26
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.25
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	95.24
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	95.24
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	95.24
PRK14528	186	adenylate kinase; Provisional	95.23
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.23
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	95.23
CHL00060	494	atpB ATP synthase CF1 beta subunit	95.22
PRK00698	205	tmk thymidylate kinase; Validated	95.22
PLN02674	244	adenylate kinase	95.22
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	95.21
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	95.2
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	95.2
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	95.2
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	95.18
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	95.18
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	95.18
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	95.18
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	95.17
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	95.17
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	95.17
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	95.17
PRK02496	184	adk adenylate kinase; Provisional	95.16
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	95.16
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	95.16
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	95.16
PRK00023	225	cmk cytidylate kinase; Provisional	95.15
PRK08058	329	DNA polymerase III subunit delta'; Validated	95.15
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	95.14
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.12
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	95.12
PRK09302	509	circadian clock protein KaiC; Reviewed	95.12
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	95.12
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	95.12
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	95.11

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=99.97  E-value=1.3e-29  Score=242.52  Aligned_cols=237  Identities=28%  Similarity=0.363  Sum_probs=188.2

Q ss_pred             HHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhccccChhHHHHHHHHHHHHhhhHhHHHHHHHHHHHHHH
Q 041190           16 LVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFATEAFRRKL   95 (261)
Q Consensus        16 l~~~l~~~~~~~~~~~~~v~~~i~~L~~~l~~i~~~l~~a~~~~~~~~~~~~wl~~lr~~ayd~ed~ld~~~~~~~~~~~   95 (261)
                      .++++.+.+..++..+.++++.+..|++.|..++.++++++..+........|...++++.|++||+++.+.......+.
T Consensus         8 ~~~~~~~~l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~   87 (889)
T KOG4658|consen    8 GVEKLDQLLNRESECLDGKDNYILELKENLKALQSALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKA   87 (889)
T ss_pred             ehhhHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566667777788899999999999999999999999999999888999999999999999999999999988865433


Q ss_pred             Hhhcc------------cCCC----------hhHH------hhcccC----CCC-----CCCcCCCCCCCCCccccccch
Q 041190           96 LLLEQ------------ADRQ----------PTAT------ARLRYG----RVQ-----ERPLSTPSLVDEEEVYGREKD  138 (261)
Q Consensus        96 ~~~~~------------~~~~----------~~~~------~rl~~~----~~~-----~~~~~~~~~~~~~~~~gr~~~  138 (261)
                      .+...            ...+          +++.      +.+...    ...     .....+.+..+... +|.+..
T Consensus        88 ~~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~~~~-VG~e~~  166 (889)
T KOG4658|consen   88 NDLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSESD-VGLETM  166 (889)
T ss_pred             hHHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCcccc-ccHHHH
Confidence            22111            0000          1111      222211    111     11123333334444 999999


Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccc-cccccceeEEEeeCCCCCHHHHHHHHHHHhcC-C-
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAG-VKKYFSFRACAYVSEDFDAVGVTKVILQAAAG-S-  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~-~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~-~-  215 (261)
                      ++++.+.|..++      ..+++|+||||+||||||++++|+.. +.++|+.++||.||++++...++.+|+..++. . 
T Consensus       167 ~~kl~~~L~~d~------~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~  240 (889)
T KOG4658|consen  167 LEKLWNRLMEDD------VGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDE  240 (889)
T ss_pred             HHHHHHHhccCC------CCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCc
Confidence            999999998753      28999999999999999999999987 89999999999999999999999999999983 2 


Q ss_pred             -CCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcccCC
Q 041190          216 -ADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFKA  261 (261)
Q Consensus       216 -~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l~~  261 (261)
                       ......++++..|.+.|++|||||||||||+..  +|+.|..|||.
T Consensus       241 ~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~--dw~~I~~~~p~  285 (889)
T KOG4658|consen  241 EWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEV--DWDKIGVPFPS  285 (889)
T ss_pred             ccchhhHHHHHHHHHHHhccCceEEEEecccccc--cHHhcCCCCCC
Confidence             223345789999999999999999999999984  89999999984

>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=99.84  E-value=1.6e-20  Score=160.72  Aligned_cols=120  Identities=37%  Similarity=0.515  Sum_probs=98.4

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG  214 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~  214 (261)
                      |+.++++|.+.|...    .++.++|+|+||||+||||||+.+|++..++.+|+.++|+++++..+...++..|+.+++.
T Consensus         1 re~~~~~l~~~L~~~----~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~   76 (287)
T PF00931_consen    1 REKEIEKLKDWLLDN----SNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGE   76 (287)
T ss_dssp             -HHHHHHHHHHHHTT----TTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHhhCC----CCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccc
Confidence            678899999999873    2578999999999999999999999987788999999999999999999999999999993


Q ss_pred             C---C-CCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcccC
Q 041190          215 S---A-DVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFK  260 (261)
Q Consensus       215 ~---~-~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l~  260 (261)
                      .   . ...+...+...+++.|.++++||||||||+.  ..|+.+...++
T Consensus        77 ~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~--~~~~~l~~~~~  124 (287)
T PF00931_consen   77 PDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDE--EDLEELREPLP  124 (287)
T ss_dssp             C-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SH--HHH-------H
T ss_pred             cccccccccccccccccchhhhccccceeeeeeeccc--ccccccccccc
Confidence            3   2 4567888999999999999999999999997  48988876664

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=99.52  E-value=7.5e-14  Score=139.76  Aligned_cols=121  Identities=24%  Similarity=0.396  Sum_probs=86.2

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEe---eCCC------
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAY---VSED------  198 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~---v~~~------  198 (261)
                      ....++|++.+++++..+|...    ...+++++|+||||+||||||+.+|+.  +..+|+..+|+.   ++..      
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            4456999999999999988542    346899999999999999999999997  677898887764   1111      


Q ss_pred             -----CC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          199 -----FD-AVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       199 -----~~-~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                           ++ ...+...++.++....+. .... ...+++.+.+||+||||||||+.  +.|+.+...
T Consensus       256 ~~~~~~~~~~~l~~~~l~~il~~~~~-~~~~-~~~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~  317 (1153)
T PLN03210        256 ANPDDYNMKLHLQRAFLSEILDKKDI-KIYH-LGAMEERLKHRKVLIFIDDLDDQ--DVLDALAGQ  317 (1153)
T ss_pred             ccccccchhHHHHHHHHHHHhCCCCc-ccCC-HHHHHHHHhCCeEEEEEeCCCCH--HHHHHHHhh
Confidence                 11 123445555555422111 1111 14578889999999999999986  588887654

syringae 6; Provisional

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.15  E-value=3.3e-10  Score=100.33  Aligned_cols=121  Identities=15%  Similarity=0.073  Sum_probs=86.2

Q ss_pred             CCCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc-ccc---ceeEEEeeCCCCC
Q 041190          125 SLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK-KYF---SFRACAYVSEDFD  200 (261)
Q Consensus       125 ~~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f---~~~~wv~v~~~~~  200 (261)
                      +.+.+..++||+.+.+.|..+|....  .+.....+.|+|++|+|||++++.++++.... ...   -..+|+++....+
T Consensus        10 ~~~~p~~l~gRe~e~~~l~~~l~~~~--~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~   87 (365)
T TIGR02928        10 PDYVPDRIVHRDEQIEELAKALRPIL--RGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDT   87 (365)
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHH--cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCC
Confidence            34455689999999999999987521  12344678999999999999999999863211 111   1346788887777


Q ss_pred             HHHHHHHHHHHh---cC--CCCCCCHHHHHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          201 AVGVTKVILQAA---AG--SADVNDLNLLQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       201 ~~~i~~~i~~~l---~~--~~~~~~~~~~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      ...++..|++++   +.  +....+..++...+.+.+  .+++++||||+++..
T Consensus        88 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        88 LYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence            888999999988   31  112234555556666666  366899999999987

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.15  E-value=3.4e-10  Score=101.26  Aligned_cols=120  Identities=19%  Similarity=0.112  Sum_probs=87.8

Q ss_pred             CCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHH
Q 041190          126 LVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVT  205 (261)
Q Consensus       126 ~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~  205 (261)
                      ...+..++||+++.+.|...|...-  .+.....+.|+|++|+|||++++.++++.......-..+++++....+...++
T Consensus        26 ~~~P~~l~~Re~e~~~l~~~l~~~~--~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~  103 (394)
T PRK00411         26 DYVPENLPHREEQIEELAFALRPAL--RGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIF  103 (394)
T ss_pred             CCcCCCCCCHHHHHHHHHHHHHHHh--CCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHH
Confidence            3456779999999999999985421  12334557899999999999999999874332212235677777777888899


Q ss_pred             HHHHHHhcC-C--CCCCCHHHHHHHHHHHhC--CCeEEEEEeCCCCC
Q 041190          206 KVILQAAAG-S--ADVNDLNLLQLQLENQLK--NKKFLLVLDDMWSE  247 (261)
Q Consensus       206 ~~i~~~l~~-~--~~~~~~~~~~~~l~~~l~--~kr~LiVlDdvw~~  247 (261)
                      ..|+.++.. .  ....+..++...+.+.+.  ++..+||||+++..
T Consensus       104 ~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l  150 (394)
T PRK00411        104 SEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYL  150 (394)
T ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHh
Confidence            999999873 2  123356677777777775  45689999999875

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

Probab=98.96  E-value=1.7e-08  Score=85.57  Aligned_cols=97  Identities=25%  Similarity=0.238  Sum_probs=65.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH-----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQ-----  231 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~-----  231 (261)
                      .+++.|+|++|+|||||++.+++..... .+ ..+|+ +....+..+++..|+..++......+...+...+...     
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~  119 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQE-RV-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQF  119 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCC-Ce-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            4588999999999999999999874321 11 12333 2334577788888988887332333333333333332     


Q ss_pred             hCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          232 LKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       232 l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      ..+++++||+||+|...+..|+.++
T Consensus       120 ~~~~~~vliiDe~~~l~~~~~~~l~  144 (269)
T TIGR03015       120 AAGKRALLVVDEAQNLTPELLEELR  144 (269)
T ss_pred             hCCCCeEEEEECcccCCHHHHHHHH
Confidence            2688899999999999877777665

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.

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

Probab=98.96  E-value=1.4e-09  Score=81.97  Aligned_cols=101  Identities=20%  Similarity=0.162  Sum_probs=71.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccc---cccceeEEEeeCCCCCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVK---KYFSFRACAYVSEDFDAVGVTKVILQAAA-GSADVNDLNLLQLQLENQL  232 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~~f~~~~wv~v~~~~~~~~i~~~i~~~l~-~~~~~~~~~~~~~~l~~~l  232 (261)
                      -+++.|+|.+|+|||++++.+.+.....   ..-...+|++++...+...+...|+..++ ......+..++...+.+.+
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            4689999999999999999998863210   00123569999888899999999999999 3333467777778888888


Q ss_pred             CCC-eEEEEEeCCCCC-ChhhHHHhhc
Q 041190          233 KNK-KFLLVLDDMWSE-NYDVWTNLCK  257 (261)
Q Consensus       233 ~~k-r~LiVlDdvw~~-~~~~w~~l~~  257 (261)
                      ... ..+||+||+... ..+.++.|+.
T Consensus        84 ~~~~~~~lviDe~~~l~~~~~l~~l~~  110 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHLFSDEFLEFLRS  110 (131)
T ss_dssp             HHCTEEEEEEETTHHHHTHHHHHHHHH
T ss_pred             HhcCCeEEEEeChHhcCCHHHHHHHHH
Confidence            654 459999999876 5555555543

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

Probab=98.88  E-value=1.8e-08  Score=88.80  Aligned_cols=119  Identities=20%  Similarity=0.121  Sum_probs=90.8

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      -+..+.+|+.+.+++...|...-  .+....-+.|+|.+|+|||+.++.|.+..+....=...++|++-...+...++..
T Consensus        15 iP~~l~~Re~ei~~l~~~l~~~~--~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~   92 (366)
T COG1474          15 IPEELPHREEEINQLASFLAPAL--RGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSK   92 (366)
T ss_pred             CcccccccHHHHHHHHHHHHHHh--cCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHH
Confidence            34448999999999999887643  2333344999999999999999999987432211111789999999999999999


Q ss_pred             HHHHhc-CCCCCCCHHHHHHHHHHHhC--CCeEEEEEeCCCCCC
Q 041190          208 ILQAAA-GSADVNDLNLLQLQLENQLK--NKKFLLVLDDMWSEN  248 (261)
Q Consensus       208 i~~~l~-~~~~~~~~~~~~~~l~~~l~--~kr~LiVlDdvw~~~  248 (261)
                      |++.++ .+....+..+....+.+.+.  ++.++||||++....
T Consensus        93 i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~  136 (366)
T COG1474          93 ILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALV  136 (366)
T ss_pred             HHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhc
Confidence            999997 44445566667777777774  689999999998764

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

Probab=98.81  E-value=8.2e-09  Score=86.30  Aligned_cols=90  Identities=13%  Similarity=0.053  Sum_probs=63.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC--CCHHHHHHHHHHHhc-CCCCCCCHH------HHHHH
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED--FDAVGVTKVILQAAA-GSADVNDLN------LLQLQ  227 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~i~~~i~~~l~-~~~~~~~~~------~~~~~  227 (261)
                      -..+.|+|++|+|||||++.+|++.... +|+..+|+.+++.  ++..++++.+...+- ...+.....      .....
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~   94 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEK   94 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHH
Confidence            4578999999999999999999985444 8999999997776  788888888844333 222222211      12222


Q ss_pred             HHHH-hCCCeEEEEEeCCCCC
Q 041190          228 LENQ-LKNKKFLLVLDDMWSE  247 (261)
Q Consensus       228 l~~~-l~~kr~LiVlDdvw~~  247 (261)
                      ...+ -.+++.++++|++-.-
T Consensus        95 a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          95 AKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHCCCCEEEEEECHHHh
Confidence            2222 2589999999999765

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.77  E-value=2e-08  Score=88.06  Aligned_cols=87  Identities=14%  Similarity=0.076  Sum_probs=61.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC--CHHHHHHHHHHHhc-CCCCCCCHHH---------HH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF--DAVGVTKVILQAAA-GSADVNDLNL---------LQ  225 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~--~~~~i~~~i~~~l~-~~~~~~~~~~---------~~  225 (261)
                      .-..|+|++|+|||||++.||++.... +|++++||.+++..  .+.++++.+...+- ...+.....+         ..
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~A  248 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKA  248 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHH
Confidence            357889999999999999999985444 89999999998887  67777777764332 2222222211         11


Q ss_pred             HHHHHHhCCCeEEEEEeCCCCC
Q 041190          226 LQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       226 ~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      ..++  ..++++||++|++-.-
T Consensus       249 e~~~--e~G~dVlL~iDsItR~  268 (416)
T PRK09376        249 KRLV--EHGKDVVILLDSITRL  268 (416)
T ss_pred             HHHH--HcCCCEEEEEEChHHH
Confidence            2222  3689999999999654

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

Probab=98.77  E-value=1.8e-08  Score=80.22  Aligned_cols=51  Identities=25%  Similarity=0.363  Sum_probs=34.3

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK  184 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  184 (261)
                      .|+||+++.+.+...|.. .  .....+++.|+|++|+|||+|.+.++......
T Consensus         1 ~fvgR~~e~~~l~~~l~~-~--~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDA-A--QSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGG-T--SS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH-H--HcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            379999999999999952 1  34456899999999999999999998874433

>PTZ00202 tuzin; Provisional

Probab=98.67  E-value=2.7e-06  Score=75.65  Aligned_cols=108  Identities=18%  Similarity=0.169  Sum_probs=73.0

Q ss_pred             CCCCCCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCH
Q 041190          122 STPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDA  201 (261)
Q Consensus       122 ~~~~~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  201 (261)
                      ....+.+...|+||+.+...|...|...+   .....++.|.|++|+|||||++.+.....    + ...+++..   +.
T Consensus       254 ~~~lPa~~~~FVGReaEla~Lr~VL~~~d---~~~privvLtG~~G~GKTTLlR~~~~~l~----~-~qL~vNpr---g~  322 (550)
T PTZ00202        254 LQSAPAVIRQFVSREAEESWVRQVLRRLD---TAHPRIVVFTGFRGCGKSSLCRSAVRKEG----M-PAVFVDVR---GT  322 (550)
T ss_pred             ccCCCCCccCCCCcHHHHHHHHHHHhccC---CCCceEEEEECCCCCCHHHHHHHHHhcCC----c-eEEEECCC---CH
Confidence            34445667889999999999999996533   22346999999999999999999987633    1 12223333   67


Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHHHHh-----C-CCeEEEEE
Q 041190          202 VGVTKVILQAAAGSADVNDLNLLQLQLENQL-----K-NKKFLLVL  241 (261)
Q Consensus       202 ~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l-----~-~kr~LiVl  241 (261)
                      .++++.++.+|+... .....++...|.+.+     . +++.+||+
T Consensus       323 eElLr~LL~ALGV~p-~~~k~dLLrqIqeaLl~~~~e~GrtPVLII  367 (550)
T PTZ00202        323 EDTLRSVVKALGVPN-VEACGDLLDFISEACRRAKKMNGETPLLVL  367 (550)
T ss_pred             HHHHHHHHHHcCCCC-cccHHHHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            899999999999321 122233333333333     2 67777776

>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=98.63  E-value=3.2e-07  Score=69.47  Aligned_cols=95  Identities=24%  Similarity=0.167  Sum_probs=56.5

Q ss_pred             cccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc
Q 041190          134 GREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA  213 (261)
Q Consensus       134 gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~  213 (261)
                      |++.....+...+...      ....+.|+|++|+|||++++.+++...  ..-...+++..++..........+...  
T Consensus         2 ~~~~~~~~i~~~~~~~------~~~~v~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~~~~~~~~~~~~~~~~~--   71 (151)
T cd00009           2 GQEEAIEALREALELP------PPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGHF--   71 (151)
T ss_pred             chHHHHHHHHHHHhCC------CCCeEEEECCCCCCHHHHHHHHHHHhh--cCCCCeEEEehhhhhhhhHHHHHhhhh--
Confidence            5677778888877542      346788999999999999999998742  111234566655533322211111000  


Q ss_pred             CCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          214 GSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       214 ~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                               ............+..+|++||++..
T Consensus        72 ---------~~~~~~~~~~~~~~~~lilDe~~~~   96 (151)
T cd00009          72 ---------LVRLLFELAEKAKPGVLFIDEIDSL   96 (151)
T ss_pred             ---------hHhHHHHhhccCCCeEEEEeChhhh
Confidence                     0011112223456789999999975

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.62  E-value=2.4e-07  Score=88.11  Aligned_cols=121  Identities=18%  Similarity=0.092  Sum_probs=82.7

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc---ccccc--eeEEEeeCCCCCH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV---KKYFS--FRACAYVSEDFDA  201 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~---~~~f~--~~~wv~v~~~~~~  201 (261)
                      +-+..+.||+++.++|...|...-. +.....++.|+|++|+|||++++.|.+....   +....  ..++|++..-.+.
T Consensus       752 YVPD~LPhREeEIeeLasfL~paIk-gsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp  830 (1164)
T PTZ00112        752 VVPKYLPCREKEIKEVHGFLESGIK-QSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHP  830 (1164)
T ss_pred             cCCCcCCChHHHHHHHHHHHHHHHh-cCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCH
Confidence            4456789999999999998876321 1223468899999999999999999876321   11222  2467888776778


Q ss_pred             HHHHHHHHHHhc--CCCCCCCHHHHHHHHHHHhC---CCeEEEEEeCCCCCC
Q 041190          202 VGVTKVILQAAA--GSADVNDLNLLQLQLENQLK---NKKFLLVLDDMWSEN  248 (261)
Q Consensus       202 ~~i~~~i~~~l~--~~~~~~~~~~~~~~l~~~l~---~kr~LiVlDdvw~~~  248 (261)
                      ..++..|..++.  .+.......+....+...+.   ....+||||||....
T Consensus       831 ~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~  882 (1164)
T PTZ00112        831 NAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLI  882 (1164)
T ss_pred             HHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhC
Confidence            888999998885  22223334445555555442   234699999998764

>TIGR00767 rho transcription termination factor Rho

Probab=98.58  E-value=2.8e-07  Score=81.26  Aligned_cols=90  Identities=11%  Similarity=0.047  Sum_probs=63.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC--CCHHHHHHHHHHHhc-CCCCCCCHH------HHHHH
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED--FDAVGVTKVILQAAA-GSADVNDLN------LLQLQ  227 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~i~~~i~~~l~-~~~~~~~~~------~~~~~  227 (261)
                      -..+.|+|++|+|||||++.+++.... ++|+..+|+.+.+.  .++.++++.++..+- ...+.....      .+...
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            346899999999999999999998543 37999999998865  688888888865544 222221111      11122


Q ss_pred             HHHH-hCCCeEEEEEeCCCCC
Q 041190          228 LENQ-LKNKKFLLVLDDMWSE  247 (261)
Q Consensus       228 l~~~-l~~kr~LiVlDdvw~~  247 (261)
                      ...+ -.+++.+|++|++-.-
T Consensus       247 Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       247 AKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHcCCCeEEEEEChhHH
Confidence            2222 3689999999999654

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

>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=98.52  E-value=1.9e-07  Score=76.87  Aligned_cols=44  Identities=34%  Similarity=0.437  Sum_probs=36.1

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |+||+++.+.|.+++...      ....+.|+|+.|+|||+|++.+.+..
T Consensus         1 F~gR~~el~~l~~~l~~~------~~~~~~l~G~rg~GKTsLl~~~~~~~   44 (234)
T PF01637_consen    1 FFGREKELEKLKELLESG------PSQHILLYGPRGSGKTSLLKEFINEL   44 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--------SSEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHhh------cCcEEEEEcCCcCCHHHHHHHHHHHh
Confidence            689999999999998653      34789999999999999999999874

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

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.40  E-value=9.7e-07  Score=79.59  Aligned_cols=99  Identities=21%  Similarity=0.261  Sum_probs=58.2

Q ss_pred             ccccccchHHH---HHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          131 EVYGREKDKEV---IVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       131 ~~~gr~~~~~~---l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      +++|.+..+..   |..++...      ....+.++|++|+||||||+.+.+..  ...|     +.++.......-++.
T Consensus        13 d~vGq~~~v~~~~~L~~~i~~~------~~~~ilL~GppGtGKTtLA~~ia~~~--~~~~-----~~l~a~~~~~~~ir~   79 (413)
T PRK13342         13 EVVGQEHLLGPGKPLRRMIEAG------RLSSMILWGPPGTGKTTLARIIAGAT--DAPF-----EALSAVTSGVKDLRE   79 (413)
T ss_pred             HhcCcHHHhCcchHHHHHHHcC------CCceEEEECCCCCCHHHHHHHHHHHh--CCCE-----EEEecccccHHHHHH
Confidence            47777666444   77776432      34567889999999999999998863  2222     222222111111222


Q ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          208 ILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       208 i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      +++.+.               .....+++.+|+||+++......++.|..
T Consensus        80 ii~~~~---------------~~~~~g~~~vL~IDEi~~l~~~~q~~LL~  114 (413)
T PRK13342         80 VIEEAR---------------QRRSAGRRTILFIDEIHRFNKAQQDALLP  114 (413)
T ss_pred             HHHHHH---------------HhhhcCCceEEEEechhhhCHHHHHHHHH
Confidence            222221               00114578899999999887555555543

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

Probab=98.39  E-value=2.9e-06  Score=73.57  Aligned_cols=112  Identities=21%  Similarity=0.195  Sum_probs=81.9

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHH
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i  208 (261)
                      ++.+.+|+.+...+..++...+   ..-++.+-|+|-.|+|||.+.+.+++....     ..+|+++-+.++...++..|
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 EPNVPCRESQIRRLKSLLGNNS---CTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKI   76 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCC---cccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHH
Confidence            4678899999999999997753   234667799999999999999999997522     36899999999999999999


Q ss_pred             HHHhc-CCCCCCC----HHHHHHHHHHHh-------CCCeEEEEEeCCCCCC
Q 041190          209 LQAAA-GSADVND----LNLLQLQLENQL-------KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       209 ~~~l~-~~~~~~~----~~~~~~~l~~~l-------~~kr~LiVlDdvw~~~  248 (261)
                      +.+.+ .+.++..    .+.+...+..+-       +++.++||||++....
T Consensus        77 L~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lr  128 (438)
T KOG2543|consen   77 LNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALR  128 (438)
T ss_pred             HHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhh
Confidence            99985 2222211    121222222111       2578999999997653

>PF05729 NACHT: NACHT domain

Probab=98.39  E-value=8e-07  Score=69.23  Aligned_cols=86  Identities=22%  Similarity=0.300  Sum_probs=50.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccc----cceeEEEeeCCCCCHH---HHHHHHHHHhcCCCCCCCHHHHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKY----FSFRACAYVSEDFDAV---GVTKVILQAAAGSADVNDLNLLQLQLEN  230 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~---~i~~~i~~~l~~~~~~~~~~~~~~~l~~  230 (261)
                      +++.|+|.+|+||||+++.++........    +...+|++........   .+...|..+....  ......   .+..
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~--~~~~~~---~~~~   75 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPES--IAPIEE---LLQE   75 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccc--hhhhHH---HHHH
Confidence            47899999999999999999887543332    3345566665533322   2333333332211  111111   1212


Q ss_pred             H-hCCCeEEEEEeCCCCCC
Q 041190          231 Q-LKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       231 ~-l~~kr~LiVlDdvw~~~  248 (261)
                      . ...++++||||++....
T Consensus        76 ~~~~~~~~llilDglDE~~   94 (166)
T PF05729_consen   76 LLEKNKRVLLILDGLDELE   94 (166)
T ss_pred             HHHcCCceEEEEechHhcc
Confidence            2 25789999999998765

>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=72.46  Aligned_cols=99  Identities=25%  Similarity=0.293  Sum_probs=59.5

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      +.+..++|....+..   ++.      ..++.-.-.||++|+||||||+.+...  ...+|     ..+|...+-.+=++
T Consensus        27 vGQ~HLlg~~~~lrr---~v~------~~~l~SmIl~GPPG~GKTTlA~liA~~--~~~~f-----~~~sAv~~gvkdlr   90 (436)
T COG2256          27 VGQEHLLGEGKPLRR---AVE------AGHLHSMILWGPPGTGKTTLARLIAGT--TNAAF-----EALSAVTSGVKDLR   90 (436)
T ss_pred             cChHhhhCCCchHHH---HHh------cCCCceeEEECCCCCCHHHHHHHHHHh--hCCce-----EEeccccccHHHHH
Confidence            445555665544444   332      235677788999999999999999886  44444     33343333222233


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          207 VILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      .++++..               +....+++.+|++|+|-.-+....+.+.
T Consensus        91 ~i~e~a~---------------~~~~~gr~tiLflDEIHRfnK~QQD~lL  125 (436)
T COG2256          91 EIIEEAR---------------KNRLLGRRTILFLDEIHRFNKAQQDALL  125 (436)
T ss_pred             HHHHHHH---------------HHHhcCCceEEEEehhhhcChhhhhhhh
Confidence            3333321               2233589999999999876644444443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.24  E-value=4.9e-05  Score=71.84  Aligned_cols=124  Identities=23%  Similarity=0.255  Sum_probs=76.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccc---eeEEEeeCCC---CCHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS---FRACAYVSED---FDAVG  203 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~---~~~wv~v~~~---~~~~~  203 (261)
                      +.++|++..+..+...+..      +....+.|+|++|+||||||+.+++..+....+.   ...|+.+...   .+...
T Consensus       154 ~~iiGqs~~~~~l~~~ia~------~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~  227 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVAS------PFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPRE  227 (615)
T ss_pred             HhceeCcHHHHHHHHHHhc------CCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHH
Confidence            3588999888888877743      2345799999999999999999988743333331   2345554321   12222


Q ss_pred             HHHHH---------------HHHhc-CCC----------------CCCC-HHHHHHHHHHHhCCCeEEEEEeCCCCCChh
Q 041190          204 VTKVI---------------LQAAA-GSA----------------DVND-LNLLQLQLENQLKNKKFLLVLDDMWSENYD  250 (261)
Q Consensus       204 i~~~i---------------~~~l~-~~~----------------~~~~-~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~  250 (261)
                      +...+               +...+ ...                +... ....+..+...+++++++++.|+.|..++.
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               11111 000                0111 123577889999999999999988887766


Q ss_pred             hHHHhhccc
Q 041190          251 VWTNLCKPF  259 (261)
Q Consensus       251 ~w~~l~~~l  259 (261)
                      .|+.++..|
T Consensus       308 ~~~~ik~~~  316 (615)
T TIGR02903       308 VPKYIKKLF  316 (615)
T ss_pred             cchhhhhhc
Confidence            787765443

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.

>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=98.24  E-value=4.4e-06  Score=68.05  Aligned_cols=52  Identities=31%  Similarity=0.400  Sum_probs=35.6

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|.+.-++++.-++..... .+..+.-+-.||++|+||||||+.+.+..
T Consensus        23 L~efiGQ~~l~~~l~i~i~aa~~-r~~~l~h~lf~GPPG~GKTTLA~IIA~e~   74 (233)
T PF05496_consen   23 LDEFIGQEHLKGNLKILIRAAKK-RGEALDHMLFYGPPGLGKTTLARIIANEL   74 (233)
T ss_dssp             CCCS-S-HHHHHHHHHHHHHHHC-TTS---EEEEESSTTSSHHHHHHHHHHHC
T ss_pred             HHHccCcHHHHhhhHHHHHHHHh-cCCCcceEEEECCCccchhHHHHHHHhcc
Confidence            35789998888887665543111 23467788999999999999999999983

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.20  E-value=3e-06  Score=73.25  Aligned_cols=51  Identities=31%  Similarity=0.448  Sum_probs=39.9

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|++..++.|..++..... ....+..+.++|++|+|||+||+.+.+..
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~-~~~~~~~~ll~Gp~G~GKT~la~~ia~~~   54 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKM-RQEALDHLLLYGPPGLGKTTLAHIIANEM   54 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999998864221 12345567899999999999999998873

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=98.18  E-value=1e-05  Score=74.46  Aligned_cols=98  Identities=27%  Similarity=0.291  Sum_probs=61.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .+++|.+..++.|.+|+....  .+...+.+.|+|++|+||||+|+.+.+...    |+ .+-++.+...+.. .+..++
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~--~g~~~~~lLL~GppG~GKTtla~ala~el~----~~-~ielnasd~r~~~-~i~~~i   85 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWL--KGKPKKALLLYGPPGVGKTSLAHALANDYG----WE-VIELNASDQRTAD-VIERVA   85 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHh--cCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CC-EEEEcccccccHH-HHHHHH
Confidence            468999999999999987532  122367899999999999999999998732    22 2334555433332 233333


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCC
Q 041190          210 QAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~  248 (261)
                      .......             ..+..++-+||||++....
T Consensus        86 ~~~~~~~-------------sl~~~~~kvIiIDEaD~L~  111 (482)
T PRK04195         86 GEAATSG-------------SLFGARRKLILLDEVDGIH  111 (482)
T ss_pred             HHhhccC-------------cccCCCCeEEEEecCcccc
Confidence            3222100             0011366788888887764

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

Probab=98.17  E-value=7e-06  Score=73.64  Aligned_cols=108  Identities=15%  Similarity=0.105  Sum_probs=71.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .++++.+...+.+...|...        +.+.++|++|+|||++|+.+++.......|+...||++++.++..+++..+ 
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            45777888899999988753        467889999999999999999875444567778899999887765544311 


Q ss_pred             HHhcCCCCCCC--HHHHHHHHHHHhC--CCeEEEEEeCCCCCCh
Q 041190          210 QAAAGSADVND--LNLLQLQLENQLK--NKKFLLVLDDMWSENY  249 (261)
Q Consensus       210 ~~l~~~~~~~~--~~~~~~~l~~~l~--~kr~LiVlDdvw~~~~  249 (261)
                         .+....-.  ..-....+.....  +++|++|+|++-..+.
T Consensus       246 ---rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani  286 (459)
T PRK11331        246 ---RPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANL  286 (459)
T ss_pred             ---CCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCH
Confidence               11100000  0111222333322  4689999999987763

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

Probab=98.17  E-value=1.5e-05  Score=70.95  Aligned_cols=119  Identities=18%  Similarity=0.138  Sum_probs=84.7

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..+..+.||+.++..+.+|+..--  +.+..+-+.|.|.+|.|||.+...|+.+......--+++++++..-.....++.
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hl--e~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~  224 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHL--ELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFK  224 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhh--hcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHH
Confidence            456779999999999999987632  345667899999999999999999998843221212457888777667888899


Q ss_pred             HHHHHhcC-CCCCCCHHHHHHHHHHHhCCC--eEEEEEeCCCCC
Q 041190          207 VILQAAAG-SADVNDLNLLQLQLENQLKNK--KFLLVLDDMWSE  247 (261)
Q Consensus       207 ~i~~~l~~-~~~~~~~~~~~~~l~~~l~~k--r~LiVlDdvw~~  247 (261)
                      .|...+.+ ...+....+....+.+.....  -||+|||++...
T Consensus       225 kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L  268 (529)
T KOG2227|consen  225 KIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHL  268 (529)
T ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHH
Confidence            99988841 112222244555565555433  599999998654

>PF13173 AAA_14: AAA domain

Probab=98.16  E-value=4.1e-06  Score=62.94  Aligned_cols=76  Identities=21%  Similarity=0.179  Sum_probs=48.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeE
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKF  237 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~  237 (261)
                      +++.|.|+.|+|||||+++++++..   .....++++...........               .+ +...+.+...+++.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~---------------~~-~~~~~~~~~~~~~~   63 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLAD---------------PD-LLEYFLELIKPGKK   63 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhh---------------hh-hHHHHHHhhccCCc
Confidence            6899999999999999999988733   22345667765532211000               00 22334444445788


Q ss_pred             EEEEeCCCCCChhhHHH
Q 041190          238 LLVLDDMWSENYDVWTN  254 (261)
Q Consensus       238 LiVlDdvw~~~~~~w~~  254 (261)
                      +|+||++....  .|..
T Consensus        64 ~i~iDEiq~~~--~~~~   78 (128)
T PF13173_consen   64 YIFIDEIQYLP--DWED   78 (128)
T ss_pred             EEEEehhhhhc--cHHH
Confidence            89999998874  4543

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.12  E-value=6e-06  Score=72.20  Aligned_cols=51  Identities=33%  Similarity=0.475  Sum_probs=40.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|++..++.+..++..... .+.....+.++|++|+||||||+.+.+..
T Consensus        25 ~~~vG~~~~~~~l~~~l~~~~~-~~~~~~~~ll~GppG~GKT~la~~ia~~l   75 (328)
T PRK00080         25 DEFIGQEKVKENLKIFIEAAKK-RGEALDHVLLYGPPGLGKTTLANIIANEM   75 (328)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHh-cCCCCCcEEEECCCCccHHHHHHHHHHHh
Confidence            4699999999999888764211 12345678899999999999999999874

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

Probab=98.10  E-value=7.5e-06  Score=70.76  Aligned_cols=95  Identities=21%  Similarity=0.279  Sum_probs=59.2

Q ss_pred             CCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHH
Q 041190          126 LVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVT  205 (261)
Q Consensus       126 ~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~  205 (261)
                      .+.+..++|.+.-   |.+++..      +.+.-+-+||++|+||||||+.+.+..+...    ..+|..|....-..=.
T Consensus       140 yvGQ~hlv~q~gl---lrs~ieq------~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dv  206 (554)
T KOG2028|consen  140 YVGQSHLVGQDGL---LRSLIEQ------NRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDV  206 (554)
T ss_pred             hcchhhhcCcchH---HHHHHHc------CCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHH
Confidence            3445556665433   3444433      3567788999999999999999998755443    3356666554433334


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          206 KVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       206 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      ++|+++...              -..+..+|-+|++|+|-.-
T Consensus       207 R~ife~aq~--------------~~~l~krkTilFiDEiHRF  234 (554)
T KOG2028|consen  207 RDIFEQAQN--------------EKSLTKRKTILFIDEIHRF  234 (554)
T ss_pred             HHHHHHHHH--------------HHhhhcceeEEEeHHhhhh
Confidence            455554331              1124578899999998654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.05  E-value=2.6e-05  Score=58.28  Aligned_cols=88  Identities=23%  Similarity=0.110  Sum_probs=47.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCC-e
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNK-K  236 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~k-r  236 (261)
                      ..+.|+|++|+||||+++.+.......  .....++..+........... ...................+....+.. .
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~--~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPP--GGGVIYIDGEDILEEVLDQLL-LIIVGGKKASGSGELRLRLALALARKLKP   79 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCC--CCCEEEECCEEccccCHHHHH-hhhhhccCCCCCHHHHHHHHHHHHHhcCC
Confidence            578999999999999999998873322  112344444332221111111 011111112222222333444444444 4


Q ss_pred             EEEEEeCCCCCC
Q 041190          237 FLLVLDDMWSEN  248 (261)
Q Consensus       237 ~LiVlDdvw~~~  248 (261)
                      .+|++|++....
T Consensus        80 ~viiiDei~~~~   91 (148)
T smart00382       80 DVLILDEITSLL   91 (148)
T ss_pred             CEEEEECCcccC
Confidence            999999999875

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.

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

Probab=98.02  E-value=6.5e-05  Score=63.93  Aligned_cols=108  Identities=15%  Similarity=0.060  Sum_probs=74.6

Q ss_pred             chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc----ccceeEEEeeCCCCCHHHHHHHHHHHh
Q 041190          137 KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK----YFSFRACAYVSEDFDAVGVTKVILQAA  212 (261)
Q Consensus       137 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~i~~~i~~~l  212 (261)
                      ...+.|-++|...   .......+.|+|.+|.|||++++.....--...    .--.++.|.++..++...++..|++++
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 EALDRLEELLEYP---KRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEAL  120 (302)
T ss_pred             HHHHHHHHHHhCC---cccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHh
Confidence            3455566666543   355677899999999999999999885421111    111466788899999999999999999


Q ss_pred             c-CCCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          213 A-GSADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       213 ~-~~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                      + +.........+.......++ -+--+||+|++-+.
T Consensus       121 gaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~l  157 (302)
T PF05621_consen  121 GAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNL  157 (302)
T ss_pred             CcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHH
Confidence            9 43344455555555545553 24557889999764

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

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.01  E-value=3.9e-05  Score=67.09  Aligned_cols=45  Identities=18%  Similarity=0.310  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|++..++.|..++...      ..+.+.++|++|+||||+|+.+.+.
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~------~~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSP------NLPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCC------CCceEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999988543      3345789999999999999998876

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

Probab=98.00  E-value=2.5e-05  Score=74.71  Aligned_cols=45  Identities=29%  Similarity=0.433  Sum_probs=33.6

Q ss_pred             CccccccchHH---HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKE---VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~---~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+.   .+..++...      ++..+.++|++|+||||||+.+++.
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~------~~~slLL~GPpGtGKTTLA~aIA~~   75 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKAD------RVGSLILYGPPGVGKTTLARIIANH   75 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHH
Confidence            35788776653   455666432      4556789999999999999999986

>PRK08118 topology modulation protein; Reviewed

Probab=97.98  E-value=4.5e-06  Score=65.79  Aligned_cols=34  Identities=26%  Similarity=0.306  Sum_probs=28.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccc-cccceeEE
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVK-KYFSFRAC  192 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~w  192 (261)
                      -|.|+|++|+||||||+.+++..... -+|+...|
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            58999999999999999999986654 45777764

>PLN03025 replication factor C subunit; Provisional

Probab=97.94  E-value=7.4e-05  Score=65.11  Aligned_cols=45  Identities=18%  Similarity=0.278  Sum_probs=35.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|..++...      +.+.+-++|++|+||||+|+.+.+.
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~------~~~~lll~Gp~G~GKTtla~~la~~   57 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDG------NMPNLILSGPPGTGKTTSILALAHE   57 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHH
Confidence            35788888888888877542      3344678999999999999999876

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

Probab=97.91  E-value=1.7e-05  Score=59.26  Aligned_cols=22  Identities=41%  Similarity=0.452  Sum_probs=20.1

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |-++|++|+|||++|+.+.+..
T Consensus         1 ill~G~~G~GKT~l~~~la~~l   22 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL   22 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT
T ss_pred             CEEECcCCCCeeHHHHHHHhhc
Confidence            5689999999999999999983

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 ....

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.90  E-value=0.00014  Score=71.96  Aligned_cols=87  Identities=21%  Similarity=0.203  Sum_probs=59.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc-CCCC----------C---CC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA-GSAD----------V---ND  220 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~-~~~~----------~---~~  220 (261)
                      ..+++.|+|++|.||||++.+..+.      +...+|+++... .+...++..++..+. ....          .   .+
T Consensus        31 ~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~  104 (903)
T PRK04841         31 NYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYAS  104 (903)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCC
Confidence            5789999999999999999998754      225889999644 455667777777775 1110          0   12


Q ss_pred             HHHHHHHHHHHhC--CCeEEEEEeCCCCCC
Q 041190          221 LNLLQLQLENQLK--NKKFLLVLDDMWSEN  248 (261)
Q Consensus       221 ~~~~~~~l~~~l~--~kr~LiVlDdvw~~~  248 (261)
                      ...+...+...+.  +.+++|||||+-..+
T Consensus       105 ~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~  134 (903)
T PRK04841        105 LSSLFAQLFIELADWHQPLYLVIDDYHLIT  134 (903)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEEeCcCcCC
Confidence            2233333333332  678999999997765

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.88  E-value=0.00014  Score=62.97  Aligned_cols=45  Identities=24%  Similarity=0.330  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|++..++.+..++...      ..+.+.++|++|+||||+++.+.+.
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~------~~~~~ll~G~~G~GKt~~~~~l~~~   61 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEK------NMPHLLFAGPPGTGKTTAALALARE   61 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCC------CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            45889999999999998543      2345799999999999999999876

>PRK06893 DNA replication initiation factor; Validated

Probab=97.88  E-value=1.9e-05  Score=65.42  Aligned_cols=38  Identities=21%  Similarity=0.010  Sum_probs=27.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeC
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVS  196 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  196 (261)
                      .+.+.++|++|+|||+|++.+++..  ........|+++.
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~~--~~~~~~~~y~~~~   76 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNHY--LLNQRTAIYIPLS   76 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH--HHcCCCeEEeeHH
Confidence            3578999999999999999999873  2222234566653

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=9.1e-06  Score=74.81  Aligned_cols=47  Identities=34%  Similarity=0.383  Sum_probs=38.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+..++.|..++....     -.+.+.++|++|+||||+|+.+.+..
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-----l~ha~Lf~GppGtGKTTlA~~lA~~l   60 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-----LGHAYLFSGPRGVGKTTTARLIAMAV   60 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            358999988999988886532     34567999999999999999998764

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=0.0001  Score=71.16  Aligned_cols=47  Identities=26%  Similarity=0.335  Sum_probs=38.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+..++.|.+++....     -.+.+-++|++|+||||+|+.+.+..
T Consensus        16 ddIIGQe~Iv~~LknaI~~~r-----l~HAyLFtGPpGtGKTTLARiLAk~L   62 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQR-----LHHAYLFTGTRGVGKTSLARLFAKGL   62 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-----CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            468999999999999986532     23456799999999999999998763

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.85  E-value=7e-05  Score=66.43  Aligned_cols=47  Identities=23%  Similarity=0.287  Sum_probs=38.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+..++.+.+.+....     -.+.+.++|++|+||||+|+.+.+..
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~-----~~h~~L~~Gp~G~GKTtla~~la~~l   62 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGR-----IHHAWLLSGTRGVGKTTIARLLAKSL   62 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCC-----CCeEEEEecCCCCCHHHHHHHHHHHh
Confidence            468899999999999886532     34567899999999999999998763

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.81  E-value=7.2e-05  Score=68.80  Aligned_cols=47  Identities=30%  Similarity=0.357  Sum_probs=37.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+.-+..|...+...     .-.+.+-++|++|+||||+|+.+.+..
T Consensus        21 ~dliGq~~vv~~L~~ai~~~-----ri~~a~Lf~Gp~G~GKTT~ArilAk~L   67 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILND-----RLAGGYLLTGIRGVGKTTSARIIAKAV   67 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----CCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            35789998888888877543     234678899999999999999998763

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.81  E-value=0.00017  Score=62.69  Aligned_cols=107  Identities=14%  Similarity=0.176  Sum_probs=64.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc----ccccccceeEEEee-CCCCCHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA----GVKKYFSFRACAYV-SEDFDAVGV  204 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~----~~~~~f~~~~wv~v-~~~~~~~~i  204 (261)
                      .+++|.+..++.+...+..+     .-.+..-++|+.|+||||+|+.+++..    ....|.|+..|... +......+ 
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~-----~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-   77 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKN-----RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-   77 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcC-----CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-
Confidence            35788888889999998643     234677899999999999999887742    12345666666552 33334444 


Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          205 TKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       205 ~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      .+++.+.+...+               ..+++-++|+|++...+.+.|+.|..
T Consensus        78 ir~~~~~~~~~p---------------~~~~~kv~iI~~ad~m~~~a~naLLK  115 (313)
T PRK05564         78 IRNIIEEVNKKP---------------YEGDKKVIIIYNSEKMTEQAQNAFLK  115 (313)
T ss_pred             HHHHHHHHhcCc---------------ccCCceEEEEechhhcCHHHHHHHHH
Confidence            334444443110               11344455555555555455655543

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.80  E-value=0.00017  Score=66.81  Aligned_cols=46  Identities=30%  Similarity=0.364  Sum_probs=37.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|...+....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~diiGq~~~v~~L~~~i~~~r-----l~ha~Lf~Gp~GvGKTTlAr~lAk~   61 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQK-----VHHAYLFTGTRGVGKTTLGRLLAKC   61 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            358899999999999886532     2455778999999999999999764

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.79  E-value=7.1e-05  Score=71.04  Aligned_cols=46  Identities=26%  Similarity=0.346  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++..+.     -.+.+-++|..|+||||+|+.+.+.
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR-----L~HAyLFtGPpGvGKTTlAriLAKa   61 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR-----LHHAYLFTGTRGVGKTTLSRIFAKA   61 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999986532     2445679999999999999988765

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.79  E-value=4.9e-05  Score=62.60  Aligned_cols=54  Identities=20%  Similarity=0.129  Sum_probs=35.7

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      +...+.+..++..      .....+.++|++|+|||+||+.+++...  ......++++++.
T Consensus        23 ~~~~~~l~~~~~~------~~~~~lll~G~~G~GKT~la~~~~~~~~--~~~~~~~~i~~~~   76 (226)
T TIGR03420        23 AELLAALRQLAAG------KGDRFLYLWGESGSGKSHLLQAACAAAE--ERGKSAIYLPLAE   76 (226)
T ss_pred             HHHHHHHHHHHhc------CCCCeEEEECCCCCCHHHHHHHHHHHHH--hcCCcEEEEeHHH
Confidence            4456666666532      2356889999999999999999988632  2222344555443

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.

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

Probab=97.78  E-value=7.6e-05  Score=61.70  Aligned_cols=110  Identities=25%  Similarity=0.298  Sum_probs=66.2

Q ss_pred             CCCCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHH
Q 041190          124 PSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVG  203 (261)
Q Consensus       124 ~~~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  203 (261)
                      +..+....++|.+.+++.|++=...--  .+....-+-++|..|+|||++++.+.+....+.   .+ -|.|+..     
T Consensus        21 ~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl--~G~pannvLL~G~rGtGKSSlVkall~~y~~~G---LR-lIev~k~-----   89 (249)
T PF05673_consen   21 PDPIRLDDLIGIERQKEALIENTEQFL--QGLPANNVLLWGARGTGKSSLVKALLNEYADQG---LR-LIEVSKE-----   89 (249)
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHH--cCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC---ce-EEEECHH-----
Confidence            334556679999988888776221100  122455677899999999999999988632221   22 2444431     


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCCh-hhHHHhhccc
Q 041190          204 VTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY-DVWTNLCKPF  259 (261)
Q Consensus       204 i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~-~~w~~l~~~l  259 (261)
                                   +..++..+...|+  -+..||+|++||+.=... .....|++.|
T Consensus        90 -------------~L~~l~~l~~~l~--~~~~kFIlf~DDLsFe~~d~~yk~LKs~L  131 (249)
T PF05673_consen   90 -------------DLGDLPELLDLLR--DRPYKFILFCDDLSFEEGDTEYKALKSVL  131 (249)
T ss_pred             -------------HhccHHHHHHHHh--cCCCCEEEEecCCCCCCCcHHHHHHHHHh
Confidence                         1223334444444  246799999999864432 2455666544

>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=97.78  E-value=0.0001  Score=61.11  Aligned_cols=35  Identities=26%  Similarity=0.267  Sum_probs=27.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEe
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAY  194 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~  194 (261)
                      --+.|+|.+|+|||||...+...  ....|....+++
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~--~~~~f~~I~l~t   48 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYY--LRHKFDHIFLIT   48 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHh--hcccCCEEEEEe
Confidence            45789999999999999999877  667786555543

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

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.76  E-value=0.00012  Score=66.53  Aligned_cols=121  Identities=15%  Similarity=0.162  Sum_probs=66.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .+++|.+..+..|..++....     -.+.+-++|++|+||||+|+.+.+.........   ...+..+.+...+...+.
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-----IGHAYIFFGPRGVGKTTIARILAKRLNCENPIG---NEPCNECTSCLEITKGIS   89 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHhcCcccccC---ccccCCCcHHHHHHccCC
Confidence            458999988999999886532     234688999999999999999987632211100   001111111112111110


Q ss_pred             HHhc--CC---CCCCCHHHHHHHHHHH-hCCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          210 QAAA--GS---ADVNDLNLLQLQLENQ-LKNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       210 ~~l~--~~---~~~~~~~~~~~~l~~~-l~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                      ..+.  ..   ....+..++...+... ..++.-++|+|++...+.+.++.|...
T Consensus        90 ~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKt  144 (484)
T PRK14956         90 SDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKT  144 (484)
T ss_pred             ccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHH
Confidence            0010  00   0111222333333221 245667999999999988788876543

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.76  E-value=0.00017  Score=59.50  Aligned_cols=88  Identities=17%  Similarity=0.038  Sum_probs=53.6

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHH----hcC---CCCCCCHH---H
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQA----AAG---SADVNDLN---L  223 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~----l~~---~~~~~~~~---~  223 (261)
                      -+.-.++.|+|.+|+|||+++.++....  ...-...+|+... .++...+. .+...    +..   -....+..   +
T Consensus        20 i~~g~i~~i~G~~GsGKT~l~~~la~~~--~~~~~~v~yi~~e-~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (225)
T PRK09361         20 FERGTITQIYGPPGSGKTNICLQLAVEA--AKNGKKVIYIDTE-GLSPERFK-QIAGEDFEELLSNIIIFEPSSFEEQSE   95 (225)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHH--HHCCCeEEEEECC-CCCHHHHH-HHHhhChHhHhhCeEEEeCCCHHHHHH
Confidence            3456799999999999999999987652  2223456788876 45554432 22221    110   01122332   2


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCC
Q 041190          224 LQLQLENQLKNKKFLLVLDDMW  245 (261)
Q Consensus       224 ~~~~l~~~l~~kr~LiVlDdvw  245 (261)
                      ....+...+..+--++|+|.+-
T Consensus        96 ~i~~~~~~~~~~~~lvVIDsi~  117 (225)
T PRK09361         96 AIRKAEKLAKENVGLIVLDSAT  117 (225)
T ss_pred             HHHHHHHHHHhcccEEEEeCcH
Confidence            3344444454677899999984

>PRK07261 topology modulation protein; Provisional

Probab=97.75  E-value=9.8e-05  Score=58.37  Aligned_cols=35  Identities=26%  Similarity=0.255  Sum_probs=25.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccc-cccceeEEE
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVK-KYFSFRACA  193 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv  193 (261)
                      -|.|+|++|+||||||+.+....... -+.|...|-
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~   37 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQ   37 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEec
Confidence            47899999999999999997664332 134545553

>PRK08116 hypothetical protein; Validated

Probab=97.74  E-value=0.00011  Score=62.34  Aligned_cols=82  Identities=26%  Similarity=0.206  Sum_probs=47.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeE
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKF  237 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~  237 (261)
                      .-+.++|.+|+|||+||..+++..  .......++++      ..+++..+....... ...+..+    +.+.+.+-. 
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l--~~~~~~v~~~~------~~~ll~~i~~~~~~~-~~~~~~~----~~~~l~~~d-  180 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANEL--IEKGVPVIFVN------FPQLLNRIKSTYKSS-GKEDENE----IIRSLVNAD-  180 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH--HHcCCeEEEEE------HHHHHHHHHHHHhcc-ccccHHH----HHHHhcCCC-
Confidence            358899999999999999999973  22222344554      334455554443311 1112222    333344333 


Q ss_pred             EEEEeCCCCCChhhHH
Q 041190          238 LLVLDDMWSENYDVWT  253 (261)
Q Consensus       238 LiVlDdvw~~~~~~w~  253 (261)
                      ||||||+-......|.
T Consensus       181 lLviDDlg~e~~t~~~  196 (268)
T PRK08116        181 LLILDDLGAERDTEWA  196 (268)
T ss_pred             EEEEecccCCCCCHHH
Confidence            8999999544334564

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.73  E-value=3.7e-05  Score=68.19  Aligned_cols=53  Identities=23%  Similarity=0.114  Sum_probs=39.3

Q ss_pred             CCCccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|.+..++.|.+.+...-..       +-...+-+.++|++|+|||++|+.+++.
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            3456889999999999876432100       1123455889999999999999999987

Many proteins may score above the trusted cutoff because an internal

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.72  E-value=0.00019  Score=65.60  Aligned_cols=46  Identities=28%  Similarity=0.393  Sum_probs=36.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|...+....     -.+.+-++|++|+||||+|+.+.+.
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            458998888888888775432     2356789999999999999999775

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.71  E-value=7e-05  Score=67.02  Aligned_cols=53  Identities=21%  Similarity=0.084  Sum_probs=39.3

Q ss_pred             CCCccccccchHHHHHHHhhCCCC-------CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDL-------NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|++..+++|.+.+...-.       -+-...+-+.++|++|+|||++|+.+++.
T Consensus       129 ~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            334688999999999887643110       01234566889999999999999999986

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.71  E-value=0.00015  Score=59.08  Aligned_cols=89  Identities=11%  Similarity=0.101  Sum_probs=55.5

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHh-c---------CCCCCCCHHH
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAA-A---------GSADVNDLNL  223 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l-~---------~~~~~~~~~~  223 (261)
                      -+.-+++.|+|++|+|||+++.++...  ........+|+.... ++...+.+. .... .         ...+..+...
T Consensus         9 i~~g~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~   84 (209)
T TIGR02237         9 VERGTITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGV   84 (209)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHH
Confidence            456789999999999999999988765  222345678888876 665554443 2221 1         1111122223


Q ss_pred             HHHHHHHHhCC-CeEEEEEeCCCC
Q 041190          224 LQLQLENQLKN-KKFLLVLDDMWS  246 (261)
Q Consensus       224 ~~~~l~~~l~~-kr~LiVlDdvw~  246 (261)
                      ....+.+.+.. +.-+||+|.+-.
T Consensus        85 ~~~~l~~~~~~~~~~lvVIDSis~  108 (209)
T TIGR02237        85 AIQKTSKFIDRDSASLVVVDSFTA  108 (209)
T ss_pred             HHHHHHHHHhhcCccEEEEeCcHH
Confidence            35555555543 567999999864

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

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.71  E-value=0.00029  Score=61.15  Aligned_cols=46  Identities=24%  Similarity=0.242  Sum_probs=38.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.+..++...     .-..++.++|++|+||||+|+.+++.
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~-----~~~~~lll~G~~G~GKT~la~~l~~~   66 (316)
T PHA02544         21 DECILPAADKETFKSIVKKG-----RIPNMLLHSPSPGTGKTTVAKALCNE   66 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcC-----CCCeEEEeeCcCCCCHHHHHHHHHHH
Confidence            46899999999999998643     23568888999999999999999886

>TIGR00763 lon ATP-dependent protease La

Probab=97.70  E-value=0.0023  Score=62.34  Aligned_cols=51  Identities=29%  Similarity=0.391  Sum_probs=37.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+.-++.|.+++.........+..++.++|++|+|||++|+.+.+.
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~  370 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKA  370 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            347888888888888664321111223457899999999999999999887

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.

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.69  E-value=0.00029  Score=62.01  Aligned_cols=104  Identities=15%  Similarity=0.082  Sum_probs=64.8

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccccccee-EEEeeCCCC-CHHHHHHHHHHHhc-C
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFR-ACAYVSEDF-DAVGVTKVILQAAA-G  214 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~-~wv~v~~~~-~~~~i~~~i~~~l~-~  214 (261)
                      -...+++.+..-.     +-.-..|+|.+|+|||||++.+.+.... ++-+.. +|+.+.+.. .+.++++.+...+. .
T Consensus       119 ~~~RvID~l~PiG-----kGQR~LIvG~pGtGKTTLl~~la~~i~~-~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvas  192 (380)
T PRK12608        119 LSMRVVDLVAPIG-----KGQRGLIVAPPRAGKTVLLQQIAAAVAA-NHPEVHLMVLLIDERPEEVTDMRRSVKGEVYAS  192 (380)
T ss_pred             hhHhhhhheeecC-----CCceEEEECCCCCCHHHHHHHHHHHHHh-cCCCceEEEEEecCCCCCHHHHHHHHhhhEEee
Confidence            3445777776532     1234599999999999999998886321 122443 677777654 67788888877666 2


Q ss_pred             CCCCCCHHH-----HHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          215 SADVNDLNL-----LQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       215 ~~~~~~~~~-----~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      ..+......     ....+-+++  .+++++||+|++-..
T Consensus       193 t~de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr~  232 (380)
T PRK12608        193 TFDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRL  232 (380)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHHH
Confidence            222222111     112222223  589999999999543

>PRK12377 putative replication protein; Provisional

Probab=97.69  E-value=0.00017  Score=60.38  Aligned_cols=80  Identities=20%  Similarity=0.086  Sum_probs=46.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeE
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKF  237 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~  237 (261)
                      ..+.++|.+|+|||+||..+.+...  .....+.+++++      +++..+-....   +......+    .+.+ .+--
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~--~~g~~v~~i~~~------~l~~~l~~~~~---~~~~~~~~----l~~l-~~~d  165 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLL--AKGRSVIVVTVP------DVMSRLHESYD---NGQSGEKF----LQEL-CKVD  165 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH--HcCCCeEEEEHH------HHHHHHHHHHh---ccchHHHH----HHHh-cCCC
Confidence            5789999999999999999998742  222234555543      34444433322   11122222    2222 4667


Q ss_pred             EEEEeCCCCCChhhHH
Q 041190          238 LLVLDDMWSENYDVWT  253 (261)
Q Consensus       238 LiVlDdvw~~~~~~w~  253 (261)
                      ||||||+-......|.
T Consensus       166 LLiIDDlg~~~~s~~~  181 (248)
T PRK12377        166 LLVLDEIGIQRETKNE  181 (248)
T ss_pred             EEEEcCCCCCCCCHHH
Confidence            8999999554333454

>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=97.69  E-value=1.9e-05  Score=59.99  Aligned_cols=87  Identities=21%  Similarity=0.129  Sum_probs=49.2

Q ss_pred             EeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHHHHhCCCeEE
Q 041190          160 IPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG-SADVNDLNLLQLQLENQLKNKKFL  238 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~-~~~~~~~~~~~~~l~~~l~~kr~L  238 (261)
                      |-++|++|+|||+||+.+....  ..   ...-+.++...+..+++...--.-+. .........   .+     .+..+
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~--~~---~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~---a~-----~~~~i   68 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL--GR---PVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVR---AM-----RKGGI   68 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH--TC---EEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCT---TH-----HEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh--hc---ceEEEEeccccccccceeeeeecccccccccccccc---cc-----cceeE
Confidence            5789999999999999998863  11   12336777776766554321111000 000000000   00     18899


Q ss_pred             EEEeCCCCCChhhHHHhhccc
Q 041190          239 LVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       239 iVlDdvw~~~~~~w~~l~~~l  259 (261)
                      +|||++....++.+..|...|
T Consensus        69 l~lDEin~a~~~v~~~L~~ll   89 (139)
T PF07728_consen   69 LVLDEINRAPPEVLESLLSLL   89 (139)
T ss_dssp             EEESSCGG--HHHHHTTHHHH
T ss_pred             EEECCcccCCHHHHHHHHHHH
Confidence            999999987766777665544

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.

>PRK08727 hypothetical protein; Validated

Probab=97.68  E-value=0.00016  Score=60.11  Aligned_cols=38  Identities=24%  Similarity=0.195  Sum_probs=27.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      ..+.++|.+|+|||+|++.+++..  ........|+++.+
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~--~~~~~~~~y~~~~~   79 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAA--EQAGRSSAYLPLQA   79 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEEeHHH
Confidence            459999999999999999998763  22222345666543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.67  E-value=0.00031  Score=58.23  Aligned_cols=92  Identities=18%  Similarity=0.104  Sum_probs=56.7

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccc----cceeEEEeeCCCCCHHHHHHHHHHHhcCC----------CCCC
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKY----FSFRACAYVSEDFDAVGVTKVILQAAAGS----------ADVN  219 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~i~~~i~~~l~~~----------~~~~  219 (261)
                      -+.-.++.|+|++|+|||+|+.++.-.......    ....+|+...+.++...+.. +++..+..          ....
T Consensus        16 i~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~-~~~~~~~~~~~~~~~i~~~~~~   94 (235)
T cd01123          16 IETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQ-IAERFGLDPEEVLDNIYVARAY   94 (235)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHH-HHHHhccChHhHhcCEEEEecC
Confidence            345689999999999999999999744212221    24678998888777655433 33333210          0112


Q ss_pred             CHH---HHHHHHHHHh-CC-CeEEEEEeCCCC
Q 041190          220 DLN---LLQLQLENQL-KN-KKFLLVLDDMWS  246 (261)
Q Consensus       220 ~~~---~~~~~l~~~l-~~-kr~LiVlDdvw~  246 (261)
                      +..   .+...+...+ +. +--|||+|.+..
T Consensus        95 ~~~~l~~~l~~l~~~l~~~~~~~liVIDSis~  126 (235)
T cd01123          95 NSDHQLQLLEELEAILIESSRIKLVIVDSVTA  126 (235)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCeeEEEEeCcHH
Confidence            222   3334444444 34 778999999975

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 .

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.66  E-value=0.00037  Score=65.51  Aligned_cols=46  Identities=24%  Similarity=0.322  Sum_probs=38.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++....     -.+.+-++|++|+||||+|+.+.+.
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr-----l~HAyLF~GPpGvGKTTlAriLAK~   60 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR-----LHHAYLFTGTRGVGKTTIARILAKC   60 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999997532     2467889999999999999988765

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.65  E-value=0.00012  Score=67.31  Aligned_cols=52  Identities=23%  Similarity=0.129  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCC-------CCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL-------NSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.|.+..+++|.+.+...-.       -+-+..+-+.++|++|+|||++|+.+++..
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL  240 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSL  240 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhh
Confidence            4577888888888887542100       012234558899999999999999999874

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.63  E-value=0.00042  Score=65.03  Aligned_cols=46  Identities=24%  Similarity=0.320  Sum_probs=37.9

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++....     -.+.+-++|..|+||||+|+.+.+.
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-----LpHA~LFtGP~GvGKTTLAriLAka   61 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-----LHHAYLFTGTRGVGKTTLSRILAKS   61 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-----CceEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999996542     3456788999999999999988765

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

Probab=97.63  E-value=0.00024  Score=68.76  Aligned_cols=44  Identities=25%  Similarity=0.301  Sum_probs=36.8

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++||+.+.+.++..|....      ..-+-++|++|+|||++|+.+.+.
T Consensus       183 ~~igr~~ei~~~~~~L~~~~------~~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       183 PLIGREDELERTIQVLCRRK------KNNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             cccCcHHHHHHHHHHHhcCC------CCceEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999997642      233568999999999999999876

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.61  E-value=0.00028  Score=59.66  Aligned_cols=50  Identities=22%  Similarity=0.269  Sum_probs=33.3

Q ss_pred             ccccccchHHHHHHHhhC---------CCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLG---------DDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~---------~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.+.-++.|.++...         ......+....+.++|++|+||||+|+.+.+.
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~   65 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKL   65 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHH
Confidence            478877666666543211         01112344567889999999999999999765

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.61  E-value=0.00057  Score=63.54  Aligned_cols=46  Identities=28%  Similarity=0.372  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++....     -.+.+-++|++|+||||+|+.+.+.
T Consensus        16 ~divGq~~v~~~L~~~i~~~~-----~~ha~Lf~Gp~G~GKTt~A~~lAk~   61 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR-----LHHAYLFTGTRGVGKTTLARILAKS   61 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            358899999999999886532     2345678999999999999988765

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.61  E-value=0.00049  Score=63.64  Aligned_cols=46  Identities=24%  Similarity=0.283  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+.-++.|.+++....     -...+-++|++|+||||+|+.+.+.
T Consensus        16 ~divGq~~v~~~L~~~~~~~~-----l~ha~Lf~Gp~G~GKTt~A~~lAk~   61 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY-----LHHAYLFTGTRGVGKTTISRILAKC   61 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-----CCeeEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999996532     2346789999999999999888765

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.60  E-value=0.0037  Score=57.59  Aligned_cols=25  Identities=32%  Similarity=0.315  Sum_probs=21.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.++.++|++|+||||++..+...
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~  373 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQR  373 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999887653

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=97.59  E-value=0.00016  Score=67.57  Aligned_cols=107  Identities=20%  Similarity=0.258  Sum_probs=65.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .+=+|.++-++.|++.|.-......-+-+++..||++|+|||.|++.|.+.  ....| .+  +.+++-.+..+|...  
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~a--l~Rkf-vR--~sLGGvrDEAEIRGH--  395 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKA--LGRKF-VR--ISLGGVRDEAEIRGH--  395 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHH--hCCCE-EE--EecCccccHHHhccc--
Confidence            345788999999999886543223344579999999999999999999987  44444 12  233443333322211  


Q ss_pred             HHhcCCCCCCCH-HHHHHHHHHHhCCCeEEEEEeCCCCCC
Q 041190          210 QAAAGSADVNDL-NLLQLQLENQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       210 ~~l~~~~~~~~~-~~~~~~l~~~l~~kr~LiVlDdvw~~~  248 (261)
                          ..+..+++ ..+++-++ ...-++-|++||++....
T Consensus       396 ----RRTYIGamPGrIiQ~mk-ka~~~NPv~LLDEIDKm~  430 (782)
T COG0466         396 ----RRTYIGAMPGKIIQGMK-KAGVKNPVFLLDEIDKMG  430 (782)
T ss_pred             ----cccccccCChHHHHHHH-HhCCcCCeEEeechhhcc
Confidence                11111221 22222222 235678899999998875

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.59  E-value=0.00045  Score=65.01  Aligned_cols=46  Identities=24%  Similarity=0.365  Sum_probs=37.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+.-+..|.+++....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r-----l~ha~Lf~Gp~GvGKTtlAr~lAk~   61 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR-----LHHAYLFTGTRGVGKTTVSRILAKS   61 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            458898888899999886532     3466789999999999999988544

>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=97.58  E-value=5.7e-05  Score=55.79  Aligned_cols=23  Identities=43%  Similarity=0.511  Sum_probs=20.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +|.|.|++|+||||+|+.+.+..
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999998863

...

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.58  E-value=0.00026  Score=66.86  Aligned_cols=46  Identities=24%  Similarity=0.350  Sum_probs=38.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|.+++....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r-----l~Ha~Lf~GP~GvGKTTlAriLAk~   61 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR-----LHHAYLLTGTRGVGKTTIARILAKS   61 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            468999999999999986532     2457889999999999999988765

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.57  E-value=0.00055  Score=61.48  Aligned_cols=47  Identities=21%  Similarity=0.192  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+.-++.|..++...     .-.+.+-++|++|+||||+|+.+.+..
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~-----~~~ha~lf~Gp~G~GKtt~A~~~a~~l   62 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMG-----RVGHGYIFSGLRGVGKTTAARVFAKAV   62 (397)
T ss_pred             hhccChHHHHHHHHHHHHhC-----CcceeEEEECCCCCCHHHHHHHHHHHh
Confidence            46889988889999888643     223457789999999999999887653

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.54  E-value=0.00027  Score=69.17  Aligned_cols=45  Identities=29%  Similarity=0.376  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++||+++++.++..|....      ..-+.++|++|+|||++|+.+...
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~------~~n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRT------KNNPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccc------cCCeEEECCCCCCHHHHHHHHHHH
Confidence            348999999999999997642      223469999999999999988775

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

Probab=97.53  E-value=0.00028  Score=56.18  Aligned_cols=80  Identities=28%  Similarity=0.272  Sum_probs=43.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCe
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKK  236 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr  236 (261)
                      ..-+.++|.+|+|||.||..+.+..- ...+ ...|+++      .+    ++..+...............    +. +-
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~-~~g~-~v~f~~~------~~----L~~~l~~~~~~~~~~~~~~~----l~-~~  109 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAI-RKGY-SVLFITA------SD----LLDELKQSRSDGSYEELLKR----LK-RV  109 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHH-HTT---EEEEEH------HH----HHHHHHCCHCCTTHCHHHHH----HH-TS
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhc-cCCc-ceeEeec------Cc----eeccccccccccchhhhcCc----cc-cc
Confidence            35699999999999999999987531 1222 2445543      23    33344422222233333322    22 34


Q ss_pred             EEEEEeCCCCCChhhHH
Q 041190          237 FLLVLDDMWSENYDVWT  253 (261)
Q Consensus       237 ~LiVlDdvw~~~~~~w~  253 (261)
                      =|+||||+-......|.
T Consensus       110 dlLilDDlG~~~~~~~~  126 (178)
T PF01695_consen  110 DLLILDDLGYEPLSEWE  126 (178)
T ss_dssp             SCEEEETCTSS---HHH
T ss_pred             cEecccccceeeecccc
Confidence            57789999877555554

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.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.53  E-value=0.00063  Score=63.56  Aligned_cols=46  Identities=24%  Similarity=0.440  Sum_probs=37.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.+.+.+....     -.+.+-++|++|+||||+|+.+.+.
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~r-----l~hA~Lf~GP~GvGKTTlA~~lAk~   61 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNK-----LTHAYIFSGPRGIGKTSIAKIFAKA   61 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999886532     2457889999999999999998765

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.52  E-value=8.8e-05  Score=64.91  Aligned_cols=53  Identities=17%  Similarity=0.240  Sum_probs=43.0

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..+++|.++.++++++++.......+.+-+++.++|++|+||||||+.+.+..
T Consensus        50 ~~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       50 DHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             chhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34799999999999999877432123456889999999999999999998774

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

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

Probab=97.52  E-value=0.0012  Score=54.41  Aligned_cols=91  Identities=16%  Similarity=0.000  Sum_probs=57.2

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhcccccccc------ceeEEEeeCCCCCHHHHHHHHHHHhcCC----------CC
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF------SFRACAYVSEDFDAVGVTKVILQAAAGS----------AD  217 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f------~~~~wv~v~~~~~~~~i~~~i~~~l~~~----------~~  217 (261)
                      -+.-.++.|+|.+|+|||+|+.++.....  ..-      ...+|+.....++...+. .+.......          ..
T Consensus        16 ~~~g~v~~I~G~~GsGKT~l~~~ia~~~~--~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~   92 (226)
T cd01393          16 IPTGRITEIFGEFGSGKTQLCLQLAVEAQ--LPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVAR   92 (226)
T ss_pred             CcCCcEEEEeCCCCCChhHHHHHHHHHhh--cccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEe
Confidence            34567999999999999999998865421  122      346788887777765544 333332210          11


Q ss_pred             CCCHHHHHHHHHHHhC----CCeEEEEEeCCCCC
Q 041190          218 VNDLNLLQLQLENQLK----NKKFLLVLDDMWSE  247 (261)
Q Consensus       218 ~~~~~~~~~~l~~~l~----~kr~LiVlDdvw~~  247 (261)
                      ..+.+++...+.....    .+--|||+|.+...
T Consensus        93 ~~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis~l  126 (226)
T cd01393          93 PYNGEQQLEIVEELERIMSSGRVDLVVVDSVAAL  126 (226)
T ss_pred             CCCHHHHHHHHHHHHHHhhcCCeeEEEEcCcchh
Confidence            2345555555555442    45569999999653

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.

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.48  E-value=0.00016  Score=68.06  Aligned_cols=50  Identities=24%  Similarity=0.290  Sum_probs=39.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.++.++.+..+|..... ......++.++|++|+||||+++.+...
T Consensus        84 del~~~~~ki~~l~~~l~~~~~-~~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        84 HELAVHKKKIEEVETWLKAQVL-ENAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             HHhcCcHHHHHHHHHHHHhccc-ccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4688888888899999876422 1223457999999999999999999886

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

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.48  E-value=0.00078  Score=63.63  Aligned_cols=46  Identities=28%  Similarity=0.327  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+.-++.|...+....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~divGQe~vv~~L~~~l~~~r-----l~hAyLf~Gp~GvGKTTlAr~lAk~   61 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR-----LHHAYLFSGTRGVGKTTIARLLAKG   61 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999998886532     2345678999999999999999776

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

Probab=97.47  E-value=0.00044  Score=61.96  Aligned_cols=51  Identities=22%  Similarity=0.092  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCC-------CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL-------NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.+..+++|.+.+...-.       -+-...+-+.++|++|+|||+||+.+.+.
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            4588888888888876542100       01234567889999999999999999986

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.47  E-value=0.0004  Score=60.04  Aligned_cols=101  Identities=18%  Similarity=0.190  Sum_probs=58.1

Q ss_pred             cccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc
Q 041190          134 GREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA  213 (261)
Q Consensus       134 gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~  213 (261)
                      ++........+++..-.  ..+...-+.++|..|+|||.||..+.+..- +..+. +.+++++      .++.++-..+.
T Consensus       135 ~~~~~~~~~~~fi~~~~--~~~~~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~~-v~~~~~~------~l~~~lk~~~~  204 (306)
T PRK08939        135 DRLDALMAALDFLEAYP--PGEKVKGLYLYGDFGVGKSYLLAAIANELA-KKGVS-STLLHFP------EFIRELKNSIS  204 (306)
T ss_pred             HHHHHHHHHHHHHHHhh--ccCCCCeEEEECCCCCCHHHHHHHHHHHHH-HcCCC-EEEEEHH------HHHHHHHHHHh
Confidence            34444444555554322  122346789999999999999999998742 22232 3445543      34444444433


Q ss_pred             CCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHH
Q 041190          214 GSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWT  253 (261)
Q Consensus       214 ~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~  253 (261)
                          ..+..+....    + .+-=||||||+-......|.
T Consensus       205 ----~~~~~~~l~~----l-~~~dlLiIDDiG~e~~s~~~  235 (306)
T PRK08939        205 ----DGSVKEKIDA----V-KEAPVLMLDDIGAEQMSSWV  235 (306)
T ss_pred             ----cCcHHHHHHH----h-cCCCEEEEecCCCccccHHH
Confidence                1122222222    2 35678999999876656674

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

Probab=97.47  E-value=0.0035  Score=58.92  Aligned_cols=108  Identities=21%  Similarity=0.259  Sum_probs=67.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .+=+|.++-++.|.++|--....++-+-+++..+|++|+|||.+++.|...  ....| +|  +++++-.+..+|...  
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~A--LnRkF-fR--fSvGG~tDvAeIkGH--  483 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARA--LNRKF-FR--FSVGGMTDVAEIKGH--  483 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHH--hCCce-EE--EeccccccHHhhccc--
Confidence            445788899999999987755445667889999999999999999999887  43333 12  234444343332211  


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCC
Q 041190          210 QAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~  248 (261)
                         ....-..-...+++.+++ .+-.+-|+.||+|...-
T Consensus       484 ---RRTYVGAMPGkiIq~LK~-v~t~NPliLiDEvDKlG  518 (906)
T KOG2004|consen  484 ---RRTYVGAMPGKIIQCLKK-VKTENPLILIDEVDKLG  518 (906)
T ss_pred             ---ceeeeccCChHHHHHHHh-hCCCCceEEeehhhhhC
Confidence               001111122233333333 34567788899997653

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

Probab=97.43  E-value=0.00065  Score=65.73  Aligned_cols=118  Identities=16%  Similarity=0.216  Sum_probs=69.2

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.|...+.....   +.+....++.++|++|+|||+||+.+....     +...+.+++++-....    
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            4578888888888887764211   012335578899999999999999998763     1223444544421111    


Q ss_pred             HHHHHhcCCCC--CCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSAD--VNDLNLLQLQLENQLK-NKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~--~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      .+..-++....  ..+.   ...+.+.++ ....+|+||++....++.++.|...|
T Consensus       525 ~~~~lig~~~gyvg~~~---~~~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~l  577 (731)
T TIGR02639       525 TVSRLIGAPPGYVGFEQ---GGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVM  577 (731)
T ss_pred             cHHHHhcCCCCCcccch---hhHHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhh
Confidence            11122231111  1111   112333443 34469999999999888888776544

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.42  E-value=0.00086  Score=56.03  Aligned_cols=83  Identities=17%  Similarity=0.168  Sum_probs=48.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCe
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKK  236 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr  236 (261)
                      ...+.++|.+|+|||+|+..+.+....  .-...++++      ..+++..+-.... . .......    +.+.+. +.
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~--~g~~v~~it------~~~l~~~l~~~~~-~-~~~~~~~----~l~~l~-~~  163 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLL--RGKSVLIIT------VADIMSAMKDTFS-N-SETSEEQ----LLNDLS-NV  163 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEE------HHHHHHHHHHHHh-h-ccccHHH----HHHHhc-cC
Confidence            357899999999999999999987322  112334443      3444444433322 1 1112222    333344 44


Q ss_pred             EEEEEeCCCCCChhhHHH
Q 041190          237 FLLVLDDMWSENYDVWTN  254 (261)
Q Consensus       237 ~LiVlDdvw~~~~~~w~~  254 (261)
                      =||||||+-......|..
T Consensus       164 dlLvIDDig~~~~s~~~~  181 (244)
T PRK07952        164 DLLVIDEIGVQTESRYEK  181 (244)
T ss_pred             CEEEEeCCCCCCCCHHHH
Confidence            588889998876566753

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.41  E-value=0.00046  Score=57.45  Aligned_cols=24  Identities=17%  Similarity=0.210  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.|+|++|+|||+|++.+++.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~   68 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAE   68 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999999886

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.41  E-value=0.00024  Score=56.30  Aligned_cols=26  Identities=46%  Similarity=0.667  Sum_probs=23.3

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++..+|.++|++|+||||+|+.+++.
T Consensus         5 ~~~~~I~i~G~~GsGKst~a~~l~~~   30 (176)
T PRK05541          5 PNGYVIWITGLAGSGKTTIAKALYER   30 (176)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            35579999999999999999999886

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

Probab=97.41  E-value=0.0006  Score=57.38  Aligned_cols=82  Identities=24%  Similarity=0.119  Sum_probs=48.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNK  235 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~k  235 (261)
                      +..-+.++|.+|+|||.||..+.+..- +..+. +.+++      ..+++.++......   ......+...+     .+
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~s-v~f~~------~~el~~~Lk~~~~~---~~~~~~l~~~l-----~~  167 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KAGIS-VLFIT------APDLLSKLKAAFDE---GRLEEKLLREL-----KK  167 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCe-EEEEE------HHHHHHHHHHHHhc---CchHHHHHHHh-----hc
Confidence            345689999999999999999988743 32232 23344      33444444443331   11122222212     24


Q ss_pred             eEEEEEeCCCCCChhhHH
Q 041190          236 KFLLVLDDMWSENYDVWT  253 (261)
Q Consensus       236 r~LiVlDdvw~~~~~~w~  253 (261)
                      -=|+||||+-......|.
T Consensus       168 ~dlLIiDDlG~~~~~~~~  185 (254)
T COG1484         168 VDLLIIDDIGYEPFSQEE  185 (254)
T ss_pred             CCEEEEecccCccCCHHH
Confidence            458889999887655664

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.40  E-value=0.0018  Score=57.13  Aligned_cols=46  Identities=22%  Similarity=0.297  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++...     .-.+.+-++|++|+||||+|+.+.+.
T Consensus        14 ~~iig~~~~~~~l~~~~~~~-----~~~~~~Ll~G~~G~GKt~~a~~la~~   59 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNG-----RIAHAYLFSGPRGTGKTSIARIFAKA   59 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcC-----CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            46799999999999988643     23457789999999999999888655

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.40  E-value=0.0018  Score=60.74  Aligned_cols=46  Identities=26%  Similarity=0.268  Sum_probs=37.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++...     .-.+.+-++|+.|+||||+|+.+.+.
T Consensus        13 ~eivGq~~i~~~L~~~i~~~-----r~~ha~Lf~Gp~G~GKTt~A~~lAk~   58 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAG-----RINHAYLFSGPRGCGKTSSARILARS   58 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999653     23456789999999999999988765

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.39  E-value=0.0012  Score=57.54  Aligned_cols=92  Identities=15%  Similarity=0.123  Sum_probs=57.7

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhcccccccc----ceeEEEeeCCCCCHHHHHHHHHHHhcCCC----------CCC
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF----SFRACAYVSEDFDAVGVTKVILQAAAGSA----------DVN  219 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~~~wv~v~~~~~~~~i~~~i~~~l~~~~----------~~~  219 (261)
                      -+.-.++-|+|++|+|||+++.+++-.......+    ...+|+...++++...+.. +++.++...          ...
T Consensus        99 i~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g~~~~~~l~~i~~~~~~  177 (317)
T PRK04301         99 IETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALGLDPDEVLDNIHVARAY  177 (317)
T ss_pred             ccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcCCChHhhhccEEEEeCC
Confidence            3456899999999999999999887542221111    3578999988888777654 344444110          111


Q ss_pred             CH---HHHHHHHHHHhCC--CeEEEEEeCCCC
Q 041190          220 DL---NLLQLQLENQLKN--KKFLLVLDDMWS  246 (261)
Q Consensus       220 ~~---~~~~~~l~~~l~~--kr~LiVlDdvw~  246 (261)
                      +.   ..+...+...+..  +--|||+|.+-.
T Consensus       178 ~~~~~~~~~~~l~~~i~~~~~~~lvVIDSisa  209 (317)
T PRK04301        178 NSDHQMLLAEKAEELIKEGENIKLVIVDSLTA  209 (317)
T ss_pred             CHHHHHHHHHHHHHHHhccCceeEEEEECchH
Confidence            11   2334455555543  445999999865

>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=97.39  E-value=0.0014  Score=54.02  Aligned_cols=50  Identities=26%  Similarity=0.360  Sum_probs=31.6

Q ss_pred             CCccccc-cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGR-EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr-~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ++.++|. ++..-.....+....   +.....+.|+|..|+|||.|.+.+++..
T Consensus         8 dnfv~g~~N~~a~~~~~~ia~~~---~~~~~~l~l~G~~G~GKTHLL~Ai~~~~   58 (219)
T PF00308_consen    8 DNFVVGESNELAYAAAKAIAENP---GERYNPLFLYGPSGLGKTHLLQAIANEA   58 (219)
T ss_dssp             CCS--TTTTHHHHHHHHHHHHST---TTSSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             ccCCcCCcHHHHHHHHHHHHhcC---CCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            3445564 333334444443321   2345668999999999999999999873

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.

>PRK06696 uridine kinase; Validated

Probab=97.38  E-value=0.00023  Score=58.76  Aligned_cols=43  Identities=21%  Similarity=0.191  Sum_probs=34.2

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |..-+++|.+.+...   ...+..+|+|.|.+|+||||||+.+.+.
T Consensus         3 ~~~~~~~la~~~~~~---~~~~~~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696          3 RKQLIKELAEHILTL---NLTRPLRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             HHHHHHHHHHHHHHh---CCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            555677777777653   2346789999999999999999999876

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.38  E-value=0.0012  Score=64.40  Aligned_cols=47  Identities=26%  Similarity=0.249  Sum_probs=37.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+..++.|..++....     -.+.+.++|+.|+||||+|+.+.+..
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-----i~Ha~Lf~Gp~G~GKTt~A~~lAr~L   61 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-----INHAYLFSGPRGCGKTSSARILARSL   61 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-----CCceEEEECCCCCCHHHHHHHHHHHh
Confidence            368899999999999986532     23567899999999999999887653

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

Probab=97.37  E-value=0.0052  Score=59.76  Aligned_cols=51  Identities=25%  Similarity=0.326  Sum_probs=39.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.+|.+.-++.|+++|.........+..++.++|++|+||||+++.+...
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~  372 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKA  372 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999998887422112234568999999999999999999876

>PRK08181 transposase; Validated

Probab=97.37  E-value=0.00045  Score=58.57  Aligned_cols=23  Identities=26%  Similarity=0.225  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-+.++|++|+|||.||..+.+.
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~  129 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLA  129 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHH
Confidence            34899999999999999999875

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

Probab=97.36  E-value=0.00082  Score=55.04  Aligned_cols=108  Identities=19%  Similarity=0.128  Sum_probs=63.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .++||.++-++.|.-+-..      .+.+-+-|.||+|+||||-+..+.+..--..+=+...=.+.|......-+...|-
T Consensus        27 ~dIVGNe~tv~rl~via~~------gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK  100 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKE------GNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIK  100 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHc------CCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHH
Confidence            4689998888877665543      3577889999999999996665554311111112233345555444433332221


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHh-CCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          210 QAAAGSADVNDLNLLQLQLENQL-KNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l-~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                       .+.+.             +-.| .++--+|+||+..+........++.
T Consensus       101 -~FAQ~-------------kv~lp~grhKIiILDEADSMT~gAQQAlRR  135 (333)
T KOG0991|consen  101 -MFAQK-------------KVTLPPGRHKIIILDEADSMTAGAQQALRR  135 (333)
T ss_pred             -HHHHh-------------hccCCCCceeEEEeeccchhhhHHHHHHHH
Confidence             11100             0001 2566789999999988666666654

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.36  E-value=0.0014  Score=61.75  Aligned_cols=46  Identities=22%  Similarity=0.331  Sum_probs=38.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+.+...     .-..-+-++|+.|+||||+|+.+.+.
T Consensus        24 ~dliGq~~~v~~L~~~~~~g-----ri~ha~L~~Gp~GvGKTt~Ar~lAk~   69 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETG-----RIAQAFMLTGVRGVGKTTTARILARA   69 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcC-----CCCceEEEECCCCCCHHHHHHHHHHh
Confidence            46899999999999988653     23456888999999999999998765

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.36  E-value=0.00053  Score=67.20  Aligned_cols=123  Identities=14%  Similarity=0.156  Sum_probs=68.4

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.|...+.....   +.+.....+.++|++|+|||+||+.+.+..  -..-...+-+..+.-.....   
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l--~~~~~~~~~~d~s~~~~~~~---  583 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYF--FGSEDAMIRLDMSEYMEKHT---  583 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHh--cCCccceEEEEchhcccccc---
Confidence            5688999999999887764211   123334566789999999999999887642  11111122333333211111   


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHhCCCe-EEEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSADVNDLNLLQLQLENQLKNKK-FLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr-~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                       +..-++.+......++ ...+.+.++.++ .+|+||++....++.++.|...|
T Consensus       584 -~~~l~g~~~gyvg~~~-~~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~l  635 (821)
T CHL00095        584 -VSKLIGSPPGYVGYNE-GGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQIL  635 (821)
T ss_pred             -HHHhcCCCCcccCcCc-cchHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHh
Confidence             1111221111000000 112344444444 68999999999888888876654

>cd01394 radB RadB

Probab=97.36  E-value=0.0014  Score=53.71  Aligned_cols=90  Identities=20%  Similarity=0.030  Sum_probs=51.9

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHH----hcC---CCCCCCHHHH--
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQA----AAG---SADVNDLNLL--  224 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~----l~~---~~~~~~~~~~--  224 (261)
                      -+.-.++.|+|.+|+||||++.++.....  ..-...+|+.....+.  +-+..++..    +..   -.+..+..++  
T Consensus        16 i~~g~i~~i~G~~GsGKT~l~~~~a~~~~--~~g~~v~yi~~e~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (218)
T cd01394          16 VERGTVTQVYGPPGTGKTNIAIQLAVETA--GQGKKVAYIDTEGLSS--ERFRQIAGDRPERAASSIIVFEPMDFNEQGR   91 (218)
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEECCCCCH--HHHHHHHhHChHhhhcCEEEEeCCCHHHHHH
Confidence            34568999999999999999999876521  2222456776655443  222333322    110   0122233222  


Q ss_pred             -HHHHHHHhCCCeEEEEEeCCCCC
Q 041190          225 -QLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       225 -~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                       ...+...+..+.-+||+|.+-..
T Consensus        92 ~~~~~~~~~~~~~~lvvIDsi~~l  115 (218)
T cd01394          92 AIQETETFADEKVDLVVVDSATAL  115 (218)
T ss_pred             HHHHHHHHHhcCCcEEEEechHHh
Confidence             33455555555679999998543

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

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.35  E-value=0.0015  Score=59.92  Aligned_cols=45  Identities=20%  Similarity=0.282  Sum_probs=36.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhh
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.+.-++.|.+.+..+.     -..-+-++|++|+||||+|+.+.+
T Consensus        13 ~dliGQe~vv~~L~~a~~~~r-----i~ha~Lf~Gp~G~GKTT~ArilAk   57 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNK-----IPQSILLVGASGVGKTTCARIISL   57 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCceEEEECCCCccHHHHHHHHHH
Confidence            468999988888888885432     234788999999999999988865

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

Probab=97.35  E-value=0.0012  Score=60.85  Aligned_cols=101  Identities=17%  Similarity=0.206  Sum_probs=63.3

Q ss_pred             CCccccccchHHHHHHHhhCCCC-C-----CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHH
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDL-N-----SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAV  202 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~-~-----~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  202 (261)
                      -.++-|.+....+|.+++..-.. .     +-...+=+-++|++|+|||.||+.+.+...+  .|     +.++.+    
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~v--Pf-----~~isAp----  257 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGV--PF-----LSISAP----  257 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCC--ce-----Eeecch----
Confidence            34577888888888887765211 0     1123445788999999999999999998443  33     333332    


Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCC
Q 041190          203 GVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       203 ~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~  248 (261)
                          +|.    ....+.+...+-..+.+.-..-.+++++|++.-..
T Consensus       258 ----eiv----SGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI~  295 (802)
T KOG0733|consen  258 ----EIV----SGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAIT  295 (802)
T ss_pred             ----hhh----cccCcccHHHHHHHHHHHhccCCeEEEeecccccc
Confidence                111    11223344444444455557789999999997654

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

Probab=97.35  E-value=0.00043  Score=58.75  Aligned_cols=113  Identities=21%  Similarity=0.207  Sum_probs=71.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEE-EeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRAC-AYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~w-v~v~~~~~~~~i~~~i  208 (261)
                      .+++|.+..+..|.+.+...      .......||++|+|||+-|.......-..+.|.|++. .++|......-+..++
T Consensus        36 de~~gQe~vV~~L~~a~~~~------~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Ki  109 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLRR------ILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKI  109 (346)
T ss_pred             HhhcchHHHHHHHHHHHhhc------CCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhh
Confidence            46889999999999988763      4678889999999999988777665433456777653 5666544332111111


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHh--CCCe-EEEEEeCCCCCChhhHHHhhcc
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQL--KNKK-FLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l--~~kr-~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                      -          +...+........  .-+. -+||||+..+...+.|..|+..
T Consensus       110 k----------~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~  152 (346)
T KOG0989|consen  110 K----------NFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRT  152 (346)
T ss_pred             c----------CHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHH
Confidence            1          1111111010000  0122 5789999999999999988754

>PRK05642 DNA replication initiation factor; Validated

Probab=97.34  E-value=0.00074  Score=56.16  Aligned_cols=24  Identities=29%  Similarity=0.346  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.|+|.+|+|||+|++.+++.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~   68 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLR   68 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999999875

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.34  E-value=0.0008  Score=66.09  Aligned_cols=45  Identities=20%  Similarity=0.306  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++||+.++..++..|....      ...+-++|++|+|||++|+.+...
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            348999999999999997643      234558999999999999988776

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.34  E-value=0.00052  Score=64.70  Aligned_cols=46  Identities=22%  Similarity=0.286  Sum_probs=37.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|..++...     .-.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~-----~i~~a~Lf~Gp~G~GKTtlA~~lA~~   61 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEG-----RVAHAYLFTGPRGVGKTSTARILAKA   61 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhC-----CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999888643     22456789999999999999999765

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.33  E-value=0.00071  Score=55.85  Aligned_cols=25  Identities=24%  Similarity=0.319  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....+.++|++|+|||+||+.+++.
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3467889999999999999999886

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.33  E-value=0.0024  Score=57.53  Aligned_cols=76  Identities=21%  Similarity=0.187  Sum_probs=42.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCe
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKK  236 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr  236 (261)
                      ...+.|+|++|+|||+|++.+++....+..=....+++.      .++...+...+..    .....    +.+.+++ .
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~------~~~~~~~~~~~~~----~~~~~----~~~~~~~-~  200 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS------EKFTNDFVNALRN----NKMEE----FKEKYRS-V  200 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH------HHHHHHHHHHHHc----CCHHH----HHHHHHh-C
Confidence            457899999999999999999987322111112345543      3334444444431    12222    2233322 2


Q ss_pred             EEEEEeCCCCC
Q 041190          237 FLLVLDDMWSE  247 (261)
Q Consensus       237 ~LiVlDdvw~~  247 (261)
                      -+|+|||+...
T Consensus       201 dlLiiDDi~~l  211 (405)
T TIGR00362       201 DLLLIDDIQFL  211 (405)
T ss_pred             CEEEEehhhhh
Confidence            37788888754

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).

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

Probab=97.32  E-value=0.0014  Score=55.47  Aligned_cols=88  Identities=19%  Similarity=0.279  Sum_probs=53.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccc-eeEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH-----
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFS-FRACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN-----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~-----  222 (261)
                      .-++|.|.+|+|||||++.+++.  ...+|. ..+++-+.+... ..++..++...=. .       ..+.....     
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            46899999999999999999998  433454 455667776543 3455555543211 1       11111111     


Q ss_pred             HHHHHHHHHh---CCCeEEEEEeCCCCC
Q 041190          223 LLQLQLENQL---KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ~~~~~l~~~l---~~kr~LiVlDdvw~~  247 (261)
                      ...-.+-+++   .++.+|+++||+-.-
T Consensus       148 ~~a~~~AEyfr~~~g~~Vl~~~Dsltr~  175 (274)
T cd01133         148 LTGLTMAEYFRDEEGQDVLLFIDNIFRF  175 (274)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEeChhHH
Confidence            1122344555   389999999998553

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.

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

Probab=97.32  E-value=0.00018  Score=60.34  Aligned_cols=53  Identities=36%  Similarity=0.528  Sum_probs=43.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV  183 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  183 (261)
                      .+++|.++-++++.=++..... .+..+--+.++|++|.||||||.-+.+...+
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~-r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgv   78 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKK-RGEALDHVLLFGPPGLGKTTLAHIIANELGV   78 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHh-cCCCcCeEEeeCCCCCcHHHHHHHHHHHhcC
Confidence            4689999999998887766433 4566888999999999999999999987543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.32  E-value=0.001  Score=65.37  Aligned_cols=123  Identities=15%  Similarity=0.155  Sum_probs=69.6

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.+...+.....   +.+....++.++|++|+|||++|+.+....  .......+.++++.-.....   
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            4589999999999998875321   012335678899999999999999998752  11111223344444222111   


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                       ...-++.++.....++ ...+.+.++ ....+|+||++-...++.|+.|...|
T Consensus       640 -~~~l~g~~~g~~g~~~-~g~l~~~v~~~p~~vlllDeieka~~~v~~~Ll~~l  691 (852)
T TIGR03346       640 -VARLIGAPPGYVGYEE-GGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLLQVL  691 (852)
T ss_pred             -HHHhcCCCCCccCccc-ccHHHHHHHcCCCcEEEEeccccCCHHHHHHHHHHH
Confidence             1111231111101000 012233332 23459999999999888888776554

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.32  E-value=0.00061  Score=66.76  Aligned_cols=121  Identities=17%  Similarity=0.156  Sum_probs=68.6

Q ss_pred             CccccccchHHHHHHHhhCCC---CCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.+.+.+....   .+.+....++.++|++|+|||.||+.+...  .-......+-++++.-...    .
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~--l~~~~~~~~~~dmse~~~~----~  639 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAEL--LYGGEQNLITINMSEFQEA----H  639 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHH--HhCCCcceEEEeHHHhhhh----h
Confidence            468999999999998886421   112344568899999999999999888664  2111112222333321110    0


Q ss_pred             HHHHHhcCCCC--CC-CHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSAD--VN-DLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~--~~-~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      .+..-++.++.  +. ....+...++   +....+|+||++-...++.++.|...|
T Consensus       640 ~~~~l~g~~~gyvg~~~~g~L~~~v~---~~p~svvllDEieka~~~v~~~Llq~l  692 (852)
T TIGR03345       640 TVSRLKGSPPGYVGYGEGGVLTEAVR---RKPYSVVLLDEVEKAHPDVLELFYQVF  692 (852)
T ss_pred             hhccccCCCCCcccccccchHHHHHH---hCCCcEEEEechhhcCHHHHHHHHHHh
Confidence            11111221111  11 1122333333   256689999999988888887765443

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.

>CHL00181 cbbX CbbX; Provisional

Probab=97.31  E-value=0.0011  Score=56.84  Aligned_cols=50  Identities=30%  Similarity=0.214  Sum_probs=32.0

Q ss_pred             ccccccchHHHHHHHhh---CC------CCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLL---GD------DLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~---~~------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.+..+++|.++..   -.      ..........+.++|++|+||||+|+.+++.
T Consensus        24 ~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~   82 (287)
T CHL00181         24 ELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADI   82 (287)
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            57887766666555421   11      0001112335788999999999999999764

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.30  E-value=0.0019  Score=57.29  Aligned_cols=46  Identities=20%  Similarity=0.332  Sum_probs=37.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.+...+...     .-.+.+-++|++|+||||+|+.+.+.
T Consensus        17 ~~iig~~~~~~~l~~~i~~~-----~~~~~~L~~G~~G~GKt~~a~~la~~   62 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENN-----HLAQALLFCGPRGVGKTTCARILARK   62 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcC-----CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999988653     23468889999999999999988665

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=97.29  E-value=0.0024  Score=54.22  Aligned_cols=93  Identities=19%  Similarity=0.068  Sum_probs=63.4

Q ss_pred             CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHH-hc-----CCCCCCCHHHHHH
Q 041190          153 SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQA-AA-----GSADVNDLNLLQL  226 (261)
Q Consensus       153 ~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~-l~-----~~~~~~~~~~~~~  226 (261)
                      +-+.-+++-|+|+.|+||||+|-+++-.  .+..-...+|+..-+.++...+.. +... +.     ...+.....++..
T Consensus        56 Gl~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~~-l~~~~~d~l~v~~~~~~e~q~~i~~  132 (279)
T COG0468          56 GLPRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAKQ-LGVDLLDNLLVSQPDTGEQQLEIAE  132 (279)
T ss_pred             CcccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHHH-HHHhhhcceeEecCCCHHHHHHHHH
Confidence            4567789999999999999999998766  344444789999999999877543 3333 33     1222223334455


Q ss_pred             HHHHHhCCCeEEEEEeCCCCCC
Q 041190          227 QLENQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       227 ~l~~~l~~kr~LiVlDdvw~~~  248 (261)
                      .+......+--|||+|.|-..-
T Consensus       133 ~~~~~~~~~i~LvVVDSvaa~~  154 (279)
T COG0468         133 KLARSGAEKIDLLVVDSVAALV  154 (279)
T ss_pred             HHHHhccCCCCEEEEecCcccc
Confidence            5555555567899999986643

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.29  E-value=0.011  Score=53.55  Aligned_cols=24  Identities=29%  Similarity=0.351  Sum_probs=19.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -+++.++|++|+||||++..+...
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~  244 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAAR  244 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999988776543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.29  E-value=0.00089  Score=65.78  Aligned_cols=121  Identities=15%  Similarity=0.138  Sum_probs=68.1

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.|...+.....   +.+....++.++|++|+|||++|+.+.+..  ...-...+.++++.-.. ..   
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l--~~~~~~~i~id~se~~~-~~---  641 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM--FDSDDAMVRIDMSEFME-KH---  641 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHh--hcCCCcEEEEEhHHhhh-hh---
Confidence            4588999888888888764211   012334578899999999999999998652  11111223444443211 11   


Q ss_pred             HHHHHhcCCCC--CCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSAD--VNDLNLLQLQLENQLK-NKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~--~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      .+..-++.+..  ..+..   ..+.+.++ ...-+|+|||+-...++.|+.|...|
T Consensus       642 ~~~~LiG~~pgy~g~~~~---g~l~~~v~~~p~~vLllDEieka~~~v~~~Ll~il  694 (857)
T PRK10865        642 SVSRLVGAPPGYVGYEEG---GYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVL  694 (857)
T ss_pred             hHHHHhCCCCcccccchh---HHHHHHHHhCCCCeEEEeehhhCCHHHHHHHHHHH
Confidence            11111231111  11111   12233332 23369999999988888887775544

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

Probab=97.29  E-value=0.0012  Score=57.98  Aligned_cols=28  Identities=32%  Similarity=0.398  Sum_probs=24.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      ..+..+.|||++|+|||.+|+.+++...
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg  173 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMG  173 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcC
Confidence            4578999999999999999999999843

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.27  E-value=0.00028  Score=69.16  Aligned_cols=45  Identities=24%  Similarity=0.390  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++||+.++..++..|....      ..-+-++|++|+||||+|+.+.+.
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            358999999999999997643      233459999999999999999876

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.27  E-value=0.00077  Score=61.30  Aligned_cols=25  Identities=40%  Similarity=0.402  Sum_probs=22.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...+.|+|++|+|||+|++.+.+..
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l  154 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYV  154 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHH
Confidence            4569999999999999999999873

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.27  E-value=0.0054  Score=58.74  Aligned_cols=102  Identities=23%  Similarity=0.193  Sum_probs=67.4

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-CCC
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-GSA  216 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~~~  216 (261)
                      +..|++.|..     ..+.+.+-|..|.|.|||||+-+....  . ..=..+.|.++.++- +...++..++..++ ..+
T Consensus        24 R~rL~~~L~~-----~~~~RL~li~APAGfGKttl~aq~~~~--~-~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p   95 (894)
T COG2909          24 RPRLLDRLRR-----ANDYRLILISAPAGFGKTTLLAQWREL--A-ADGAAVAWLSLDESDNDPARFLSYLIAALQQATP   95 (894)
T ss_pred             cHHHHHHHhc-----CCCceEEEEeCCCCCcHHHHHHHHHHh--c-CcccceeEeecCCccCCHHHHHHHHHHHHHHhCc
Confidence            4456666654     447899999999999999999888652  1 112358999987754 57788888888887 111


Q ss_pred             C-------------CCCHHHHHHHHHHHhC--CCeEEEEEeCCCCCC
Q 041190          217 D-------------VNDLNLLQLQLENQLK--NKKFLLVLDDMWSEN  248 (261)
Q Consensus       217 ~-------------~~~~~~~~~~l~~~l~--~kr~LiVlDdvw~~~  248 (261)
                      +             ..+...+...+..-+.  .++.++||||.--..
T Consensus        96 ~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~  142 (894)
T COG2909          96 TLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLIS  142 (894)
T ss_pred             cccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccC
Confidence            1             1223334444444332  567899999975543

>PRK10867 signal recognition particle protein; Provisional

Probab=97.26  E-value=0.0027  Score=57.40  Aligned_cols=25  Identities=36%  Similarity=0.400  Sum_probs=19.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhh
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ....+|.++|++|+||||.+..+..
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHH
Confidence            3478999999999999996655543

>TIGR00959 ffh signal recognition particle protein

Probab=97.26  E-value=0.0027  Score=57.31  Aligned_cols=25  Identities=32%  Similarity=0.305  Sum_probs=20.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.++.++|++|+||||++..+...
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            4689999999999999987666443

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.24  E-value=0.001  Score=65.47  Aligned_cols=44  Identities=20%  Similarity=0.289  Sum_probs=36.3

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++||+.++..++..|....      ...+-++|++|+|||++|+.+...
T Consensus       174 ~~igr~~ei~~~~~~l~r~~------~~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       174 PVIGRDEEIRRTIQVLSRRT------KNNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             cCCCcHHHHHHHHHHHhcCC------CCceEEEcCCCCCHHHHHHHHHHH
Confidence            48999999999999997642      233447999999999999988776

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.

>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=97.23  E-value=0.00027  Score=55.86  Aligned_cols=88  Identities=18%  Similarity=0.085  Sum_probs=50.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCH---HHHHHHHHHHhcCCCCCCCHHHHHHHHHHHh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDA---VGVTKVILQAAAGSADVNDLNLLQLQLENQL  232 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~---~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l  232 (261)
                      ...++.++|++|+|||.||+.+.+-..+ +....-+-++++.-...   ..+...+...   .  +.....         
T Consensus         2 p~~~~ll~GpsGvGKT~la~~la~~l~~-~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~---~--~~~v~~---------   66 (171)
T PF07724_consen    2 PKSNFLLAGPSGVGKTELAKALAELLFV-GSERPLIRIDMSEYSEGDDVESSVSKLLGS---P--PGYVGA---------   66 (171)
T ss_dssp             -SEEEEEESSTTSSHHHHHHHHHHHHT--SSCCEEEEEEGGGHCSHHHCSCHCHHHHHH---T--TCHHHH---------
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHhcc-CCccchHHHhhhcccccchHHhhhhhhhhc---c--cceeec---------
Confidence            3568899999999999999999876322 23334455555553231   1111111111   0  011110         


Q ss_pred             CCCeEEEEEeCCCCCCh-----------hhHHHhhccc
Q 041190          233 KNKKFLLVLDDMWSENY-----------DVWTNLCKPF  259 (261)
Q Consensus       233 ~~kr~LiVlDdvw~~~~-----------~~w~~l~~~l  259 (261)
                       ...-+|+||++....+           ..|+.|...|
T Consensus        67 -~~~gVVllDEidKa~~~~~~~~~v~~~~V~~~LL~~l  103 (171)
T PF07724_consen   67 -EEGGVVLLDEIDKAHPSNSGGADVSGEGVQNSLLQLL  103 (171)
T ss_dssp             -HHHTEEEEETGGGCSHTTTTCSHHHHHHHHHHHHHHH
T ss_pred             -cchhhhhhHHHhhccccccccchhhHHHHHHHHHHHh
Confidence             0111999999999988           7788776554

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 ....

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

Probab=97.23  E-value=0.00099  Score=63.70  Aligned_cols=123  Identities=16%  Similarity=0.178  Sum_probs=74.6

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..+..+.+.+.....   +.+..+......|++|+|||.||+.+...  .-+.-+.-+-+.+|+- ...   .
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~--Lfg~e~aliR~DMSEy-~Ek---H  564 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA--LFGDEQALIRIDMSEY-MEK---H  564 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHH--hcCCCccceeechHHH-HHH---H
Confidence            4589999999999988876421   23556778888999999999999988764  2111123333444441 111   1


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHhCCCeE-EEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSADVNDLNLLQLQLENQLKNKKF-LLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~-LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      .+-+-++.++.--..++ -..|.+..+.++| +|.||+|-..-|+..+-+...|
T Consensus       565 sVSrLIGaPPGYVGyee-GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVl  617 (786)
T COG0542         565 SVSRLIGAPPGYVGYEE-GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVL  617 (786)
T ss_pred             HHHHHhCCCCCCceecc-ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHh
Confidence            22222342221111111 2346667778877 8999999888777776655443

>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=97.23  E-value=0.0022  Score=51.87  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=19.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++++.++|+.|+||||.+-++...
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~   24 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAAR   24 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHH
Confidence            378999999999999976666554

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 ....

>PRK13531 regulatory ATPase RavA; Provisional

Probab=97.23  E-value=0.00053  Score=62.32  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|+++.++.+.-.+..+        .-+.+.|++|+|||++|+.+....
T Consensus        20 ~~i~gre~vI~lll~aalag--------~hVLL~GpPGTGKT~LAraLa~~~   63 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSG--------ESVFLLGPPGIAKSLIARRLKFAF   63 (498)
T ss_pred             hhccCcHHHHHHHHHHHccC--------CCEEEECCCChhHHHHHHHHHHHh
Confidence            35899999999988888764        358899999999999999998753

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.22  E-value=0.0025  Score=57.01  Aligned_cols=51  Identities=14%  Similarity=0.119  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCCC----CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLN----SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~----~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+.+......    ...-.+-+-++|++|+|||++|+.+.+.
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~   59 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAA   59 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            35889999999999999763200    0012456889999999999999888654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.22  E-value=0.0018  Score=55.43  Aligned_cols=85  Identities=22%  Similarity=0.161  Sum_probs=45.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccc-cccceeEEEeeCCC-CCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVK-KYFSFRACAYVSED-FDAVGVTKVILQAAA-GSADVNDLNLLQLQLENQL  232 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~-~~~~~~~~~~~~~~l~~~l  232 (261)
                      +..++.++|++|+||||++..+......+ ..+ .+..|+.... ....+.+....+.++ +.....+...+...+.. +
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~-~  270 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNK-KVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDR-L  270 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCC-eEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHH-c
Confidence            45799999999999999998887653222 122 2334544331 122333333333344 22222344455444443 3


Q ss_pred             CCCeEEEEEeC
Q 041190          233 KNKKFLLVLDD  243 (261)
Q Consensus       233 ~~kr~LiVlDd  243 (261)
                      .+ .=+|++|.
T Consensus       271 ~~-~d~vliDt  280 (282)
T TIGR03499       271 RD-KDLILIDT  280 (282)
T ss_pred             cC-CCEEEEeC
Confidence            43 34777775

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.21  E-value=0.0031  Score=59.32  Aligned_cols=47  Identities=26%  Similarity=0.331  Sum_probs=36.9

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.+..+..|.+.+...     .-...+.++|+.|+||||+|+.+.+..
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~-----ri~ha~Lf~GPpG~GKTtiArilAk~L   62 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQEN-----RVAPAYLFSGTRGVGKTTIARIFAKAL   62 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcC-----CCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            35789888888888888643     224677789999999999999887763

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.21  E-value=0.0029  Score=54.91  Aligned_cols=93  Identities=16%  Similarity=0.134  Sum_probs=56.7

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccc----cceeEEEeeCCCCCHHHHHHHHHHHhcCCC----------CCC
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKY----FSFRACAYVSEDFDAVGVTKVILQAAAGSA----------DVN  219 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~----------~~~  219 (261)
                      -+.-.++-|+|++|+|||+++.+++-.......    -...+||...++++...+.+ +++.++...          ...
T Consensus        92 i~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~~-~~~~~gl~~~~~~~~i~i~~~~  170 (310)
T TIGR02236        92 IETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQ-MAEARGLDPDEVLKNIYVARAY  170 (310)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhhceEEEecC
Confidence            345689999999999999999988755322110    12578999988888777543 344433100          011


Q ss_pred             CH---HHHHHHHHHHhCC---CeEEEEEeCCCCC
Q 041190          220 DL---NLLQLQLENQLKN---KKFLLVLDDMWSE  247 (261)
Q Consensus       220 ~~---~~~~~~l~~~l~~---kr~LiVlDdvw~~  247 (261)
                      +.   ..+...+.+.+..   +--+||+|.+-..
T Consensus       171 ~~~~~~~lld~l~~~i~~~~~~~~lVVIDSisa~  204 (310)
T TIGR02236       171 NSNHQMLLVEKAEDLIKELNNPVKLLIVDSLTSH  204 (310)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCceEEEEecchHh
Confidence            11   1233445555533   2449999998754

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.

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

Probab=97.20  E-value=0.0021  Score=55.74  Aligned_cols=98  Identities=18%  Similarity=0.146  Sum_probs=59.5

Q ss_pred             CccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAV  202 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  202 (261)
                      ..+-|.++++++|.+...-.-.+       +-..++=|-+||++|+|||-||+.|.+.  ....|     +.|..+    
T Consensus       151 ~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~--T~AtF-----IrvvgS----  219 (406)
T COG1222         151 EDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ--TDATF-----IRVVGS----  219 (406)
T ss_pred             hhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhc--cCceE-----EEeccH----
Confidence            45667888888888865432100       2234556789999999999999999998  44344     444332    


Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          203 GVTKVILQAAAGSADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       203 ~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                      ++.++.         .++-..+.+.+.+.-+ ...++|++|++..-
T Consensus       220 ElVqKY---------iGEGaRlVRelF~lArekaPsIIFiDEIDAI  256 (406)
T COG1222         220 ELVQKY---------IGEGARLVRELFELAREKAPSIIFIDEIDAI  256 (406)
T ss_pred             HHHHHH---------hccchHHHHHHHHHHhhcCCeEEEEechhhh
Confidence            111111         1122334444444443 45788999988653

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

Probab=97.19  E-value=0.00033  Score=67.51  Aligned_cols=44  Identities=27%  Similarity=0.324  Sum_probs=36.4

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++||+.++..++..|....      ..-+-++|++|+|||++|+.+...
T Consensus       187 ~liGR~~ei~~~i~iL~r~~------~~n~LLvGppGvGKT~lae~la~~  230 (758)
T PRK11034        187 PLIGREKELERAIQVLCRRR------KNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_pred             cCcCCCHHHHHHHHHHhccC------CCCeEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999997742      123357999999999999999865

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.19  E-value=0.0039  Score=56.49  Aligned_cols=27  Identities=30%  Similarity=0.231  Sum_probs=23.2

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.++.++|.+|+||||++..+....
T Consensus        93 ~~p~vI~lvG~~GsGKTTtaakLA~~L  119 (437)
T PRK00771         93 LKPQTIMLVGLQGSGKTTTAAKLARYF  119 (437)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            357899999999999999998887653

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.18  E-value=0.0032  Score=59.46  Aligned_cols=46  Identities=24%  Similarity=0.233  Sum_probs=36.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|...+..+.     -...+-++|+.|+||||+|+.+.+.
T Consensus        16 ~eivGQe~i~~~L~~~i~~~r-----i~ha~Lf~Gp~GvGKttlA~~lAk~   61 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDR-----VGHGYIFSGLRGVGKTTAARVFAKA   61 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeeEEEECCCCCCHHHHHHHHHHH
Confidence            468899988899999886432     2355889999999999999888665

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.18  E-value=0.0033  Score=57.48  Aligned_cols=26  Identities=35%  Similarity=0.374  Sum_probs=22.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....+.|+|++|+|||+|++.+.+..
T Consensus       147 ~~~~l~l~G~~G~GKThL~~ai~~~~  172 (450)
T PRK00149        147 AYNPLFIYGGVGLGKTHLLHAIGNYI  172 (450)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            34568999999999999999999873

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.16  E-value=0.0055  Score=49.01  Aligned_cols=24  Identities=25%  Similarity=0.279  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+-++|+.|+||||+|+.+.+.
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~~~~~   37 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALALAKA   37 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            467889999999999999888665

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.

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

Probab=97.16  E-value=0.0019  Score=60.77  Aligned_cols=76  Identities=28%  Similarity=0.342  Sum_probs=54.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHh-
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQL-  232 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l-  232 (261)
                      .+.-+++-++|++|.||||||+-|.++...+     ++=|++|...+...+-..|...+....              .+ 
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkqaGYs-----VvEINASDeRt~~~v~~kI~~avq~~s--------------~l~  383 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQAGYS-----VVEINASDERTAPMVKEKIENAVQNHS--------------VLD  383 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHhcCce-----EEEecccccccHHHHHHHHHHHHhhcc--------------ccc
Confidence            4567899999999999999999999874432     556889998888777776666554111              11 


Q ss_pred             -CCCeEEEEEeCCCCCC
Q 041190          233 -KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       233 -~~kr~LiVlDdvw~~~  248 (261)
                       .++..-+|+|++.-..
T Consensus       384 adsrP~CLViDEIDGa~  400 (877)
T KOG1969|consen  384 ADSRPVCLVIDEIDGAP  400 (877)
T ss_pred             cCCCcceEEEecccCCc
Confidence             1456667788887653

>PRK06526 transposase; Provisional

Probab=97.14  E-value=0.00055  Score=57.60  Aligned_cols=23  Identities=30%  Similarity=0.183  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-+.++|++|+|||+||..+...
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHH
Confidence            45899999999999999999765

>PRK06921 hypothetical protein; Provisional

Probab=97.14  E-value=0.0034  Score=53.24  Aligned_cols=37  Identities=22%  Similarity=0.072  Sum_probs=26.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccc-cceeEEEee
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKY-FSFRACAYV  195 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-f~~~~wv~v  195 (261)
                      ...+.++|.+|+|||+|+..+.+..  ... -..+++++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l--~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANEL--MRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHH--hhhcCceEEEEEH
Confidence            4678999999999999999999873  222 223455554

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.13  E-value=0.005  Score=56.70  Aligned_cols=46  Identities=24%  Similarity=0.252  Sum_probs=36.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+.-+..|.+.+....     -.+.+-++|+.|+||||+|+.+...
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            358899999999999996532     2345678999999999999988664

>TIGR02012 tigrfam_recA protein RecA

Probab=97.13  E-value=0.0016  Score=56.55  Aligned_cols=98  Identities=19%  Similarity=0.063  Sum_probs=60.8

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC-----
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG-----  214 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~-----  214 (261)
                      ..|-.+|...   +-+.-+++-|+|++|+||||||.++....  ...-...+|+...+.++..     .+++++-     
T Consensus        41 ~~LD~~Lg~G---Glp~G~iteI~G~~GsGKTtLaL~~~~~~--~~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l  110 (321)
T TIGR02012        41 LSLDLALGVG---GLPRGRIIEIYGPESSGKTTLALHAIAEA--QKAGGTAAFIDAEHALDPV-----YARKLGVDIDNL  110 (321)
T ss_pred             HHHHHHhcCC---CCcCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEEcccchhHHH-----HHHHcCCCHHHe
Confidence            4444555311   34566899999999999999998876652  2223346788877765553     2334431     


Q ss_pred             -CCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          215 -SADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       215 -~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                       -..+...++....+...++ +.--+||+|.|-..
T Consensus       111 ~v~~p~~~eq~l~~~~~li~~~~~~lIVIDSv~al  145 (321)
T TIGR02012       111 LVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAAL  145 (321)
T ss_pred             EEecCCCHHHHHHHHHHHhhccCCcEEEEcchhhh
Confidence             1123345555555555553 56779999998754

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.13  E-value=0.0038  Score=58.74  Aligned_cols=46  Identities=20%  Similarity=0.289  Sum_probs=37.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|.+.+....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~~-----~~hayLf~Gp~G~GKtt~A~~lak~   61 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTGR-----VAHAFLFTGARGVGKTSTARILAKA   61 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999886532     2356678999999999999888765

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

Probab=97.13  E-value=0.00074  Score=61.11  Aligned_cols=51  Identities=24%  Similarity=0.141  Sum_probs=36.7

Q ss_pred             CccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.+..+++|.+.+...-..       +-....-+.++|++|+|||++|+.+.+.
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            35778888888888876421000       1123455779999999999999999986

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.12  E-value=0.051  Score=48.25  Aligned_cols=25  Identities=28%  Similarity=0.339  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++.++|+.|+||||++..+...
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~  229 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQ  229 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999998888654

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

Probab=97.12  E-value=0.0016  Score=53.48  Aligned_cols=108  Identities=24%  Similarity=0.298  Sum_probs=64.2

Q ss_pred             CCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHH
Q 041190          126 LVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVT  205 (261)
Q Consensus       126 ~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~  205 (261)
                      .+.-..++|.+.+++.|.+=-..--  .+....-+-+||..|+||+.|++.+.+.  +.+..- + -|.|... +     
T Consensus        56 ~i~L~~l~Gvd~qk~~L~~NT~~F~--~G~pANnVLLwGaRGtGKSSLVKA~~~e--~~~~gl-r-LVEV~k~-d-----  123 (287)
T COG2607          56 PIDLADLVGVDRQKEALVRNTEQFA--EGLPANNVLLWGARGTGKSSLVKALLNE--YADEGL-R-LVEVDKE-D-----  123 (287)
T ss_pred             CcCHHHHhCchHHHHHHHHHHHHHH--cCCcccceEEecCCCCChHHHHHHHHHH--HHhcCC-e-EEEEcHH-H-----
Confidence            3455678999888888776222110  1234456789999999999999999887  322221 1 3344331 0     


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCC-hhhHHHhhccc
Q 041190          206 KVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSEN-YDVWTNLCKPF  259 (261)
Q Consensus       206 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~-~~~w~~l~~~l  259 (261)
                                  ..+...+...|+  ....||+|++||+.=+. ...+..|+++|
T Consensus       124 ------------l~~Lp~l~~~Lr--~~~~kFIlFcDDLSFe~gd~~yK~LKs~L  164 (287)
T COG2607         124 ------------LATLPDLVELLR--ARPEKFILFCDDLSFEEGDDAYKALKSAL  164 (287)
T ss_pred             ------------HhhHHHHHHHHh--cCCceEEEEecCCCCCCCchHHHHHHHHh
Confidence                        111112222221  24789999999997543 24667777665

>PRK07667 uridine kinase; Provisional

Probab=97.12  E-value=0.00077  Score=54.33  Aligned_cols=38  Identities=16%  Similarity=0.276  Sum_probs=29.6

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.|.+.+...    .++..+|+|.|.+|+||||+|+.+...
T Consensus         3 ~~~~~~~~~~~----~~~~~iIgI~G~~gsGKStla~~L~~~   40 (193)
T PRK07667          3 TNELINIMKKH----KENRFILGIDGLSRSGKTTFVANLKEN   40 (193)
T ss_pred             HHHHHHHHHhc----CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45667666543    234589999999999999999999875

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.11  E-value=0.00092  Score=61.81  Aligned_cols=52  Identities=23%  Similarity=0.229  Sum_probs=34.8

Q ss_pred             CCccccccchHHHHHHHhh---CCCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLL---GDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~---~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|.+..++++.+++.   ....   -+....+-+.++|++|+|||+||+.+.+.
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            3467888777766665443   1100   01223345889999999999999999886

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.

>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=97.11  E-value=0.0004  Score=51.52  Aligned_cols=21  Identities=43%  Similarity=0.615  Sum_probs=19.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|.|++|+||||+|+.+.+.
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            689999999999999999876

...

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.11  E-value=0.0033  Score=53.19  Aligned_cols=95  Identities=19%  Similarity=0.179  Sum_probs=49.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHH--------HHHh----cCCCCCCCHHHHHH
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVI--------LQAA----AGSADVNDLNLLQL  226 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i--------~~~l----~~~~~~~~~~~~~~  226 (261)
                      .+-+.|++|+|||+||+.+.+.  ...   ....+++....+..+++...        ...+    .......+..-...
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~--lg~---~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   97 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARK--RDR---PVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDN   97 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH--hCC---CEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCc
Confidence            4568999999999999999864  211   22345555554444443221        0110    00000000000000


Q ss_pred             HHHHHhCCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          227 QLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       227 ~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      .+.... .+...++||++....++.+..|...|
T Consensus        98 ~l~~A~-~~g~~lllDEi~r~~~~~q~~Ll~~L  129 (262)
T TIGR02640        98 RLTLAV-REGFTLVYDEFTRSKPETNNVLLSVF  129 (262)
T ss_pred             hHHHHH-HcCCEEEEcchhhCCHHHHHHHHHHh
Confidence            111111 13468999999998877777666544

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).

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=97.09  E-value=0.00044  Score=55.75  Aligned_cols=23  Identities=43%  Similarity=0.507  Sum_probs=20.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ||+|.|++|+||||+|+.+....
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L   23 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQIL   23 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            69999999999999999998763

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 ....

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

Probab=97.09  E-value=0.003  Score=53.26  Aligned_cols=102  Identities=25%  Similarity=0.211  Sum_probs=61.6

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc---cc-ceeEEEeeCCCCCHHHHHHHHHHHhcCC
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK---YF-SFRACAYVSEDFDAVGVTKVILQAAAGS  215 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~---~f-~~~~wv~v~~~~~~~~i~~~i~~~l~~~  215 (261)
                      ..|-++|..    +-+.-.+.-|+|++|+|||.|+-+++-......   .. ...+|+.-...|+...+. +|++..+..
T Consensus        25 ~~lD~~L~G----Gi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~   99 (256)
T PF08423_consen   25 KSLDELLGG----GIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLD   99 (256)
T ss_dssp             HHHHHHTTS----SEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-
T ss_pred             HHHHHhhCC----CCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccc
Confidence            345555533    233456999999999999999988865432221   12 347899999999988865 455554310


Q ss_pred             ----------CCCCCHHHHH---HHHHHHh-CCCeEEEEEeCCCC
Q 041190          216 ----------ADVNDLNLLQ---LQLENQL-KNKKFLLVLDDMWS  246 (261)
Q Consensus       216 ----------~~~~~~~~~~---~~l~~~l-~~kr~LiVlDdvw~  246 (261)
                                ....+..++.   ..+...+ .++--|||+|.+-.
T Consensus       100 ~~~~l~~I~v~~~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaa  144 (256)
T PF08423_consen  100 PEEILDNIFVIRVFDLEELLELLEQLPKLLSESKIKLIVIDSIAA  144 (256)
T ss_dssp             HHHHHHTEEEEE-SSHHHHHHHHHHHHHHHHHSCEEEEEEETSSH
T ss_pred             cchhhhceeeeecCCHHHHHHHHHHHHhhccccceEEEEecchHH
Confidence                      0122333333   3333333 45677999999855

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 ....

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

Probab=97.08  E-value=0.0013  Score=63.62  Aligned_cols=117  Identities=16%  Similarity=0.144  Sum_probs=67.7

Q ss_pred             ccccccchHHHHHHHhhCCC---CCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      .++|.+..++.|.+.+....   .+.+.....+.++|++|+|||++|+.+....  ...   .+.++++.-....    .
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l--~~~---~i~id~se~~~~~----~  529 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL--GIE---LLRFDMSEYMERH----T  529 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh--CCC---cEEeechhhcccc----c
Confidence            47888888888888876421   0023345678999999999999999997763  122   2334444321111    1


Q ss_pred             HHHHhcCCCC--CCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          208 ILQAAAGSAD--VNDLNLLQLQLENQLK-NKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       208 i~~~l~~~~~--~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      +..-++.+..  ..+..   ..+.+.++ ....+|+||++....++.|+.|...|
T Consensus       530 ~~~LiG~~~gyvg~~~~---g~L~~~v~~~p~sVlllDEieka~~~v~~~LLq~l  581 (758)
T PRK11034        530 VSRLIGAPPGYVGFDQG---GLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVM  581 (758)
T ss_pred             HHHHcCCCCCccccccc---chHHHHHHhCCCcEEEeccHhhhhHHHHHHHHHHH
Confidence            1111231111  11111   12233333 34579999999999888888776544

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.07  E-value=0.0056  Score=55.75  Aligned_cols=26  Identities=35%  Similarity=0.393  Sum_probs=22.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....+.|+|++|+|||+|++.+.+..
T Consensus       140 ~~npl~L~G~~G~GKTHLl~Ai~~~l  165 (445)
T PRK12422        140 PFNPIYLFGPEGSGKTHLMQAAVHAL  165 (445)
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHH
Confidence            35678999999999999999999873

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

Probab=97.07  E-value=0.0013  Score=57.08  Aligned_cols=98  Identities=19%  Similarity=0.062  Sum_probs=61.1

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC-----
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG-----  214 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~-----  214 (261)
                      ..|-.+|...   +-+.-+++-|+|++|+||||||.+++-..  ...-...+|+...+.++..     .+..++.     
T Consensus        41 ~~LD~~Lg~G---Glp~G~iteI~Gp~GsGKTtLal~~~~~~--~~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l  110 (325)
T cd00983          41 LSLDIALGIG---GYPKGRIIEIYGPESSGKTTLALHAIAEA--QKLGGTVAFIDAEHALDPV-----YAKKLGVDLDNL  110 (325)
T ss_pred             HHHHHHhcCC---CccCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCCEEEECccccHHHH-----HHHHcCCCHHHh
Confidence            3444555411   34566799999999999999999887552  2223456788887766653     2333331     


Q ss_pred             -CCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          215 -SADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       215 -~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                       -..+.+.++....+...++ +.--|||+|.|-..
T Consensus       111 ~v~~p~~~eq~l~i~~~li~s~~~~lIVIDSvaal  145 (325)
T cd00983         111 LISQPDTGEQALEIADSLVRSGAVDLIVVDSVAAL  145 (325)
T ss_pred             eecCCCCHHHHHHHHHHHHhccCCCEEEEcchHhh
Confidence             1123445555555555543 46779999998654

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=97.07  E-value=0.00054  Score=55.87  Aligned_cols=25  Identities=36%  Similarity=0.549  Sum_probs=23.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..+|+|.|.+|+|||||++.++..
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999999999999999876

>CHL00176 ftsH cell division protein; Validated

Probab=97.06  E-value=0.001  Score=63.13  Aligned_cols=99  Identities=17%  Similarity=0.148  Sum_probs=54.9

Q ss_pred             CccccccchHHHHHHH---hhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHH
Q 041190          130 EEVYGREKDKEVIVGL---LLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVG  203 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~---L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  203 (261)
                      .++.|.++.++++.+.   |.....   -+....+-+.++|++|+|||+||+.+.+...+  +     ++.++..    .
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~--p-----~i~is~s----~  251 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEV--P-----FFSISGS----E  251 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCC--C-----eeeccHH----H
Confidence            4577877666665554   332210   01223456899999999999999999886321  2     2333221    1


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          204 VTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       204 i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      +.    ....    ......+...+.......+++|+|||+...
T Consensus       252 f~----~~~~----g~~~~~vr~lF~~A~~~~P~ILfIDEID~l  287 (638)
T CHL00176        252 FV----EMFV----GVGAARVRDLFKKAKENSPCIVFIDEIDAV  287 (638)
T ss_pred             HH----HHhh----hhhHHHHHHHHHHHhcCCCcEEEEecchhh
Confidence            10    0000    011122333344455678899999999643

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.06  E-value=0.0039  Score=47.91  Aligned_cols=40  Identities=25%  Similarity=0.223  Sum_probs=28.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD  200 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  200 (261)
                      ++.|+|++|+||||+++.+.....  ..-...+|+.......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIA--TKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHH--hcCCEEEEEECCcchH
Confidence            367999999999999999987632  2223566777665443

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.

>PRK09354 recA recombinase A; Provisional

Probab=97.05  E-value=0.0025  Score=55.82  Aligned_cols=99  Identities=18%  Similarity=0.060  Sum_probs=63.1

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC----
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG----  214 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~----  214 (261)
                      ...|-.+|...   +-+.-+++-|+|++|+|||||+-+++...  ...-...+|+...+.++..     .++.++.    
T Consensus        45 i~~LD~~LG~G---Gip~G~IteI~G~~GsGKTtLal~~~~~~--~~~G~~~~yId~E~s~~~~-----~a~~lGvdld~  114 (349)
T PRK09354         45 SLALDIALGIG---GLPRGRIVEIYGPESSGKTTLALHAIAEA--QKAGGTAAFIDAEHALDPV-----YAKKLGVDIDN  114 (349)
T ss_pred             cHHHHHHhcCC---CCcCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEECCccchHHH-----HHHHcCCCHHH
Confidence            34455556412   34567899999999999999999887652  2233456788888777653     2344431    


Q ss_pred             --CCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          215 --SADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       215 --~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                        -..+...++....+...++ ++--|||+|.|-..
T Consensus       115 lli~qp~~~Eq~l~i~~~li~s~~~~lIVIDSvaaL  150 (349)
T PRK09354        115 LLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAAL  150 (349)
T ss_pred             eEEecCCCHHHHHHHHHHHhhcCCCCEEEEeChhhh
Confidence              1123345555555555553 56779999998755

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.05  E-value=0.0056  Score=57.35  Aligned_cols=46  Identities=17%  Similarity=0.159  Sum_probs=38.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|..++..+.     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~-----i~hayLf~Gp~G~GKTt~Ar~lAk~   61 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK-----IANAYIFSGPRGVGKTSSARAFARC   61 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999996532     3457889999999999999998776

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.05  E-value=0.0013  Score=63.73  Aligned_cols=53  Identities=26%  Similarity=0.164  Sum_probs=38.1

Q ss_pred             CCCccccccchHHHHHHHhhCCCC-------CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDL-------NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.++.|.+..++.|.+++...-.       -+-...+-+.++|++|+|||+||+.+.+.
T Consensus       176 ~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~  235 (733)
T TIGR01243       176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE  235 (733)
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHH
Confidence            334588999999998887642100       01123456889999999999999999886

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.04  E-value=0.003  Score=54.84  Aligned_cols=103  Identities=17%  Similarity=0.117  Sum_probs=62.8

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc----ccceeEEEeeCCCCCHHHHHHHHHHHhcCC
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK----YFSFRACAYVSEDFDAVGVTKVILQAAAGS  215 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~  215 (261)
                      ..|-++|..    +-+.-+++-|+|++|+|||+|+.+++-......    .=...+|+...++|+..++.. +++.++..
T Consensus        83 ~~LD~lLgG----Gi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~d  157 (313)
T TIGR02238        83 QALDGILGG----GIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGVD  157 (313)
T ss_pred             HHHHHHhCC----CCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCCC
Confidence            445555543    234568999999999999999988763322211    113578999999888888654 55655511


Q ss_pred             C----------CCCCHHHH---HHHHHHHh-CCCeEEEEEeCCCCC
Q 041190          216 A----------DVNDLNLL---QLQLENQL-KNKKFLLVLDDMWSE  247 (261)
Q Consensus       216 ~----------~~~~~~~~---~~~l~~~l-~~kr~LiVlDdvw~~  247 (261)
                      .          ...+.+++   ...+...+ .++--|||+|.+-..
T Consensus       158 ~~~~l~~i~~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSisal  203 (313)
T TIGR02238       158 PDAVLDNILYARAYTSEHQMELLDYLAAKFSEEPFRLLIVDSIMAL  203 (313)
T ss_pred             hHHhcCcEEEecCCCHHHHHHHHHHHHHHhhccCCCEEEEEcchHh
Confidence            1          11223333   33343334 345668999998643

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.

>PTZ00301 uridine kinase; Provisional

Probab=97.04  E-value=0.00078  Score=55.03  Aligned_cols=24  Identities=33%  Similarity=0.618  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|+|.|.+|+||||||+.+.+.
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~   26 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSE   26 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHH
Confidence            479999999999999999887654

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

Probab=97.03  E-value=0.002  Score=60.47  Aligned_cols=75  Identities=21%  Similarity=0.201  Sum_probs=48.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC--CHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF--DAVGVTKVILQAAAGSADVNDLNLLQLQLENQLK  233 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~--~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~  233 (261)
                      ...-|.+.|+.|+|||+||+.+++... +++.-....++++.-.  ....+.+.+                ...+.+++.
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l----------------~~vfse~~~  492 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFL----------------NNVFSEALW  492 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHH----------------HHHHHHHHh
Confidence            345688999999999999999998743 2222223455555421  223332222                223456677


Q ss_pred             CCeEEEEEeCCCCC
Q 041190          234 NKKFLLVLDDMWSE  247 (261)
Q Consensus       234 ~kr~LiVlDdvw~~  247 (261)
                      ....+|||||+...
T Consensus       493 ~~PSiIvLDdld~l  506 (952)
T KOG0735|consen  493 YAPSIIVLDDLDCL  506 (952)
T ss_pred             hCCcEEEEcchhhh
Confidence            88999999999654

>PRK09183 transposase/IS protein; Provisional

Probab=97.02  E-value=0.0021  Score=54.31  Aligned_cols=23  Identities=35%  Similarity=0.405  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+.|+|++|+|||+||..+.+.
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHH
Confidence            45779999999999999999765

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=97.01  E-value=0.0047  Score=53.74  Aligned_cols=103  Identities=16%  Similarity=0.028  Sum_probs=60.7

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc----ccceeEEEeeCCCCCHHHHHHHHHHHhcCC
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK----YFSFRACAYVSEDFDAVGVTKVILQAAAGS  215 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~  215 (261)
                      ..|-.+|..    +-+.-.++.|+|.+|+|||+|+..++.......    .-...+|+...+.++..++ ..+.+.++..
T Consensus        83 ~~lD~ll~g----Gi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~~  157 (316)
T TIGR02239        83 KELDKLLGG----GIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGLN  157 (316)
T ss_pred             HHHHHHhcC----CCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCCC
Confidence            445555543    234678999999999999999998875321111    1124689988887777664 3344444411


Q ss_pred             C----------CCCCHHHH---HHHHHHHh-CCCeEEEEEeCCCCC
Q 041190          216 A----------DVNDLNLL---QLQLENQL-KNKKFLLVLDDMWSE  247 (261)
Q Consensus       216 ~----------~~~~~~~~---~~~l~~~l-~~kr~LiVlDdvw~~  247 (261)
                      .          ...+.+++   ...+...+ ..+--|||+|.+-..
T Consensus       158 ~~~~l~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~LvVIDSI~al  203 (316)
T TIGR02239       158 PEDVLDNVAYARAYNTDHQLQLLQQAAAMMSESRFALLIVDSATAL  203 (316)
T ss_pred             hHHhhccEEEEecCChHHHHHHHHHHHHhhccCCccEEEEECcHHH
Confidence            0          11223333   33333334 345679999998653

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).

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.99  E-value=0.0069  Score=50.44  Aligned_cols=98  Identities=18%  Similarity=0.221  Sum_probs=57.5

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc-C----
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA-G----  214 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~-~----  214 (261)
                      ..|-++|..    +-+.-+++.|.|.+|+|||+++.++.... . ..-...+|++...  +...+.+.+. +++ .    
T Consensus         8 ~~LD~~l~G----G~~~gs~~lI~G~pGsGKT~la~~~l~~~-~-~~ge~~lyvs~ee--~~~~i~~~~~-~~g~~~~~~   78 (237)
T TIGR03877         8 PGMDEILHG----GIPERNVVLLSGGPGTGKSIFSQQFLWNG-L-QMGEPGIYVALEE--HPVQVRRNMA-QFGWDVRKY   78 (237)
T ss_pred             HhHHHHhcC----CCcCCeEEEEEcCCCCCHHHHHHHHHHHH-H-HcCCcEEEEEeeC--CHHHHHHHHH-HhCCCHHHH
Confidence            344455543    34567899999999999999998764321 1 1233567777665  4444444322 221 0    


Q ss_pred             ---------C-----------------CCCCCHHHHHHHHHHHhCC-CeEEEEEeCCCC
Q 041190          215 ---------S-----------------ADVNDLNLLQLQLENQLKN-KKFLLVLDDMWS  246 (261)
Q Consensus       215 ---------~-----------------~~~~~~~~~~~~l~~~l~~-kr~LiVlDdvw~  246 (261)
                               .                 .+..+..++...+++.+.. +.-++|+|.+-.
T Consensus        79 ~~~g~l~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSls~  137 (237)
T TIGR03877        79 EEEGKFAIVDAFTGGIGEAAEREKYVVKDPTDVRELIDVLRQAIRDINAKRVVIDSVTT  137 (237)
T ss_pred             hhcCCEEEEeccccccccccccccccccCcccHHHHHHHHHHHHHHhCCCEEEEcChhH
Confidence                     0                 0224556666667666532 344799999765

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.

>TIGR00235 udk uridine kinase

Probab=96.98  E-value=0.00073  Score=55.03  Aligned_cols=26  Identities=38%  Similarity=0.569  Sum_probs=23.1

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...+|+|+|++|+|||||++.+...
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999999999875

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK08233 hypothetical protein; Provisional

Probab=96.98  E-value=0.00066  Score=53.77  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=22.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..+|+|.|.+|+||||||+.+....
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhC
Confidence            4789999999999999999998763

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.97  E-value=0.0029  Score=59.95  Aligned_cols=101  Identities=20%  Similarity=0.100  Sum_probs=61.3

Q ss_pred             CccccccchHHHHHHHhhCCC--C----CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDD--L----NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVG  203 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~--~----~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  203 (261)
                      .++-|.++-+.+|.+-+.-.-  .    .+-.+.+=|-.||++|+|||-|||.|...  ..     ..|++|-++     
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATE--cs-----L~FlSVKGP-----  739 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATE--CS-----LNFLSVKGP-----  739 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhh--ce-----eeEEeecCH-----
Confidence            457788888888887553310  0    01223455788999999999999999886  22     235666553     


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCCh
Q 041190          204 VTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY  249 (261)
Q Consensus       204 i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~  249 (261)
                         ++++..-    +.+.+-+...+.+.=..+.|+|+||++.+..|
T Consensus       740 ---ELLNMYV----GqSE~NVR~VFerAR~A~PCVIFFDELDSlAP  778 (953)
T KOG0736|consen  740 ---ELLNMYV----GQSEENVREVFERARSAAPCVIFFDELDSLAP  778 (953)
T ss_pred             ---HHHHHHh----cchHHHHHHHHHHhhccCCeEEEeccccccCc
Confidence               2222211    12222222222333346889999999998765

>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=96.97  E-value=0.0033  Score=49.55  Aligned_cols=22  Identities=41%  Similarity=0.486  Sum_probs=19.3

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.++|++|+||||++..+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~   23 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALY   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6789999999999999888765

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.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.97  E-value=0.0021  Score=52.38  Aligned_cols=27  Identities=33%  Similarity=0.398  Sum_probs=24.1

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.+|+|.|.+|+||||+|+.++...
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~~   32 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQL   32 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHHh
Confidence            457899999999999999999998873

>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=96.96  E-value=0.00076  Score=57.38  Aligned_cols=96  Identities=19%  Similarity=0.229  Sum_probs=49.9

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCC
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVN  219 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~  219 (261)
                      ..+++.+...       -+-+.++|++|+|||++++.......- ..| ...-++.+..-+... +..+++.-.......
T Consensus        23 ~~ll~~l~~~-------~~pvLl~G~~GtGKT~li~~~l~~l~~-~~~-~~~~~~~s~~Tts~~-~q~~ie~~l~k~~~~   92 (272)
T PF12775_consen   23 SYLLDLLLSN-------GRPVLLVGPSGTGKTSLIQNFLSSLDS-DKY-LVITINFSAQTTSNQ-LQKIIESKLEKRRGR   92 (272)
T ss_dssp             HHHHHHHHHC-------TEEEEEESSTTSSHHHHHHHHHHCSTT-CCE-EEEEEES-TTHHHHH-HHHCCCTTECECTTE
T ss_pred             HHHHHHHHHc-------CCcEEEECCCCCchhHHHHhhhccCCc-ccc-ceeEeeccCCCCHHH-HHHHHhhcEEcCCCC
Confidence            4455555542       256799999999999999998865221 112 133455555333332 222222111100000


Q ss_pred             CHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHH
Q 041190          220 DLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWT  253 (261)
Q Consensus       220 ~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~  253 (261)
                      ..        .--.+|+.++++||+--..++.|.
T Consensus        93 ~~--------gP~~~k~lv~fiDDlN~p~~d~yg  118 (272)
T PF12775_consen   93 VY--------GPPGGKKLVLFIDDLNMPQPDKYG  118 (272)
T ss_dssp             EE--------EEESSSEEEEEEETTT-S---TTS
T ss_pred             CC--------CCCCCcEEEEEecccCCCCCCCCC
Confidence            00        001478999999999888776664

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.95  E-value=0.00083  Score=51.84  Aligned_cols=25  Identities=40%  Similarity=0.391  Sum_probs=21.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..-|+|.|++|+||||+++.+.+..
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHH
Confidence            3568999999999999999998763

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.95  E-value=0.00058  Score=63.13  Aligned_cols=50  Identities=26%  Similarity=0.263  Sum_probs=39.9

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++|.++.++.|++.|.......+..-+++.++|++|+||||||+.+.+-
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            58999999999999984321112334579999999999999999999875

>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=96.94  E-value=0.00076  Score=51.18  Aligned_cols=22  Identities=36%  Similarity=0.487  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|.++|++|+||||+|+.+...
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            5789999999999999999865

...

>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=96.94  E-value=0.0047  Score=50.87  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=20.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|+|.|.+|+||||+|+.+...
T Consensus         1 IigI~G~sGSGKTTla~~L~~~   22 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQAL   22 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHH
Confidence            5899999999999999999865

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

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

Probab=96.93  E-value=0.0015  Score=60.23  Aligned_cols=73  Identities=19%  Similarity=0.153  Sum_probs=46.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCe
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKK  236 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr  236 (261)
                      ..=|.+||++|+|||-||+.|.|..  .-+|     ++|-++    +++..        .-+.+...+...+...-..-.
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEa--g~NF-----isVKGP----ELlNk--------YVGESErAVR~vFqRAR~saP  605 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEA--GANF-----ISVKGP----ELLNK--------YVGESERAVRQVFQRARASAP  605 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhc--cCce-----EeecCH----HHHHH--------HhhhHHHHHHHHHHHhhcCCC
Confidence            4457889999999999999999973  3345     444442    12211        112233333334444445778


Q ss_pred             EEEEEeCCCCCC
Q 041190          237 FLLVLDDMWSEN  248 (261)
Q Consensus       237 ~LiVlDdvw~~~  248 (261)
                      |+|+||++...-
T Consensus       606 CVIFFDEiDaL~  617 (802)
T KOG0733|consen  606 CVIFFDEIDALV  617 (802)
T ss_pred             eEEEecchhhcC
Confidence            999999997654

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.93  E-value=0.0044  Score=54.39  Aligned_cols=102  Identities=18%  Similarity=0.089  Sum_probs=62.1

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc---cc-cceeEEEeeCCCCCHHHHHHHHHHHhcCC
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK---KY-FSFRACAYVSEDFDAVGVTKVILQAAAGS  215 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~~-f~~~~wv~v~~~~~~~~i~~~i~~~l~~~  215 (261)
                      ..|-++|..    +-+.-++.-|+|++|+|||+|+.+++-.....   .. -...+|+...++|+..++.. +.+.++..
T Consensus       113 ~~LD~lLgG----Gi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d  187 (344)
T PLN03187        113 QALDELLGG----GIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMD  187 (344)
T ss_pred             HhHHhhcCC----CCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCC
Confidence            344455543    23456889999999999999998886332221   11 13568999999999888654 45555511


Q ss_pred             C----------CCCCHHHH---HHHHHHHh-CCCeEEEEEeCCCC
Q 041190          216 A----------DVNDLNLL---QLQLENQL-KNKKFLLVLDDMWS  246 (261)
Q Consensus       216 ~----------~~~~~~~~---~~~l~~~l-~~kr~LiVlDdvw~  246 (261)
                      .          ...+.+++   ...+...+ ..+--|||+|.+-.
T Consensus       188 ~~~~l~~I~~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSita  232 (344)
T PLN03187        188 ADAVLDNIIYARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVIA  232 (344)
T ss_pred             hhhhcCeEEEecCCCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHH
Confidence            1          12233333   23333333 34456899999864

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.91  E-value=0.0024  Score=58.27  Aligned_cols=80  Identities=16%  Similarity=0.114  Sum_probs=46.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNK  235 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~k  235 (261)
                      ....+.|+|..|+|||+|++.+.+.......-...++++      ..++...+...+...      ......+++.++ +
T Consensus       140 ~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~------~~~f~~~~~~~l~~~------~~~~~~~~~~~~-~  206 (450)
T PRK14087        140 SYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS------GDEFARKAVDILQKT------HKEIEQFKNEIC-Q  206 (450)
T ss_pred             ccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE------HHHHHHHHHHHHHHh------hhHHHHHHHHhc-c
Confidence            345689999999999999999988522111111123333      345566666555421      011223444444 3


Q ss_pred             eEEEEEeCCCCCC
Q 041190          236 KFLLVLDDMWSEN  248 (261)
Q Consensus       236 r~LiVlDdvw~~~  248 (261)
                      .-+|+|||+-...
T Consensus       207 ~dvLiIDDiq~l~  219 (450)
T PRK14087        207 NDVLIIDDVQFLS  219 (450)
T ss_pred             CCEEEEecccccc
Confidence            3478889996653

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.91  E-value=0.0081  Score=56.96  Aligned_cols=47  Identities=23%  Similarity=0.314  Sum_probs=37.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..+..|..++....     -..-+-++|+.|+||||+|+.+.+..
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-----l~~a~Lf~Gp~G~GKttlA~~lAk~L   62 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-----IAPAYLFTGPRGTGKTSSARILAKSL   62 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-----CCceEEEECCCCCChHHHHHHHHHHh
Confidence            458899989999999886532     23467889999999999999997763

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.90  E-value=0.0033  Score=54.91  Aligned_cols=24  Identities=25%  Similarity=0.331  Sum_probs=21.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .-+.++|.+|+|||+||..+.+..
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l  207 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKEL  207 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHH
Confidence            569999999999999999998873

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.89  E-value=0.0012  Score=51.06  Aligned_cols=42  Identities=31%  Similarity=0.471  Sum_probs=31.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA  213 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~  213 (261)
                      +|.|.|++|+||||+|+.+.++....  |           .+...++++|.++.+
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~--~-----------vsaG~iFR~~A~e~g   43 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK--L-----------VSAGTIFREMARERG   43 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc--e-----------eeccHHHHHHHHHcC
Confidence            68999999999999999998874432  1           244566677766655

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.89  E-value=0.012  Score=51.61  Aligned_cols=103  Identities=14%  Similarity=0.052  Sum_probs=63.1

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccc----cceeEEEeeCCCCCHHHHHHHHHHHhcC
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKY----FSFRACAYVSEDFDAVGVTKVILQAAAG  214 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~i~~~i~~~l~~  214 (261)
                      ...|-++|..    +-+.-.++-|+|.+|+|||+|+..++-.......    -...+|+...++|...++. +|++.++.
T Consensus       109 ~~~LD~lL~G----G~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~~  183 (342)
T PLN03186        109 SRELDKILEG----GIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFGL  183 (342)
T ss_pred             CHHHHHhhcC----CCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcCC
Confidence            3445555543    2345678999999999999999888754222111    1257899999988887764 45555541


Q ss_pred             CC----------CCCCHHHHHHHH---HHHh-CCCeEEEEEeCCCC
Q 041190          215 SA----------DVNDLNLLQLQL---ENQL-KNKKFLLVLDDMWS  246 (261)
Q Consensus       215 ~~----------~~~~~~~~~~~l---~~~l-~~kr~LiVlDdvw~  246 (261)
                      ..          ...+.+.+...+   ...+ ..+--|||+|.+-.
T Consensus       184 ~~~~~l~~i~~~~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~a  229 (342)
T PLN03186        184 NGADVLENVAYARAYNTDHQSELLLEAASMMAETRFALMIVDSATA  229 (342)
T ss_pred             ChhhhccceEEEecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcHH
Confidence            11          112333333222   2223 45667999999865

>PRK06762 hypothetical protein; Provisional

Probab=96.87  E-value=0.00089  Score=52.40  Aligned_cols=23  Identities=39%  Similarity=0.544  Sum_probs=21.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|+|++|+||||+|+.+.+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999876

>PRK00625 shikimate kinase; Provisional

Probab=96.86  E-value=0.0027  Score=50.21  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.++|++|+||||+++.+.+.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999776

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.86  E-value=0.0088  Score=57.22  Aligned_cols=46  Identities=17%  Similarity=0.344  Sum_probs=37.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|...+....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-----l~HAYLF~GP~GtGKTt~AriLAk~   63 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-----ISHAYLFSGPRGTGKTSVAKIFANA   63 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            358899999999999986532     3456678999999999999988664

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

Probab=96.85  E-value=0.0035  Score=55.95  Aligned_cols=66  Identities=21%  Similarity=0.230  Sum_probs=38.9

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      .++.++|-......-...-....  .+.....+.|||..|.|||.|++.+.+.  ...+......++++.
T Consensus        86 FdnFv~g~~N~~A~aa~~~va~~--~g~~~nplfi~G~~GlGKTHLl~Aign~--~~~~~~~a~v~y~~s  151 (408)
T COG0593          86 FDNFVVGPSNRLAYAAAKAVAEN--PGGAYNPLFIYGGVGLGKTHLLQAIGNE--ALANGPNARVVYLTS  151 (408)
T ss_pred             hhheeeCCchHHHHHHHHHHHhc--cCCcCCcEEEECCCCCCHHHHHHHHHHH--HHhhCCCceEEeccH
Confidence            44556665443332222222211  2235789999999999999999999997  434443333344433

>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=96.85  E-value=0.0022  Score=54.52  Aligned_cols=82  Identities=12%  Similarity=0.120  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhc-cccChhHHHHHHHHHHHHhhhHhHHHHHHHH
Q 041190           11 VTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEK-QITKPLTKKWLGKLQNLAYDAEDMLDEFATE   89 (261)
Q Consensus        11 ~~v~~l~~~l~~~~~~~~~~~~~v~~~i~~L~~~l~~i~~~l~~a~~~-~~~~~~~~~wl~~lr~~ayd~ed~ld~~~~~   89 (261)
                      |.+..++..|.++.......+.-++++++-++.+|+.+|.||+..... +..-...+.++.++.+.||++|.++|-|..+
T Consensus       296 GyVdFlL~NLkdfq~rysdSlaflKnQiqvIQ~elesLqpFLk~V~ee~~nkh~~~ed~a~~ii~kAyevEYVVDaCi~k  375 (402)
T PF12061_consen  296 GYVDFLLKNLKDFQGRYSDSLAFLKNQIQVIQTELESLQPFLKHVVEEPHNKHDTNEDCATQIIRKAYEVEYVVDACISK  375 (402)
T ss_pred             cHHHHHHhhHHHHhccccchHHHHHHHHHHHHHHHHHhhHHHHHHHhccchhhhhhhhHHHHHHHHHhheeeeeehhhcC
Confidence            467778888888877767778889999999999999999999997544 3333448899999999999999999998665


Q ss_pred             HHH
Q 041190           90 AFR   92 (261)
Q Consensus        90 ~~~   92 (261)
                      ...
T Consensus       376 ~~P  378 (402)
T PF12061_consen  376 SVP  378 (402)
T ss_pred             CCc
Confidence            433

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.83  E-value=0.0055  Score=57.48  Aligned_cols=46  Identities=22%  Similarity=0.271  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+.+....     -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~~viGq~~v~~~L~~~i~~~~-----~~hayLf~Gp~GtGKTt~Ak~lAka   61 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQGK-----ISHAYLFSGPRGTGKTSAAKIFAKA   61 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999987532     2456678999999999999888654

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.82  E-value=0.0049  Score=54.36  Aligned_cols=48  Identities=21%  Similarity=0.342  Sum_probs=38.7

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-..++|.+.....+...+...     .-...+-++|+.|+||||+|..+.+.
T Consensus        21 ~~~~l~Gh~~a~~~L~~a~~~g-----rl~ha~L~~G~~G~GKttlA~~lA~~   68 (351)
T PRK09112         21 ENTRLFGHEEAEAFLAQAYREG-----KLHHALLFEGPEGIGKATLAFHLANH   68 (351)
T ss_pred             chhhccCcHHHHHHHHHHHHcC-----CCCeeEeeECCCCCCHHHHHHHHHHH
Confidence            3456899999999999988653     23457889999999999999887665

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.82  E-value=0.01  Score=54.28  Aligned_cols=46  Identities=26%  Similarity=0.361  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++..+.     -.+.+-++|++|+||||+|+.+.+.
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            468999999999999886532     2356778999999999999888654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.82  E-value=0.0038  Score=53.47  Aligned_cols=22  Identities=36%  Similarity=0.363  Sum_probs=18.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -+.++|++|+||||+|+.+.+.
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~   81 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQI   81 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            5789999999999999776554

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.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.82  E-value=0.0082  Score=51.46  Aligned_cols=24  Identities=29%  Similarity=0.333  Sum_probs=21.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHh
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ....+|+|.|.+|+||||+|+.+.
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~   83 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQ   83 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            456899999999999999998763

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.

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

Probab=96.80  E-value=0.0043  Score=53.26  Aligned_cols=82  Identities=11%  Similarity=0.185  Sum_probs=49.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccc--cccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCC
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVK--KYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKN  234 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~--~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  234 (261)
                      -++|-++|++|+|||+|.+.++++..++  +.|....-+.+..    ..++.+=..+     .+.-...+..+|.+.+.+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins----hsLFSKWFsE-----SgKlV~kmF~kI~ELv~d  247 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS----HSLFSKWFSE-----SGKLVAKMFQKIQELVED  247 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh----hHHHHHHHhh-----hhhHHHHHHHHHHHHHhC
Confidence            4689999999999999999999987654  3343333344322    1222221111     122344555666677765


Q ss_pred             Ce--EEEEEeCCCCC
Q 041190          235 KK--FLLVLDDMWSE  247 (261)
Q Consensus       235 kr--~LiVlDdvw~~  247 (261)
                      +.  +++.+|+|-+.
T Consensus       248 ~~~lVfvLIDEVESL  262 (423)
T KOG0744|consen  248 RGNLVFVLIDEVESL  262 (423)
T ss_pred             CCcEEEEEeHHHHHH
Confidence            54  56678888654

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.79  E-value=0.0054  Score=54.36  Aligned_cols=25  Identities=28%  Similarity=0.312  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-.++.++|++|+||||++..+...
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~  160 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAAR  160 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999888765

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.79  E-value=0.017  Score=53.61  Aligned_cols=46  Identities=22%  Similarity=0.272  Sum_probs=36.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|...+...     .-.+.+-++|+.|+||||+|+.+.+.
T Consensus        14 deiiGqe~v~~~L~~~I~~g-----rl~hayLf~Gp~G~GKTt~Ar~LAk~   59 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNN-----RLAHAYLFSGLRGSGKTSSARIFARA   59 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcC-----CCCeeEEEECCCCCcHHHHHHHHHHH
Confidence            45899998899999988643     23456689999999999999977654

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.79  E-value=0.01  Score=52.86  Aligned_cols=25  Identities=28%  Similarity=0.323  Sum_probs=21.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.++|+++|++|+||||++..+...
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~  264 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQ  264 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHH
Confidence            4579999999999999999888653

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.77  E-value=0.0099  Score=49.29  Aligned_cols=98  Identities=20%  Similarity=0.129  Sum_probs=59.1

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-++|..    +-+.-+++.|+|.+|+|||+|+.++.... .+ .=....|++..++  ...+.+.+ .+++-.   
T Consensus        11 i~~LD~~l~g----G~~~g~~~~i~G~~GsGKt~l~~~~~~~~-~~-~g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~   81 (234)
T PRK06067         11 NEELDRKLGG----GIPFPSLILIEGDHGTGKSVLSQQFVYGA-LK-QGKKVYVITTENT--SKSYLKQM-ESVKIDISD   81 (234)
T ss_pred             CHHHHHhhCC----CCcCCcEEEEECCCCCChHHHHHHHHHHH-Hh-CCCEEEEEEcCCC--HHHHHHHH-HHCCCChhH
Confidence            3445555533    34567899999999999999999985431 11 2234678887664  34444442 223200   


Q ss_pred             ------------------CCCCCHHHHHHHHHHHhCC-CeEEEEEeCCC
Q 041190          216 ------------------ADVNDLNLLQLQLENQLKN-KKFLLVLDDMW  245 (261)
Q Consensus       216 ------------------~~~~~~~~~~~~l~~~l~~-kr~LiVlDdvw  245 (261)
                                        ....+.+.+...+...+.. +.-++|+|.+-
T Consensus        82 ~~~~g~l~i~~~~~~~~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         82 FFLWGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             HHhCCCceEEeccccccccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence                              0112335666667666653 55689999986

>PRK06547 hypothetical protein; Provisional

Probab=96.77  E-value=0.0014  Score=51.83  Aligned_cols=27  Identities=37%  Similarity=0.469  Sum_probs=23.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....+|.|.|++|+||||+|+.+.+..
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999999998763

>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=96.76  E-value=0.0051  Score=50.40  Aligned_cols=83  Identities=22%  Similarity=0.257  Sum_probs=51.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCH-------
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDL-------  221 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~-------  221 (261)
                      .-++|.|.+|+|||+|++.+.++.+    -+..+++.+++.. ...++.+++...-. .       ..+....       
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            4689999999999999999988742    2234777787653 34555555533211 1       1111111       


Q ss_pred             --HHHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          222 --NLLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       222 --~~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                        -.+...+++  +++.+|+++||+-.
T Consensus        92 ~a~t~AEyfrd--~G~dVlli~Dsltr  116 (215)
T PF00006_consen   92 TALTIAEYFRD--QGKDVLLIIDSLTR  116 (215)
T ss_dssp             HHHHHHHHHHH--TTSEEEEEEETHHH
T ss_pred             cchhhhHHHhh--cCCceeehhhhhHH
Confidence              112333444  79999999999943

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 ....

>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=96.76  E-value=0.0012  Score=43.89  Aligned_cols=22  Identities=41%  Similarity=0.616  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.|.|.+|+||||+++.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999876

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.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.76  E-value=0.00091  Score=48.49  Aligned_cols=21  Identities=48%  Similarity=0.588  Sum_probs=18.9

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|++|+|||+||+.+..+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            568999999999999998776

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

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.74  E-value=0.015  Score=55.10  Aligned_cols=46  Identities=24%  Similarity=0.276  Sum_probs=37.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|..++..+.     -.+.+-++|+.|+||||+|+.+...
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~-----l~hayLf~Gp~G~GKtt~A~~lAk~   62 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK-----LAHAYLFCGPRGVGKTTCARIFAKT   62 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeeEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999986532     3456889999999999999877654

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.73  E-value=0.0026  Score=51.43  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|++|+||||+++.+...
T Consensus         2 GlilI~GptGSGKTTll~~ll~~   24 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY   24 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999987765

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.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.70  E-value=0.0013  Score=52.28  Aligned_cols=25  Identities=28%  Similarity=0.345  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.++|.|.|++|+||||+++.+.+.
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999999765

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.70  E-value=0.0056  Score=54.92  Aligned_cols=25  Identities=28%  Similarity=0.222  Sum_probs=21.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++.++|++|+||||++..+...
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999888754

>PRK14974 cell division protein FtsY; Provisional

Probab=96.70  E-value=0.01  Score=51.98  Aligned_cols=25  Identities=32%  Similarity=0.272  Sum_probs=21.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++.++|++|+||||++..+...
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~  163 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYY  163 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4689999999999999977777654

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

Probab=96.69  E-value=0.0066  Score=47.79  Aligned_cols=45  Identities=22%  Similarity=0.215  Sum_probs=32.2

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|....+..+++.+..-..    ....|.|+|..|+||+.+|+.+++.
T Consensus         1 liG~s~~m~~~~~~~~~~a~----~~~pVlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS----SDLPVLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT----STS-EEEECSTTSSHHHHHHHHHHC
T ss_pred             CEeCCHHHHHHHHHHHHHhC----CCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            46777777778777765321    2255679999999999999999985

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 ....

>PRK04328 hypothetical protein; Provisional

Probab=96.68  E-value=0.01  Score=49.77  Aligned_cols=52  Identities=19%  Similarity=0.242  Sum_probs=34.2

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED  198 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  198 (261)
                      .|-++|..    +-+.-+++.|.|.+|+|||+|+.+..... .+ .-...+|++..++
T Consensus        11 ~LD~lL~G----Gip~gs~ili~G~pGsGKT~l~~~fl~~~-~~-~ge~~lyis~ee~   62 (249)
T PRK04328         11 GMDEILYG----GIPERNVVLLSGGPGTGKSIFSQQFLWNG-LQ-MGEPGVYVALEEH   62 (249)
T ss_pred             hHHHHhcC----CCcCCcEEEEEcCCCCCHHHHHHHHHHHH-Hh-cCCcEEEEEeeCC
Confidence            44455533    23456899999999999999998865431 21 2234677877663

>PRK05439 pantothenate kinase; Provisional

Probab=96.67  E-value=0.015  Score=50.26  Aligned_cols=27  Identities=30%  Similarity=0.225  Sum_probs=23.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....-+|+|.|.+|+||||+|+.+..-
T Consensus        83 ~~~~~iIgIaG~~gsGKSTla~~L~~~  109 (311)
T PRK05439         83 QKVPFIIGIAGSVAVGKSTTARLLQAL  109 (311)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            446789999999999999999988663

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.67  E-value=0.0017  Score=50.28  Aligned_cols=25  Identities=44%  Similarity=0.430  Sum_probs=22.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..+|.++|.+|+||||||+.+.+..
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L   26 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRL   26 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998873

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 ....

>PRK04296 thymidine kinase; Provisional

Probab=96.66  E-value=0.0021  Score=51.71  Aligned_cols=85  Identities=13%  Similarity=-0.124  Sum_probs=44.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHHHHhCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSA---DVNDLNLLQLQLENQLKN  234 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~---~~~~~~~~~~~l~~~l~~  234 (261)
                      .+..|+|+.|+||||++.........  +-.....+.  +.++.......+..+++...   ......++...+++ ..+
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~--~g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~   77 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEE--RGMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGE   77 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHH--cCCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCC
Confidence            47788999999999999877765321  211222221  11121111223444444111   12234455555555 334


Q ss_pred             CeEEEEEeCCCCC
Q 041190          235 KKFLLVLDDMWSE  247 (261)
Q Consensus       235 kr~LiVlDdvw~~  247 (261)
                      +.-+||+|++--.
T Consensus        78 ~~dvviIDEaq~l   90 (190)
T PRK04296         78 KIDCVLIDEAQFL   90 (190)
T ss_pred             CCCEEEEEccccC
Confidence            4458999999654

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.66  E-value=0.0012  Score=53.28  Aligned_cols=22  Identities=41%  Similarity=0.635  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|+|.|++|+|||||++.+..-
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~   22 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQ   22 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999765

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.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.65  E-value=0.002  Score=53.37  Aligned_cols=27  Identities=30%  Similarity=0.374  Sum_probs=23.7

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+..+++|.|++|+|||||++.+..-
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~~   56 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEAL   56 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            346789999999999999999988765

>PRK03839 putative kinase; Provisional

Probab=96.65  E-value=0.0014  Score=52.03  Aligned_cols=23  Identities=43%  Similarity=0.719  Sum_probs=20.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .|.|.|++|+||||+++.+.+..
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998874

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.65  E-value=0.0016  Score=51.03  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=22.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +...|.++|++|+||||+|+.+.+..
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998863

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.64  E-value=0.013  Score=49.20  Aligned_cols=27  Identities=33%  Similarity=0.411  Sum_probs=23.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ++..+|.++||.|+||||..|.++.+.
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl   43 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHL   43 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHH
Confidence            456788899999999999999998873

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.64  E-value=0.009  Score=52.97  Aligned_cols=25  Identities=44%  Similarity=0.527  Sum_probs=20.4

Q ss_pred             CceEEeEeecCCCChHH-HHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTT-LAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTt-La~~v~~~  180 (261)
                      +-+++.++|+.|+|||| ||+.-..-
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~  227 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARY  227 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHH
Confidence            46899999999999998 77665543

>PRK04040 adenylate kinase; Provisional

Probab=96.62  E-value=0.0018  Score=51.99  Aligned_cols=24  Identities=33%  Similarity=0.619  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|+|++|+||||+++.+.+.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~   25 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEK   25 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            368999999999999999999876

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.62  E-value=0.0083  Score=54.10  Aligned_cols=87  Identities=16%  Similarity=0.158  Sum_probs=51.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHHH----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLNL----  223 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~~----  223 (261)
                      -..++|.|..|+|||||++.+.+..    ..+..+.+-+++... ..+++.+++..-+ .       ..+......    
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~~----~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRGT----TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGC  237 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccCC----CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHH
Confidence            3468999999999999999998652    124555566766543 3445555443321 1       111111111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          224 -LQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 -~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                       ..-.+-+++  +++++|+++||+-.-
T Consensus       238 ~~A~tiAEyfrd~G~~VLl~~DslTR~  264 (444)
T PRK08972        238 ETATTIAEYFRDQGLNVLLLMDSLTRY  264 (444)
T ss_pred             HHHHHHHHHHHHcCCCEEEEEcChHHH
Confidence             111233333  689999999999553

>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=96.62  E-value=0.0098  Score=51.59  Aligned_cols=100  Identities=17%  Similarity=0.050  Sum_probs=59.1

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-..|...   +-+.-+++-|+|+.|+||||||-.+...  .+..-...+|+...+.++...     +..++-.   
T Consensus        38 ~~~LD~aLg~G---G~p~G~ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e~~ld~~~-----a~~lGvdl~r  107 (322)
T PF00154_consen   38 SPALDYALGIG---GLPRGRIVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAEHALDPEY-----AESLGVDLDR  107 (322)
T ss_dssp             -HHHHHHTSSS---SEETTSEEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESSS---HHH-----HHHTT--GGG
T ss_pred             CcccchhhccC---ccccCceEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCcccchhhH-----HHhcCccccc
Confidence            34444555422   3455679999999999999999988876  333334578999988777644     3444411   


Q ss_pred             ---CCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCC
Q 041190          216 ---ADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSEN  248 (261)
Q Consensus       216 ---~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~  248 (261)
                         ..+...++..+.+..+++ +.--+||+|.|-...
T Consensus       108 llv~~P~~~E~al~~~e~lirsg~~~lVVvDSv~al~  144 (322)
T PF00154_consen  108 LLVVQPDTGEQALWIAEQLIRSGAVDLVVVDSVAALV  144 (322)
T ss_dssp             EEEEE-SSHHHHHHHHHHHHHTTSESEEEEE-CTT-B
T ss_pred             eEEecCCcHHHHHHHHHHHhhcccccEEEEecCcccC
Confidence               123344555555555553 455799999987764

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 ....

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.61  E-value=0.017  Score=54.21  Aligned_cols=24  Identities=33%  Similarity=0.445  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.|+|..|+|||.|++.+++.
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~~  337 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGHY  337 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHH
Confidence            345899999999999999999987

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.60  E-value=0.014  Score=48.94  Aligned_cols=90  Identities=18%  Similarity=0.152  Sum_probs=50.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccc-c--ccceeEEEeeCCCCCHHHHHHHHHHHhcCC-----CCCCC--HHHHH-
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVK-K--YFSFRACAYVSEDFDAVGVTKVILQAAAGS-----ADVND--LNLLQ-  225 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~--~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~-----~~~~~--~~~~~-  225 (261)
                      -.+++++|.+|+||||+++.+..=.+-. .  .|+-.-....+ .....+-..++++..+..     ..++.  -.+.+ 
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L~~pt~G~i~f~g~~i~~~~-~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQR  117 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLS-KEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQR  117 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcCcCCCCceEEEcCcchhhcc-hhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhh
Confidence            4589999999999999999998642211 0  12221111112 112333455566655511     11111  12222 


Q ss_pred             HHHHHHhCCCeEEEEEeCCCCC
Q 041190          226 LQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       226 ~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      -.|...|.-+.-|||+|+--+.
T Consensus       118 i~IARALal~P~liV~DEpvSa  139 (268)
T COG4608         118 IGIARALALNPKLIVADEPVSA  139 (268)
T ss_pred             HHHHHHHhhCCcEEEecCchhh
Confidence            2356677888889999987664

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

Probab=96.59  E-value=0.017  Score=50.03  Aligned_cols=46  Identities=20%  Similarity=0.155  Sum_probs=34.0

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|-+.....+..+.....    .....+-++|++|+||||+|..+.+.
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~----~~~halL~~Gp~G~Gktt~a~~lA~~   47 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESG----RLPHALLFYGPPGVGKTTAALALAKE   47 (325)
T ss_pred             CcccchhHHHHHHHHHHhcC----CCCceeeeeCCCCCCHHHHHHHHHHH
Confidence            35666777788888877432    12335999999999999999888765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.59  E-value=0.01  Score=57.69  Aligned_cols=51  Identities=22%  Similarity=0.092  Sum_probs=35.5

Q ss_pred             CccccccchHHHHHHHhhCCCC-------CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL-------NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.+..++.|.+.+...-.       -+....+-+.++|++|+|||++|+.+.+.
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e  510 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE  510 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            4577888787777776542100       01123445788999999999999999987

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.

>PTZ00035 Rad51 protein; Provisional

Probab=96.59  E-value=0.02  Score=50.24  Aligned_cols=103  Identities=14%  Similarity=0.023  Sum_probs=60.8

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc---c-ccceeEEEeeCCCCCHHHHHHHHHHHhcC
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK---K-YFSFRACAYVSEDFDAVGVTKVILQAAAG  214 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~-~f~~~~wv~v~~~~~~~~i~~~i~~~l~~  214 (261)
                      ...|-++|..    +-+.-.++.|+|.+|+|||+|+..++-.....   . .-...+|+...+.++..++ ..+.+.++.
T Consensus       104 ~~~LD~lLgG----Gi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~  178 (337)
T PTZ00035        104 STQLDKLLGG----GIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGL  178 (337)
T ss_pred             cHHHHHHhCC----CCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCC
Confidence            3445555643    34567899999999999999999887542211   1 1123568888777777664 334454441


Q ss_pred             CC----------CCCCHHHHHHH---HHHHh-CCCeEEEEEeCCCC
Q 041190          215 SA----------DVNDLNLLQLQ---LENQL-KNKKFLLVLDDMWS  246 (261)
Q Consensus       215 ~~----------~~~~~~~~~~~---l~~~l-~~kr~LiVlDdvw~  246 (261)
                      ..          ...+.+++...   +...+ .++--|||+|.+..
T Consensus       179 ~~~~~l~nI~~~~~~~~e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        179 DPEDVLDNIAYARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             ChHhHhhceEEEccCCHHHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence            10          11233333333   23333 35667999999975

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.57  E-value=0.0054  Score=48.78  Aligned_cols=23  Identities=39%  Similarity=0.430  Sum_probs=20.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -|.|.|++|+||||+|+.+.+..
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998873

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.57  E-value=0.015  Score=47.66  Aligned_cols=22  Identities=27%  Similarity=0.386  Sum_probs=19.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|++|+||||+|+.+...
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~   23 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEK   23 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999999775

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.55  E-value=0.0034  Score=52.02  Aligned_cols=23  Identities=30%  Similarity=0.497  Sum_probs=20.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -|.|.|++|+||||+|+.+.+..
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999997763

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.54  E-value=0.019  Score=48.85  Aligned_cols=25  Identities=36%  Similarity=0.445  Sum_probs=21.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.+++.++|++|+||||++..+...
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~   95 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANK   95 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4689999999999999988777554

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.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=96.54  E-value=0.016  Score=52.45  Aligned_cols=87  Identities=16%  Similarity=0.189  Sum_probs=47.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHh-----c--CCCCCCCHH-----HH
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAA-----A--GSADVNDLN-----LL  224 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l-----~--~~~~~~~~~-----~~  224 (261)
                      -..++|+|.+|+|||||++.+....+   .....++..--...++.++....+...     .  .+.+.....     ..
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~---pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~  241 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADA---FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLT  241 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC---CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHH
Confidence            35789999999999999998876422   222233332112234444444333322     2  122222111     11


Q ss_pred             HHHHHHHh--CCCeEEEEEeCCCC
Q 041190          225 QLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       225 ~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                      .-.+-+++  +++.+|+++||+-.
T Consensus       242 a~~iAEyfrd~G~~Vll~~DslTr  265 (450)
T PRK06002        242 ATAIAEYFRDRGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHHcCCCEEEeccchHH
Confidence            12233333  58999999999854

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.54  E-value=0.0046  Score=54.86  Aligned_cols=46  Identities=20%  Similarity=0.244  Sum_probs=36.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..|.+.+....     -...+-++|+.|+||+|+|..+.+.
T Consensus        19 ~~iiGq~~~~~~L~~~~~~~r-----l~HA~Lf~Gp~G~GK~~lA~~~A~~   64 (365)
T PRK07471         19 TALFGHAAAEAALLDAYRSGR-----LHHAWLIGGPQGIGKATLAYRMARF   64 (365)
T ss_pred             hhccChHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999886532     3456889999999999999766543

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.53  E-value=0.012  Score=53.63  Aligned_cols=88  Identities=17%  Similarity=0.200  Sum_probs=55.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHH-----H
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLN-----L  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~-----~  223 (261)
                      .-++|.|.+|+|||||+..+.+..... +-++.+++-+.+.. ...+++.++...-. .       ..+.....     .
T Consensus       144 QR~gIfa~~G~GKt~Ll~~~~~~~~~~-~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~  222 (461)
T PRK12597        144 GKTGLFGGAGVGKTVLMMELIFNISKQ-HSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVL  222 (461)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhh-CCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHH
Confidence            458999999999999999888774322 45677777777644 34555555544321 1       11111111     1


Q ss_pred             HHHHHHHHh---CCCeEEEEEeCCCC
Q 041190          224 LQLQLENQL---KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 ~~~~l~~~l---~~kr~LiVlDdvw~  246 (261)
                      ..-.+-+++   .++++|+++|++-.
T Consensus       223 ~a~tiAEyfrd~~G~~VLl~~DslTR  248 (461)
T PRK12597        223 TGLTIAEYLRDEEKEDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHhcCCceEEEeccchH
Confidence            223355555   38999999999954

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.53  E-value=0.021  Score=51.50  Aligned_cols=26  Identities=31%  Similarity=0.280  Sum_probs=21.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....+|.++|++|+||||++..+...
T Consensus        98 ~~~~vi~lvG~~GvGKTTtaaKLA~~  123 (429)
T TIGR01425        98 GKQNVIMFVGLQGSGKTTTCTKLAYY  123 (429)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34689999999999999988877543

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.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=96.50  E-value=0.015  Score=52.62  Aligned_cols=87  Identities=17%  Similarity=0.175  Sum_probs=51.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc--------CCCCCCCHHH----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA--------GSADVNDLNL----  223 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~--------~~~~~~~~~~----  223 (261)
                      -..++|+|..|+|||||++.+.+..+    -+..+.+-+++... ..++..+.+..-+        ...+......    
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            35789999999999999999987632    23445566666443 3344444433321        1112111111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          224 -LQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 -~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                       ..-.+-+++  .++.+|+++||+-.-
T Consensus       234 ~~a~tiAEyfrd~G~~Vll~~DslTr~  260 (442)
T PRK08927        234 YLTLAIAEYFRDQGKDVLCLMDSVTRF  260 (442)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCcHHH
Confidence             112233444  589999999999553

>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=96.49  E-value=0.0065  Score=51.61  Aligned_cols=23  Identities=30%  Similarity=0.289  Sum_probs=18.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..|.|+|.||+||||+|+.+...
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            46889999999999999999876

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.49  E-value=0.0022  Score=50.77  Aligned_cols=23  Identities=30%  Similarity=0.405  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|++|+|||||++.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999999998665

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.49  E-value=0.0059  Score=47.04  Aligned_cols=22  Identities=41%  Similarity=0.616  Sum_probs=19.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.|+|.+|+||||+|+.+...
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            4789999999999999998775

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=96.48  E-value=0.0066  Score=53.13  Aligned_cols=112  Identities=21%  Similarity=0.209  Sum_probs=62.5

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQ  210 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~  210 (261)
                      .++|.+.....+...+...        +-+.+.|++|+|||+||+.+.....  -   .-.+|.+.......++.....-
T Consensus        25 ~~~g~~~~~~~~l~a~~~~--------~~vll~G~PG~gKT~la~~lA~~l~--~---~~~~i~~t~~l~p~d~~G~~~~   91 (329)
T COG0714          25 VVVGDEEVIELALLALLAG--------GHVLLEGPPGVGKTLLARALARALG--L---PFVRIQCTPDLLPSDLLGTYAY   91 (329)
T ss_pred             eeeccHHHHHHHHHHHHcC--------CCEEEECCCCccHHHHHHHHHHHhC--C---CeEEEecCCCCCHHHhcCchhH
Confidence            3778776666665555543        3578999999999999999988632  1   2345666666665554433222


Q ss_pred             HhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          211 AAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       211 ~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      ..... ......-...-+   +.+-+.++.+|+++...+..-..|...|
T Consensus        92 ~~~~~-~~~~~~~~~gpl---~~~~~~ill~DEInra~p~~q~aLl~~l  136 (329)
T COG0714          92 AALLL-EPGEFRFVPGPL---FAAVRVILLLDEINRAPPEVQNALLEAL  136 (329)
T ss_pred             hhhhc-cCCeEEEecCCc---ccccceEEEEeccccCCHHHHHHHHHHH
Confidence            21100 000000000000   0111169999999998876655555443

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.48  E-value=0.0088  Score=53.58  Aligned_cols=52  Identities=23%  Similarity=0.283  Sum_probs=37.7

Q ss_pred             CccccccchHHHHHHHhhCC--------CCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGD--------DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.++.++.+.-.+...        ...+....+-|.++|++|+|||++|+.+....
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l   71 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLA   71 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            45889988888887666531        00012234678899999999999999998873

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.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.48  E-value=0.0019  Score=51.72  Aligned_cols=23  Identities=39%  Similarity=0.533  Sum_probs=20.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +|+|.|.+|+||||+|+.+....
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999998763

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.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=96.47  E-value=0.014  Score=53.03  Aligned_cols=88  Identities=19%  Similarity=0.284  Sum_probs=52.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHH-----H
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLN-----L  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~-----~  223 (261)
                      .-++|.|.+|+|||||+..+........ =+..+++-+.+.. .+.+++.++...-. .       ..+.....     .
T Consensus       145 QR~gIfa~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~  223 (463)
T PRK09280        145 GKIGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVAL  223 (463)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            4589999999999999998876532221 1356677776654 34555555554321 1       11111111     1


Q ss_pred             HHHHHHHHh---CCCeEEEEEeCCCC
Q 041190          224 LQLQLENQL---KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 ~~~~l~~~l---~~kr~LiVlDdvw~  246 (261)
                      ..-.+-+++   +++++||++|++-.
T Consensus       224 ~a~tiAEyfrd~~G~~VLll~DslTR  249 (463)
T PRK09280        224 TGLTMAEYFRDVEGQDVLLFIDNIFR  249 (463)
T ss_pred             HHHHHHHHHHHhcCCceEEEecchHH
Confidence            122345555   68999999999954

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.47  E-value=0.013  Score=52.32  Aligned_cols=25  Identities=28%  Similarity=0.232  Sum_probs=21.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+++.++|++|+||||.+..+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~  197 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAI  197 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999988887654

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

Probab=96.47  E-value=0.015  Score=52.18  Aligned_cols=73  Identities=21%  Similarity=0.170  Sum_probs=42.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEE
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFL  238 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~L  238 (261)
                      ++.|+|+.++||||+++.+....  .+.   .++++..+......-+.+.+..                +.+.-..++.+
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~--~~~---~iy~~~~d~~~~~~~l~d~~~~----------------~~~~~~~~~~y   97 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGL--LEE---IIYINFDDLRLDRIELLDLLRA----------------YIELKEREKSY   97 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhC--Ccc---eEEEEecchhcchhhHHHHHHH----------------HHHhhccCCce
Confidence            99999999999999997776552  111   4555433322111111111111                11111128899


Q ss_pred             EEEeCCCCCChhhHHH
Q 041190          239 LVLDDMWSENYDVWTN  254 (261)
Q Consensus       239 iVlDdvw~~~~~~w~~  254 (261)
                      |+||+|.+..  .|..
T Consensus        98 ifLDEIq~v~--~W~~  111 (398)
T COG1373          98 IFLDEIQNVP--DWER  111 (398)
T ss_pred             EEEecccCch--hHHH
Confidence            9999999984  6754

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

Probab=96.46  E-value=0.061  Score=50.98  Aligned_cols=103  Identities=18%  Similarity=0.090  Sum_probs=60.1

Q ss_pred             CCCccccccchHHHHHHHhhCCCC------C-CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDL------N-SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD  200 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~------~-~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  200 (261)
                      .-.++-|..+.++-|.+.+.-...      . .-+...=|.++|++|+|||.||..+.....       .-+++|.++  
T Consensus       665 ~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~-------~~fisvKGP--  735 (952)
T KOG0735|consen  665 RWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSN-------LRFISVKGP--  735 (952)
T ss_pred             CceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCC-------eeEEEecCH--
Confidence            344566777777777777655320      0 112233478899999999999999987622       124556553  


Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCCh
Q 041190          201 AVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENY  249 (261)
Q Consensus       201 ~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~  249 (261)
                        +++.+.+        +.+.+.+..-+.+.-.-|.|++++|+..+..|
T Consensus       736 --ElL~KyI--------GaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAP  774 (952)
T KOG0735|consen  736 --ELLSKYI--------GASEQNVRDLFERAQSAKPCILFFDEFDSIAP  774 (952)
T ss_pred             --HHHHHHh--------cccHHHHHHHHHHhhccCCeEEEeccccccCc
Confidence              2222221        11222222222333356899999999888654

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=96.46  E-value=0.0029  Score=49.93  Aligned_cols=26  Identities=27%  Similarity=0.386  Sum_probs=23.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...+++|+|..|+|||||++.+....
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l   30 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPAL   30 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHH
Confidence            46799999999999999999998663

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=96.46  E-value=0.004  Score=57.68  Aligned_cols=55  Identities=20%  Similarity=0.182  Sum_probs=40.1

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEee
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYV  195 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v  195 (261)
                      .+-++++..||...-. .....+++.++|++|+||||.++.+.+..    .|+.+-|.+-
T Consensus        25 kkKv~eV~~wl~~~~~-~~~~~~iLlLtGP~G~GKtttv~~La~el----g~~v~Ew~np   79 (519)
T PF03215_consen   25 KKKVEEVRSWLEEMFS-GSSPKRILLLTGPSGCGKTTTVKVLAKEL----GFEVQEWINP   79 (519)
T ss_pred             HHHHHHHHHHHHHHhc-cCCCcceEEEECCCCCCHHHHHHHHHHHh----CCeeEEecCC
Confidence            4456788888875321 23345699999999999999999998862    4667778653

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=96.46  E-value=0.011  Score=49.60  Aligned_cols=96  Identities=19%  Similarity=0.143  Sum_probs=55.1

Q ss_pred             ccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVG  203 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  203 (261)
                      ++-|=.++.++|.+...-.-..       +-..++=+..+|++|+|||.+|+.|.|.  ....|     +.|-++    +
T Consensus       178 dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanr--tdacf-----irvigs----e  246 (435)
T KOG0729|consen  178 DVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANR--TDACF-----IRVIGS----E  246 (435)
T ss_pred             cccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcc--cCceE-----EeehhH----H
Confidence            3455667777777754322100       1123455788999999999999999997  33333     333221    1


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHHHHhCC-CeEEEEEeCCCC
Q 041190          204 VTKVILQAAAGSADVNDLNLLQLQLENQLKN-KKFLLVLDDMWS  246 (261)
Q Consensus       204 i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~-kr~LiVlDdvw~  246 (261)
                      +.++         ....-..+.+.|.+.-+. |-++|++|++.-
T Consensus       247 lvqk---------yvgegarmvrelf~martkkaciiffdeida  281 (435)
T KOG0729|consen  247 LVQK---------YVGEGARMVRELFEMARTKKACIIFFDEIDA  281 (435)
T ss_pred             HHHH---------HhhhhHHHHHHHHHHhcccceEEEEeecccc
Confidence            1111         111223344555555554 569999998864

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.45  E-value=0.002  Score=51.18  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=20.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|.|+|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999876

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.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=96.44  E-value=0.0021  Score=51.16  Aligned_cols=22  Identities=45%  Similarity=0.620  Sum_probs=20.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999876

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>TIGR03263 guanyl_kin guanylate kinase

Probab=96.44  E-value=0.0024  Score=50.61  Aligned_cols=23  Identities=35%  Similarity=0.667  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++.|+|++|+|||||++.+.+.
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            47899999999999999999875

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.

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=96.43  E-value=0.0052  Score=56.85  Aligned_cols=74  Identities=18%  Similarity=0.082  Sum_probs=44.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCC
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKN  234 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  234 (261)
                      ...+.+-++|++|+|||.||+.+.+.  ...+|-...     ..    .++.        ..-......+...+....+.
T Consensus       274 ~~~~giLl~GpPGtGKT~lAkava~~--~~~~fi~v~-----~~----~l~s--------k~vGesek~ir~~F~~A~~~  334 (494)
T COG0464         274 RPPKGVLLYGPPGTGKTLLAKAVALE--SRSRFISVK-----GS----ELLS--------KWVGESEKNIRELFEKARKL  334 (494)
T ss_pred             CCCCeeEEECCCCCCHHHHHHHHHhh--CCCeEEEee-----CH----HHhc--------cccchHHHHHHHHHHHHHcC
Confidence            34568899999999999999999995  334442221     11    1000        00111222222333444467


Q ss_pred             CeEEEEEeCCCCC
Q 041190          235 KKFLLVLDDMWSE  247 (261)
Q Consensus       235 kr~LiVlDdvw~~  247 (261)
                      ..+.|++|++.+.
T Consensus       335 ~p~iiFiDEiDs~  347 (494)
T COG0464         335 APSIIFIDEIDSL  347 (494)
T ss_pred             CCcEEEEEchhhh
Confidence            8899999998764

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.43  E-value=0.021  Score=48.34  Aligned_cols=90  Identities=26%  Similarity=0.228  Sum_probs=54.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcccc--ccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGV--KKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~--~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~----  222 (261)
                      .-++|.|-.|+|||+|+..+.++...  +.+-+..+++-+.+.. ...+++.++...=. .       ..+.....    
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            35789999999999999998876431  1224567888888755 34555555544311 1       11111111    


Q ss_pred             -HHHHHHHHHh---CCCeEEEEEeCCCCC
Q 041190          223 -LLQLQLENQL---KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 -~~~~~l~~~l---~~kr~LiVlDdvw~~  247 (261)
                       ...-.+-+++   +++++|+++||+-.-
T Consensus       150 ~~~a~aiAEyfrd~~g~~VLl~~D~ltr~  178 (276)
T cd01135         150 PRMALTTAEYLAYEKGKHVLVILTDMTNY  178 (276)
T ss_pred             HHHHHHHHHHHHhccCCeEEEEEcChhHH
Confidence             1122244444   378999999998654

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.

>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=96.43  E-value=0.011  Score=46.73  Aligned_cols=100  Identities=22%  Similarity=0.135  Sum_probs=53.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcccc----c----------cccceeEEEeeCCCCCHHHHHHHHHHHhc------CC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGV----K----------KYFSFRACAYVSEDFDAVGVTKVILQAAA------GS  215 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~----~----------~~f~~~~wv~v~~~~~~~~i~~~i~~~l~------~~  215 (261)
                      +-.-|.+.|+.|+||||+.+.+....-.    .          ..+...+| .+++......++...+....      ..
T Consensus        13 ~~~~ililGl~~sGKTtll~~l~~~~~~~~~pT~g~~~~~i~~~~~~~~~~-d~gG~~~~~~~w~~y~~~~~~iIfVvDs   91 (175)
T PF00025_consen   13 KEIKILILGLDGSGKTTLLNRLKNGEISETIPTIGFNIEEIKYKGYSLTIW-DLGGQESFRPLWKSYFQNADGIIFVVDS   91 (175)
T ss_dssp             SEEEEEEEESTTSSHHHHHHHHHSSSEEEEEEESSEEEEEEEETTEEEEEE-EESSSGGGGGGGGGGHTTESEEEEEEET
T ss_pred             cEEEEEEECCCccchHHHHHHhhhccccccCcccccccceeeeCcEEEEEE-eccccccccccceeeccccceeEEEEec
Confidence            4566799999999999999999764211    0          11112222 35554444444544444322      11


Q ss_pred             CCCCCHHHHHHHHHHHh-----CCCeEEEEEeCCCCCChhhHHHhh
Q 041190          216 ADVNDLNLLQLQLENQL-----KNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       216 ~~~~~~~~~~~~l~~~l-----~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      .+.....+....+.+.+     .+.++||++---........+++.
T Consensus        92 sd~~~l~e~~~~L~~ll~~~~~~~~piLIl~NK~D~~~~~~~~~i~  137 (175)
T PF00025_consen   92 SDPERLQEAKEELKELLNDPELKDIPILILANKQDLPDAMSEEEIK  137 (175)
T ss_dssp             TGGGGHHHHHHHHHHHHTSGGGTTSEEEEEEESTTSTTSSTHHHHH
T ss_pred             ccceeecccccchhhhcchhhcccceEEEEeccccccCcchhhHHH
Confidence            22333445555555544     467888887655443322334444

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.42  E-value=0.0031  Score=49.78  Aligned_cols=26  Identities=31%  Similarity=0.381  Sum_probs=22.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +..+|.++|++|+||||+|+.+....
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l   28 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKL   28 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34699999999999999999998763

>PRK08149 ATP synthase SpaL; Validated

Probab=96.41  E-value=0.02  Score=51.66  Aligned_cols=87  Identities=15%  Similarity=0.272  Sum_probs=50.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc--------CCCCCCCHH-----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA--------GSADVNDLN-----  222 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~--------~~~~~~~~~-----  222 (261)
                      -..++|+|.+|+|||||++.+.+....    +..+...+... ....++..+.+....        ...+.....     
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~~----dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~  226 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSEA----DVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAA  226 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCCC----CeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHH
Confidence            347899999999999999999875322    23333334332 244555555554322        111221111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          223 LLQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ~~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      ...-.+-+++  ++|++|+++||+-.-
T Consensus       227 ~~a~tiAE~fr~~G~~Vll~~DslTr~  253 (428)
T PRK08149        227 LVATTVAEYFRDQGKRVVLFIDSMTRY  253 (428)
T ss_pred             HHHHHHHHHHHHcCCCEEEEccchHHH
Confidence            1122233333  589999999999553

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.41  E-value=0.0066  Score=53.07  Aligned_cols=46  Identities=17%  Similarity=0.132  Sum_probs=36.8

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.......+.+.+..-.    ..-..|.|+|.+|+||+++|+.++..
T Consensus         7 ~liG~S~~~~~~~~~i~~~a----~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          7 NLLGEANSFLEVLEQVSRLA----PLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             ccEECCHHHHHHHHHHHHHh----CCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            48898888888888776632    23356889999999999999999864

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.40  E-value=0.009  Score=53.12  Aligned_cols=96  Identities=23%  Similarity=0.126  Sum_probs=55.6

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCC--
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSA--  216 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~--  216 (261)
                      ...+-+.|..    +-..-.++.|.|.+|+|||||+.++....  ...-....|++..+.  ...+. .-..+++...  
T Consensus        68 i~eLD~vLgG----Gi~~GslvLI~G~pG~GKStLllq~a~~~--a~~g~~VlYvs~EEs--~~qi~-~Ra~rlg~~~~~  138 (372)
T cd01121          68 IEELDRVLGG----GLVPGSVILIGGDPGIGKSTLLLQVAARL--AKRGGKVLYVSGEES--PEQIK-LRADRLGISTEN  138 (372)
T ss_pred             CHHHHHhhcC----CccCCeEEEEEeCCCCCHHHHHHHHHHHH--HhcCCeEEEEECCcC--HHHHH-HHHHHcCCCccc
Confidence            4455555543    23345799999999999999999987652  222234567765443  33322 2234444111  


Q ss_pred             ----CCCCHHHHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          217 ----DVNDLNLLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       217 ----~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                          ...+.+.+...+.   ..+.-+||+|.+..
T Consensus       139 l~l~~e~~le~I~~~i~---~~~~~lVVIDSIq~  169 (372)
T cd01121         139 LYLLAETNLEDILASIE---ELKPDLVIIDSIQT  169 (372)
T ss_pred             EEEEccCcHHHHHHHHH---hcCCcEEEEcchHH
Confidence                2234455544443   34667899999854

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.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.40  E-value=0.039  Score=45.46  Aligned_cols=41  Identities=20%  Similarity=0.132  Sum_probs=28.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      +.-.++.|.|.+|+|||||+..+.... .+ .-...+|++...
T Consensus        18 ~~G~~~~i~G~~G~GKT~l~~~~~~~~-~~-~g~~~~~is~e~   58 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTIFCLHFAYKG-LR-DGDPVIYVTTEE   58 (229)
T ss_pred             cCCeEEEEECCCCCChHHHHHHHHHHH-Hh-cCCeEEEEEccC
Confidence            456799999999999999998865431 11 223457777644

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.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.39  E-value=0.0079  Score=50.77  Aligned_cols=87  Identities=20%  Similarity=0.082  Sum_probs=58.1

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC-------------------
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG-------------------  214 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~-------------------  214 (261)
                      -+.-+++.|+|.+|+|||+++.+....  ...+.....||+..++  ...+++.+.+ ++.                   
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f~~qfl~~--~~~~ge~vlyvs~~e~--~~~l~~~~~~-~g~d~~~~~~~g~l~i~d~~~~   94 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIFALQFLYE--GAREGEPVLYVSTEES--PEELLENARS-FGWDLEVYIEKGKLAILDAFLS   94 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHHHHHHHHH--HHhcCCcEEEEEecCC--HHHHHHHHHH-cCCCHHHHhhcCCEEEEEcccc
Confidence            456789999999999999999887765  3445778999998884  3444444322 220                   


Q ss_pred             CCC--------CCCHHHHHHHHHHHhCC-CeEEEEEeCCC
Q 041190          215 SAD--------VNDLNLLQLQLENQLKN-KKFLLVLDDMW  245 (261)
Q Consensus       215 ~~~--------~~~~~~~~~~l~~~l~~-kr~LiVlDdvw  245 (261)
                      ...        ..+...+...|++.... +...+|+|.+-
T Consensus        95 ~~~~~~~~~~~~~~~~~l~~~I~~~~~~~~~~~~ViDsi~  134 (260)
T COG0467          95 EKGLVSIVVGDPLDLEELLDRIREIVEKEGADRVVIDSIT  134 (260)
T ss_pred             ccccccccccCCccHHHHHHHHHHHHHHhCCCEEEEeCCc
Confidence            000        12445566667666643 37788999886

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=96.38  E-value=0.22  Score=44.66  Aligned_cols=72  Identities=24%  Similarity=0.200  Sum_probs=42.7

Q ss_pred             HHHHHHHhhCCCCC---CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC--CCHHHHHHHHHHHhc
Q 041190          139 KEVIVGLLLGDDLN---SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED--FDAVGVTKVILQAAA  213 (261)
Q Consensus       139 ~~~l~~~L~~~~~~---~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~i~~~i~~~l~  213 (261)
                      .++|+++|......   ....+.||-.+|.-|+||||-+-.+.+..+. ..+  .+-+.....  +...+.++.+.++++
T Consensus        79 ~eELv~llG~~~~~~~l~~~~P~vImmvGLQGsGKTTt~~KLA~~lkk-~~~--kvllVaaD~~RpAA~eQL~~La~q~~  155 (451)
T COG0541          79 YEELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKYLKK-KGK--KVLLVAADTYRPAAIEQLKQLAEQVG  155 (451)
T ss_pred             HHHHHHHhCCCCcccccCCCCCeEEEEEeccCCChHhHHHHHHHHHHH-cCC--ceEEEecccCChHHHHHHHHHHHHcC
Confidence            56777777742211   1345789999999999999988777665322 222  222222222  344555666666665

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.38  E-value=0.0027  Score=50.20  Aligned_cols=23  Identities=22%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.+.|++|+||||+|+.+.+.
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999999876

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>cd04159 Arl10_like Arl10-like subfamily

Probab=96.37  E-value=0.016  Score=43.91  Aligned_cols=21  Identities=33%  Similarity=0.577  Sum_probs=19.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |+|+|.+|+|||||.+.+...
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            689999999999999999776

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=96.37  E-value=0.0024  Score=48.51  Aligned_cols=22  Identities=41%  Similarity=0.680  Sum_probs=20.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|.|+|++|+||||+|+.+...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~   22 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKK   22 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999876

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.36  E-value=0.0025  Score=48.86  Aligned_cols=22  Identities=27%  Similarity=0.567  Sum_probs=19.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.++|++|+||||+|+.+.+.
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            4678999999999999999876

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=96.36  E-value=0.0035  Score=47.83  Aligned_cols=39  Identities=21%  Similarity=0.332  Sum_probs=26.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      ++|.|+|..|+|||||++.+.+... +..+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~-~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELK-RRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHH-HTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh-HcCCceEEEEEccC
Confidence            4799999999999999999998743 23455554555444

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.36  E-value=0.026  Score=50.89  Aligned_cols=24  Identities=29%  Similarity=0.306  Sum_probs=20.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      +-.+++++|+.|+||||++..+..
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~  213 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAA  213 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            347999999999999999987754

>PF14516 AAA_35: AAA-like domain

Probab=96.35  E-value=0.077  Score=46.52  Aligned_cols=112  Identities=13%  Similarity=0.066  Sum_probs=69.1

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC----C-CCHH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE----D-FDAV  202 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~----~-~~~~  202 (261)
                      +.+..+.|...-+.+.+.|...       -..+.|.|+..+|||+|...+.+..+.. .+. .+++++..    . .+..
T Consensus         9 ~~~~Yi~R~~~e~~~~~~i~~~-------G~~~~I~apRq~GKTSll~~l~~~l~~~-~~~-~v~id~~~~~~~~~~~~~   79 (331)
T PF14516_consen    9 DSPFYIERPPAEQECYQEIVQP-------GSYIRIKAPRQMGKTSLLLRLLERLQQQ-GYR-CVYIDLQQLGSAIFSDLE   79 (331)
T ss_pred             CCCcccCchHHHHHHHHHHhcC-------CCEEEEECcccCCHHHHHHHHHHHHHHC-CCE-EEEEEeecCCCcccCCHH
Confidence            4445677885666666666542       2589999999999999999998774332 343 34565543    1 2456


Q ss_pred             HHHHHHHHHhcCCC------------CCCCHHHHHHHHHHHh---CCCeEEEEEeCCCCCC
Q 041190          203 GVTKVILQAAAGSA------------DVNDLNLLQLQLENQL---KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       203 ~i~~~i~~~l~~~~------------~~~~~~~~~~~l~~~l---~~kr~LiVlDdvw~~~  248 (261)
                      ..++.++..+....            ...+.......+.+.+   .+++.+|+||+|...-
T Consensus        80 ~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~  140 (331)
T PF14516_consen   80 QFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLF  140 (331)
T ss_pred             HHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhc
Confidence            56666665554111            1112233334444433   2689999999998664

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.34  E-value=0.033  Score=47.04  Aligned_cols=42  Identities=24%  Similarity=0.224  Sum_probs=29.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      -+.-+++.|+|.+|+|||+++.++.... .+ .=...++++...
T Consensus        33 ip~gs~~lI~G~pGtGKT~l~~qf~~~~-a~-~Ge~vlyis~Ee   74 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLMVEQFAVTQ-AS-RGNPVLFVTVES   74 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHHHHHHHHHH-Hh-CCCcEEEEEecC
Confidence            3456799999999999999999875431 11 122456777654

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=96.34  E-value=0.011  Score=53.01  Aligned_cols=51  Identities=22%  Similarity=0.270  Sum_probs=37.9

Q ss_pred             CccccccchHHHHHHHhhCC--------CCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGD--------DLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.+..++.+...+...        ........+.+.++|++|+|||+||+.+...
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            45899999998888877541        0001112467899999999999999999876

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.34  E-value=0.012  Score=53.78  Aligned_cols=47  Identities=34%  Similarity=0.375  Sum_probs=34.6

Q ss_pred             chHHHHHHHhhCCCC--C-CCCCceEEeEeecCCCChHHHHHHHhhcccc
Q 041190          137 KDKEVIVGLLLGDDL--N-SGPGFSVIPITGMGGLGKTTLAQLVFNDAGV  183 (261)
Q Consensus       137 ~~~~~l~~~L~~~~~--~-~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  183 (261)
                      .++++|+++|.+...  . ++.=++=|.++|++|+|||-||+.|.-...+
T Consensus       314 ~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~V  363 (752)
T KOG0734|consen  314 QELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGV  363 (752)
T ss_pred             HHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCC
Confidence            567888888876421  0 2233556889999999999999999887554

>PRK00300 gmk guanylate kinase; Provisional

Probab=96.33  E-value=0.0033  Score=50.91  Aligned_cols=24  Identities=29%  Similarity=0.468  Sum_probs=21.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+|.|+|++|+|||||++.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999876

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.32  E-value=0.0018  Score=52.07  Aligned_cols=23  Identities=39%  Similarity=0.567  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|-+.|.+|+||||+|+++..-
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~   24 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKE   24 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHH
Confidence            46778999999999999998765

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.32  E-value=0.02  Score=55.11  Aligned_cols=24  Identities=29%  Similarity=0.372  Sum_probs=20.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++.++|+.|+||||.+.++...
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~  208 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAAR  208 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhh
Confidence            479999999999999988887654

>PRK03846 adenylylsulfate kinase; Provisional

Probab=96.32  E-value=0.004  Score=50.35  Aligned_cols=26  Identities=31%  Similarity=0.321  Sum_probs=23.2

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++..++.|+|++|+||||||+.+...
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~   47 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEA   47 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45689999999999999999999775

>PRK06936 type III secretion system ATPase; Provisional

Probab=96.30  E-value=0.019  Score=51.88  Aligned_cols=84  Identities=18%  Similarity=0.196  Sum_probs=50.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH-----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN-----  222 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~-----  222 (261)
                      -..++|.|..|+|||||.+.+++...    -++.+++-+++... ..++....+..-+ .       ..+.....     
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            35789999999999999999998632    24567777777543 3333433222211 1       11111111     


Q ss_pred             ----HHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          223 ----LLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       223 ----~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                          .+...+++  .+|++|+++||+-.
T Consensus       238 ~~a~tiAEyfrd--~G~~Vll~~DslTR  263 (439)
T PRK06936        238 FVATSIAEYFRD--QGKRVLLLMDSVTR  263 (439)
T ss_pred             HHHHHHHHHHHH--cCCCEEEeccchhH
Confidence                12333333  58999999999954

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.29  E-value=0.022  Score=52.19  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..|++++|+.|+||||++.++...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~  279 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAAR  279 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHH
Confidence            479999999999999999988865

>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=96.28  E-value=0.054  Score=42.30  Aligned_cols=42  Identities=26%  Similarity=0.271  Sum_probs=28.9

Q ss_pred             cccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          134 GREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       134 gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++..+.|...+..+     .-...+-++|+.|+||+++|..+.+.
T Consensus         1 gq~~~~~~L~~~~~~~-----~l~ha~L~~G~~g~gk~~~a~~~a~~   42 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSG-----RLPHALLFHGPSGSGKKTLALAFARA   42 (162)
T ss_dssp             S-HHHHHHHHHHHHCT-----C--SEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcC-----CcceeEEEECCCCCCHHHHHHHHHHH
Confidence            4455667777777543     23456889999999999998777554

...

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=96.27  E-value=0.015  Score=52.66  Aligned_cols=89  Identities=13%  Similarity=0.178  Sum_probs=55.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH-----H
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN-----L  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~-----~  223 (261)
                      .-++|.|.+|+|||+|+..+.+... +.+-++.+++-+.+... ..+++.++...-. .       ..+.....     .
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            4689999999999999999877632 22346778888877553 4555555544311 1       11111111     1


Q ss_pred             HHHHHHHHh---CCCeEEEEEeCCCCC
Q 041190          224 LQLQLENQL---KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 ~~~~l~~~l---~~kr~LiVlDdvw~~  247 (261)
                      ..-.+-+++   +++++|+++||+-.-
T Consensus       218 ~a~tiAEyfrd~~G~~VLl~~DslTR~  244 (449)
T TIGR03305       218 TALTMAEYFRDDEKQDVLLLIDNIFRF  244 (449)
T ss_pred             HHHHHHHHHHHhcCCceEEEecChHHH
Confidence            223355555   468999999999553

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.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.27  E-value=0.0031  Score=49.26  Aligned_cols=20  Identities=50%  Similarity=0.776  Sum_probs=18.4

Q ss_pred             EEeEeecCCCChHHHHHHHh
Q 041190          159 VIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~  178 (261)
                      .|.|.|.||+||||+++.+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999885

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.25  E-value=0.023  Score=52.44  Aligned_cols=101  Identities=15%  Similarity=0.044  Sum_probs=62.4

Q ss_pred             chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC--
Q 041190          137 KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG--  214 (261)
Q Consensus       137 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~--  214 (261)
                      .....|-++|..    +-+.-+++.|.|++|+|||||+.+.....  ..+=+..+++...+  +..++...+ +.++-  
T Consensus       247 tGi~~lD~~lgG----G~~~gs~~li~G~~G~GKt~l~~~f~~~~--~~~ge~~~y~s~eE--s~~~i~~~~-~~lg~~~  317 (484)
T TIGR02655       247 SGVVRLDEMCGG----GFFKDSIILATGATGTGKTLLVSKFLENA--CANKERAILFAYEE--SRAQLLRNA-YSWGIDF  317 (484)
T ss_pred             CChHhHHHHhcC----CccCCcEEEEECCCCCCHHHHHHHHHHHH--HHCCCeEEEEEeeC--CHHHHHHHH-HHcCCCh
Confidence            345666666654    34567899999999999999998886652  11223456666555  444554443 34431  


Q ss_pred             --------------CCCCCCHHHHHHHHHHHhCC-CeEEEEEeCCCC
Q 041190          215 --------------SADVNDLNLLQLQLENQLKN-KKFLLVLDDMWS  246 (261)
Q Consensus       215 --------------~~~~~~~~~~~~~l~~~l~~-kr~LiVlDdvw~  246 (261)
                                    .+.....+.....+++.+.. +.-++|+|.+-.
T Consensus       318 ~~~~~~g~l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi~~  364 (484)
T TIGR02655       318 EEMEQQGLLKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSLSA  364 (484)
T ss_pred             HHHhhCCcEEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCHHH
Confidence                          01123346666777777643 556899999864

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.

>PRK06620 hypothetical protein; Validated

Probab=96.25  E-value=0.0035  Score=51.43  Aligned_cols=52  Identities=21%  Similarity=0.184  Sum_probs=31.9

Q ss_pred             CCCccccc-c-chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          128 DEEEVYGR-E-KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       128 ~~~~~~gr-~-~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.++|. + .....+..+-....  .++..+.+.|+|++|+|||+|++.+++..
T Consensus        15 fd~Fvvg~~N~~a~~~~~~~~~~~~--~~~~~~~l~l~Gp~G~GKThLl~a~~~~~   68 (214)
T PRK06620         15 PDEFIVSSSNDQAYNIIKNWQCGFG--VNPYKFTLLIKGPSSSGKTYLTKIWQNLS   68 (214)
T ss_pred             chhhEecccHHHHHHHHHHHHHccc--cCCCcceEEEECCCCCCHHHHHHHHHhcc
Confidence            44556665 2 23444444432111  11112678999999999999999987763

>TIGR01351 adk adenylate kinases

Probab=96.24  E-value=0.027  Score=45.86  Aligned_cols=21  Identities=29%  Similarity=0.368  Sum_probs=19.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKsT~a~~La~~   22 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEK   22 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999765

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.24  E-value=0.0068  Score=45.71  Aligned_cols=27  Identities=37%  Similarity=0.474  Sum_probs=23.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcccc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGV  183 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  183 (261)
                      -.+|.+.|.-|+||||+++.+.+....
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            458999999999999999999987443

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.

>PHA00729 NTP-binding motif containing protein

Probab=96.24  E-value=0.0045  Score=50.92  Aligned_cols=24  Identities=46%  Similarity=0.452  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|.|+|.+|+||||||..+.+.
T Consensus        17 f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         17 FVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHH
Confidence            456889999999999999999876

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=96.23  E-value=0.014  Score=50.46  Aligned_cols=113  Identities=19%  Similarity=0.150  Sum_probs=68.9

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccce-eEEEeeCCCCCHHH-HHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSF-RACAYVSEDFDAVG-VTKV  207 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~-i~~~  207 (261)
                      ..++|-.++...+..++...-.  -....-+.|+|+.|.|||+|...+..+.   +.|.. ..-|...+....++ .++.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~--~gEsnsviiigprgsgkT~li~~~Ls~~---q~~~E~~l~v~Lng~~~~dk~al~~   98 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTIL--HGESNSVIIIGPRGSGKTILIDTRLSDI---QENGENFLLVRLNGELQTDKIALKG   98 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHH--hcCCCceEEEccCCCCceEeeHHHHhhH---HhcCCeEEEEEECccchhhHHHHHH
Confidence            4588988888888888865311  1123457889999999999999888772   22322 23344544433322 3555


Q ss_pred             HHHHhc-----CCCCCCCHHHHHHHHHHHhCC------CeEEEEEeCCCCC
Q 041190          208 ILQAAA-----GSADVNDLNLLQLQLENQLKN------KKFLLVLDDMWSE  247 (261)
Q Consensus       208 i~~~l~-----~~~~~~~~~~~~~~l~~~l~~------kr~LiVlDdvw~~  247 (261)
                      |..++.     ......+..+...++...|+.      -++++|+|+..--
T Consensus        99 I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf  149 (408)
T KOG2228|consen   99 ITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLF  149 (408)
T ss_pred             HHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhcc
Confidence            666554     122334555555666666642      3588888887543

>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=96.23  E-value=0.0063  Score=53.08  Aligned_cols=53  Identities=26%  Similarity=0.327  Sum_probs=44.7

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....++|.++.++++++.+.......+..-+++.+.|+.|.|||||+..+.+-
T Consensus        59 f~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~  111 (358)
T PF08298_consen   59 FEDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRG  111 (358)
T ss_pred             ccccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999988754334567889999999999999999998775

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PTZ00494 tuzin-like protein; Provisional

Probab=96.23  E-value=0.48  Score=43.07  Aligned_cols=80  Identities=14%  Similarity=0.145  Sum_probs=61.1

Q ss_pred             CCCCCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHH
Q 041190          123 TPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAV  202 (261)
Q Consensus       123 ~~~~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  202 (261)
                      +........++.|+.+-..+...|..-   +..+++++.+.|..|+||++|.+.....+.+     ...+|.|...   +
T Consensus       364 ~~a~a~~~~~V~R~~eE~~vRqvL~ql---d~aHPRIvV~TG~~GcGKSslcRsAvrkE~~-----paV~VDVRg~---E  432 (664)
T PTZ00494        364 MLAAAAEAFEVRREDEEALVRSVLTQM---APSHPRIVALAGGSGGGRCVPCRRAVRVEGV-----ALVHVDVGGT---E  432 (664)
T ss_pred             cccccccccccchhhHHHHHHHHHhhc---cCCCCcEEEEecCCCCCchHHHHHHHHHcCC-----CeEEEEecCC---c
Confidence            334456677899998888888888765   3567899999999999999999988776444     3566776554   4


Q ss_pred             HHHHHHHHHhc
Q 041190          203 GVTKVILQAAA  213 (261)
Q Consensus       203 ~i~~~i~~~l~  213 (261)
                      +-++.+.+.++
T Consensus       433 DtLrsVVKALg  443 (664)
T PTZ00494        433 DTLRSVVRALG  443 (664)
T ss_pred             chHHHHHHHhC
Confidence            45778888888

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=96.23  E-value=0.0036  Score=49.28  Aligned_cols=22  Identities=50%  Similarity=0.629  Sum_probs=18.9

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |.|.|.+|+|||||++.+++..
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            6899999999999999998764

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.23  E-value=0.025  Score=46.85  Aligned_cols=50  Identities=20%  Similarity=0.133  Sum_probs=30.8

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHH
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i  208 (261)
                      +.-.++.|.|++|+|||||+.++.... .+.. ...++++...  +..++++.+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~-~~~g-~~~~yi~~e~--~~~~~~~~~   71 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGF-LQNG-YSVSYVSTQL--TTTEFIKQM   71 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH-HhCC-CcEEEEeCCC--CHHHHHHHH
Confidence            345699999999999999975554431 1222 2345565333  445555554

>PF11868 DUF3388: Protein of unknown function (DUF3388); InterPro: IPR024514 This domain is found in a family of bacterial proteins that are functionally uncharacterised

Probab=96.22  E-value=0.017  Score=44.39  Aligned_cols=50  Identities=24%  Similarity=0.358  Sum_probs=34.8

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHH--HHHHHhhccccccccceeEEEeeCCC
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTT--LAQLVFNDAGVKKYFSFRACAYVSED  198 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTt--La~~v~~~~~~~~~f~~~~wv~v~~~  198 (261)
                      +..-|+++|..--  ...+-.+|+|.||+-+|||.  +|-.||.+         .-|.-+|++
T Consensus        37 eLGlLVDFmaEl~--K~~Gh~lIGiRGmPRVGKTEsivAasVcAn---------KrW~f~SST   88 (192)
T PF11868_consen   37 ELGLLVDFMAELF--KEEGHKLIGIRGMPRVGKTESIVAASVCAN---------KRWLFLSST   88 (192)
T ss_pred             HhccHHHHHHHHH--HhcCceEEeecCCCccCchhHHHHHhhhcC---------ceEEEeeHH
Confidence            4555555543310  11245899999999999997  77888876         568888884

Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=96.20  E-value=0.0073  Score=56.31  Aligned_cols=45  Identities=31%  Similarity=0.495  Sum_probs=36.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+..+...+...      ...-+-|+|++|+|||++|+.+++.
T Consensus        65 ~~iiGqs~~i~~l~~al~~~------~~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGP------NPQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCC------CCceEEEECCCCCCHHHHHHHHHHH
Confidence            35899998898888876432      2345678999999999999999864

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.

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=96.20  E-value=0.0046  Score=49.93  Aligned_cols=27  Identities=48%  Similarity=0.522  Sum_probs=23.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      ...+|.|-||-|+||||||+.+.+..+
T Consensus         3 ~~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           3 VAMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             cccEEEEecccccCHHHHHHHHHHHhC
Confidence            357999999999999999999987743

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=96.19  E-value=0.0036  Score=47.49  Aligned_cols=22  Identities=32%  Similarity=0.676  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.|+|++|+|||||++.+...
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhc
Confidence            3789999999999999999876

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.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=96.18  E-value=0.02  Score=51.55  Aligned_cols=51  Identities=33%  Similarity=0.331  Sum_probs=35.7

Q ss_pred             CCccccccchHHHHHHHhhC---------CCCCCC----CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLG---------DDLNSG----PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~---------~~~~~~----~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++|.+..++.+...+..         ... .+    .....+.++|++|+|||++|+.+...
T Consensus        76 ~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~-~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~  139 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKK-SDNGVELSKSNILLIGPTGSGKTLLAQTLARI  139 (413)
T ss_pred             cceecCHHHHHHHHHHHHHHHHhhhccccccc-cccccccCCceEEEECCCCcCHHHHHHHHHHh
Confidence            34589998888888665521         000 00    12357899999999999999999865

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>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=96.16  E-value=0.0047  Score=45.14  Aligned_cols=22  Identities=32%  Similarity=0.519  Sum_probs=19.8

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |.|+|..|+|||||.+.+....
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            6899999999999999998764

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.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=96.16  E-value=0.029  Score=50.74  Aligned_cols=86  Identities=16%  Similarity=0.201  Sum_probs=48.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHHH----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLNL----  223 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~~----  223 (261)
                      -..++|.|..|+|||||++.+.+..    +.+..++..+.+.. ...+++......=. .       ..+......    
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            4578999999999999999998753    23344555555533 33344444332100 0       111111111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCCC
Q 041190          224 -LQLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 -~~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                       ..-.+-+++  +++++|+++||+-.
T Consensus       231 ~~a~tiAEyfrd~G~~VLl~~Dsltr  256 (433)
T PRK07594        231 FVATTIAEFFRDNGKRVVLLADSLTR  256 (433)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCHHH
Confidence             111233333  58999999999954

>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=96.16  E-value=0.023  Score=49.32  Aligned_cols=75  Identities=16%  Similarity=0.200  Sum_probs=47.1

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc--ccc---ceeEEEeeCCCCCHHHHHHHHHH
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK--KYF---SFRACAYVSEDFDAVGVTKVILQ  210 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~--~~f---~~~~wv~v~~~~~~~~i~~~i~~  210 (261)
                      +...+.|.+.|...+   .....+|+|.|.=|+|||++.+.+.+..+..  ..+   ..-+|-.-....-...++..|..
T Consensus         2 ~~~a~~la~~I~~~~---~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~~~~~~~~i~fn~w~~~~~~~~~~~~~~~l~~   78 (325)
T PF07693_consen    2 KPYAKALAEIIKNPD---SDDPFVIGLYGEWGSGKSSFLNMLKEELKEDNKEKYIFIYFNAWEYDGEDDLWASFLEELFD   78 (325)
T ss_pred             hHHHHHHHHHHhccC---CCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccceeeEEEccccCCCcchHHHHHHHHHHH
Confidence            345677788887642   2567899999999999999999998875433  112   12234433332234455555555


Q ss_pred             Hhc
Q 041190          211 AAA  213 (261)
Q Consensus       211 ~l~  213 (261)
                      ++.
T Consensus        79 ~l~   81 (325)
T PF07693_consen   79 QLE   81 (325)
T ss_pred             HHH
Confidence            554

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 [].

>PRK06217 hypothetical protein; Validated

Probab=96.16  E-value=0.0039  Score=49.69  Aligned_cols=25  Identities=36%  Similarity=0.469  Sum_probs=21.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhcccc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGV  183 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~  183 (261)
                      -|.|.|.+|+||||+|+.+.+....
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~   27 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDI   27 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCC
Confidence            4899999999999999999887543

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.15  E-value=0.0043  Score=49.61  Aligned_cols=23  Identities=26%  Similarity=0.348  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|++|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            37899999999999999999775

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=96.15  E-value=0.037  Score=50.26  Aligned_cols=87  Identities=17%  Similarity=0.156  Sum_probs=48.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHHH----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLNL----  223 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~~----  223 (261)
                      -..++|+|..|+|||||++.+.....    .+..+...+.... ...++...+...-. .       ..+......    
T Consensus       168 GqrigI~G~sG~GKSTLl~~I~g~~~----~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~  243 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRFTE----ADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAA  243 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC----CCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHH
Confidence            34689999999999999999976421    2233333444432 33444444433321 1       112211111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          224 -LQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 -~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                       ..-.+-+++  +++++|+++||+-.-
T Consensus       244 ~~a~aiAEyfrd~G~~VLl~~DslTR~  270 (451)
T PRK05688        244 MYCTRIAEYFRDKGKNVLLLMDSLTRF  270 (451)
T ss_pred             HHHHHHHHHHHHCCCCEEEEecchhHH
Confidence             111233333  689999999998553

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=96.14  E-value=0.0095  Score=46.41  Aligned_cols=37  Identities=27%  Similarity=0.441  Sum_probs=31.2

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....+.|.+.|..         +++.++|.+|+|||||.+.+..+.
T Consensus        23 ~~g~~~l~~~l~~---------k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   23 GEGIEELKELLKG---------KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTTHHHHHHHHTT---------SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CcCHHHHHHHhcC---------CEEEEECCCCCCHHHHHHHHHhhc
Confidence            4568888888843         689999999999999999998763

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.

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

Probab=96.14  E-value=0.015  Score=54.27  Aligned_cols=58  Identities=21%  Similarity=0.118  Sum_probs=38.8

Q ss_pred             CCCccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhcccccccc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF  187 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f  187 (261)
                      .-.++-|.++-+.+|-+...-.-..       +-...+=|-.||++|+|||++|+.+.+.  ...+|
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            3345666777777766544332100       2245667889999999999999999987  33445

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=96.14  E-value=0.0079  Score=47.90  Aligned_cols=34  Identities=26%  Similarity=0.343  Sum_probs=26.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEE
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRAC  192 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~w  192 (261)
                      .+++.|+|+.|+|||||++.+...  ....|...++
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~--~~~~~~~~v~   35 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQE--FPDKFGRVVS   35 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHH--STTTEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh--ccccccccee
Confidence            368899999999999999999987  4456644443

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 ....

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=96.13  E-value=0.031  Score=46.58  Aligned_cols=51  Identities=24%  Similarity=0.136  Sum_probs=35.4

Q ss_pred             CccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++-|.+-++.++.+...-.-..       +-..++=+.++|++|+|||-||+.|.++
T Consensus       155 ~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  155 ADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             cccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhc
Confidence            35667777777777754322100       1223455788999999999999999998

>PRK13949 shikimate kinase; Provisional

Probab=96.13  E-value=0.0042  Score=48.98  Aligned_cols=23  Identities=35%  Similarity=0.439  Sum_probs=20.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -|.|+|++|+||||+++.+.+..
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999998763

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.12  E-value=0.0081  Score=49.29  Aligned_cols=22  Identities=55%  Similarity=0.869  Sum_probs=19.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|+|+|-||+||||+|..+...
T Consensus         2 kIaI~GKGG~GKTtiaalll~~   23 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKR   23 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHH
Confidence            6899999999999999885544

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=96.12  E-value=0.0044  Score=51.10  Aligned_cols=22  Identities=41%  Similarity=0.530  Sum_probs=19.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      -.+++|+|.+|+|||||++.+.
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~   54 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLA   54 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHh
Confidence            3589999999999999999984

>CHL00195 ycf46 Ycf46; Provisional

Probab=96.12  E-value=0.018  Score=53.08  Aligned_cols=52  Identities=19%  Similarity=0.192  Sum_probs=33.8

Q ss_pred             CccccccchHHHHHHHhhC--C--CCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLG--D--DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~--~--~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.|.+..++.+......  .  ..-+-+..+-|-++|++|+|||.+|+.+.+..
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~  283 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDW  283 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            4567776666665542211  0  00012345668899999999999999998873

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=96.11  E-value=0.028  Score=50.69  Aligned_cols=87  Identities=18%  Similarity=0.175  Sum_probs=48.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc-C-------CCCCCCHHH----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA-G-------SADVNDLNL----  223 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~-~-------~~~~~~~~~----  223 (261)
                      -..++|.|..|+|||||++.+....+   . +....+.+.+. ....++..+.+..-+ .       ..+......    
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~~~---~-~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~  215 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARNTD---A-DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAA  215 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCC---C-CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHH
Confidence            35789999999999999999987532   1 22222333332 234444444433321 1       111111111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          224 -LQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 -~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                       ..-.+-+++  +++++|+++||+-.-
T Consensus       216 ~~a~~iAEyfrd~G~~Vll~~DslTr~  242 (418)
T TIGR03498       216 YTATAIAEYFRDQGKDVLLLMDSVTRF  242 (418)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchhHH
Confidence             112244444  589999999998654

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK05922 type III secretion system ATPase; Validated

Probab=96.11  E-value=0.04  Score=49.80  Aligned_cols=85  Identities=13%  Similarity=0.167  Sum_probs=47.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-CC-------CCCCCHH-----H
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-GS-------ADVNDLN-----L  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~~-------~~~~~~~-----~  223 (261)
                      ..++|+|..|+|||||.+.+.+..+    -+....+.+++.. ...+.+.+...... ..       .+.....     .
T Consensus       158 qrigI~G~nG~GKSTLL~~Ia~~~~----~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~~  233 (434)
T PRK05922        158 QRIGVFSEPGSGKSSLLSTIAKGSK----STINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAGR  233 (434)
T ss_pred             cEEEEECCCCCChHHHHHHHhccCC----CCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHHH
Confidence            4689999999999999999987522    2333333344422 23344444433322 11       1111111     1


Q ss_pred             HHHHHHHHh--CCCeEEEEEeCCCC
Q 041190          224 LQLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 ~~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                      ..-.+-+++  +++++|+++||+-.
T Consensus       234 ~a~tiAEyfrd~G~~VLl~~DslTR  258 (434)
T PRK05922        234 AAMTIAEYFRDQGHRVLFIMDSLSR  258 (434)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchhH
Confidence            122234444  58999999999954

>PTZ00185 ATPase alpha subunit; Provisional

Probab=96.10  E-value=0.028  Score=51.59  Aligned_cols=95  Identities=17%  Similarity=0.181  Sum_probs=54.0

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhccccc-----cccceeEEEeeCCCCCHHHHHHHHHHHhc--CC-------CCCCCH-
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVK-----KYFSFRACAYVSEDFDAVGVTKVILQAAA--GS-------ADVNDL-  221 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~-----~~f~~~~wv~v~~~~~~~~i~~~i~~~l~--~~-------~~~~~~-  221 (261)
                      .-++|.|-.|+|||+|| -.+.+...+.     ++-...+++-+++..+...-+.+.+++.+  ..       .+.... 
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            35789999999999996 5566653221     23345678888886543322333333332  10       111111 


Q ss_pred             --------HHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHh
Q 041190          222 --------NLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       222 --------~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l  255 (261)
                              -.+.+.+++  +++.+|||+||+-.-. ..+.++
T Consensus       270 r~~Apy~a~tiAEYFrd--~GkdVLiv~DDLTr~A-~A~REI  308 (574)
T PTZ00185        270 QYLAPYSGVTMGEYFMN--RGRHCLCVYDDLSKQA-VAYRQI  308 (574)
T ss_pred             HHHHHHHHHHHHHHHHH--cCCCEEEEEcCchHHH-HHHHHH
Confidence                    122333442  5899999999997653 445444

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=96.10  E-value=0.049  Score=47.73  Aligned_cols=47  Identities=19%  Similarity=0.097  Sum_probs=35.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVI  208 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i  208 (261)
                      ..++|.|..|+|||+|++.+.+..    +-++.+++-|.+..+ +.+++.++
T Consensus       158 qr~~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~iGERg~Ev~e~l~ef  205 (369)
T cd01134         158 GTAAIPGPFGCGKTVIQQSLSKYS----NSDIVIYVGCGERGNEMTEVLEEF  205 (369)
T ss_pred             CEEEEECCCCCChHHHHHHHHhCC----CCCEEEEEEeCCChHHHHHHHHHH
Confidence            478999999999999999998863    234677888877543 34455554

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.

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=96.10  E-value=0.0082  Score=50.15  Aligned_cols=39  Identities=28%  Similarity=0.356  Sum_probs=28.0

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....+++.|...    ..+..+|+|.|+||+||+||.-.+...
T Consensus        14 ~~~~ll~~l~~~----~g~a~~iGiTG~PGaGKSTli~~l~~~   52 (266)
T PF03308_consen   14 EARELLKRLYPH----TGRAHVIGITGPPGAGKSTLIDALIRE   52 (266)
T ss_dssp             HHHHHHHHHGGG----TT-SEEEEEEE-TTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh----cCCceEEEeeCCCCCcHHHHHHHHHHH
Confidence            455666666653    235689999999999999999887665

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.

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=96.10  E-value=0.019  Score=49.06  Aligned_cols=27  Identities=33%  Similarity=0.311  Sum_probs=23.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      .+..+.|||++|.|||-+|+.|.....
T Consensus       165 ~Pkg~ll~GppGtGKTlla~~Vaa~mg  191 (388)
T KOG0651|consen  165 PPKGLLLYGPPGTGKTLLARAVAATMG  191 (388)
T ss_pred             CCceeEEeCCCCCchhHHHHHHHHhcC
Confidence            466899999999999999999998733

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

Probab=96.10  E-value=0.024  Score=44.64  Aligned_cols=79  Identities=18%  Similarity=0.131  Sum_probs=43.9

Q ss_pred             EeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCC--CeE
Q 041190          160 IPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKN--KKF  237 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~--kr~  237 (261)
                      +.|.|.+|+|||++|.+....     ......++.-++.++. ++...|..+.......-...+....+.+.+..  +.-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~   75 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGD   75 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCC
Confidence            678999999999999988654     1234566666666654 34444444333222222222222333444421  233


Q ss_pred             EEEEeCC
Q 041190          238 LLVLDDM  244 (261)
Q Consensus       238 LiVlDdv  244 (261)
                      .|++|.+
T Consensus        76 ~VLIDcl   82 (169)
T cd00544          76 VVLIDCL   82 (169)
T ss_pred             EEEEEcH
Confidence            7999987

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK14527 adenylate kinase; Provisional

Probab=96.10  E-value=0.0055  Score=49.18  Aligned_cols=26  Identities=27%  Similarity=0.267  Sum_probs=22.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +..+|.|+|++|+||||+|+.+.+..
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998664

>PRK14738 gmk guanylate kinase; Provisional

Probab=96.08  E-value=0.0066  Score=49.42  Aligned_cols=26  Identities=19%  Similarity=0.290  Sum_probs=22.6

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++.|+|++|+|||||++.+.+.
T Consensus        11 ~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         11 AKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            46788999999999999999999753

>PRK14530 adenylate kinase; Provisional

Probab=96.08  E-value=0.0048  Score=50.54  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=20.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|+|++|+||||+++.+...
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999765

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.07  E-value=0.0056  Score=49.48  Aligned_cols=24  Identities=25%  Similarity=0.457  Sum_probs=22.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++.|.|.+|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999886

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=96.06  E-value=0.054  Score=47.23  Aligned_cols=84  Identities=18%  Similarity=0.232  Sum_probs=48.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc--------CCCCCCCHH------
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA--------GSADVNDLN------  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~--------~~~~~~~~~------  222 (261)
                      ..++|+|..|+|||||.+.+.+....    ++.+..-+... ....++....+..-+        ...+.....      
T Consensus        70 qri~I~G~sG~GKTtLl~~Ia~~~~~----~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~~  145 (326)
T cd01136          70 QRLGIFAGSGVGKSTLLGMIARGTTA----DVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAY  145 (326)
T ss_pred             cEEEEECCCCCChHHHHHHHhCCCCC----CEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHHH
Confidence            57899999999999999999876321    23333444332 344454444444321        111211111      


Q ss_pred             ---HHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          223 ---LLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ---~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                         .+...+++  ++|.+|+++||+-.-
T Consensus       146 ~a~~~AEyfr~--~g~~Vll~~Dsltr~  171 (326)
T cd01136         146 TATAIAEYFRD--QGKDVLLLMDSLTRF  171 (326)
T ss_pred             HHHHHHHHHHH--cCCCeEEEeccchHH
Confidence               22333333  589999999998553

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.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=96.06  E-value=0.004  Score=48.48  Aligned_cols=21  Identities=29%  Similarity=0.525  Sum_probs=18.8

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|++|+||||+|+.+.+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999998876

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.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.06  E-value=0.025  Score=54.59  Aligned_cols=118  Identities=16%  Similarity=0.069  Sum_probs=63.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      ..++|.......+.+.+..-.    ..-..|.|+|.+|+|||++|+.+++...- . -..-+.+++.... ...+-..++
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a----~~~~pVLI~GE~GTGK~~lA~~ih~~s~r-~-~~~~v~i~c~~~~-~~~~~~~lf  448 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVA----QSDSTVLILGETGTGKELIARAIHNLSGR-N-NRRMVKMNCAAMP-AGLLESDLF  448 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHh----CCCCCEEEECCCCcCHHHHHHHHHHhcCC-C-CCCeEEEecccCC-hhHhhhhhc
Confidence            468999888888877665432    12357899999999999999999875321 1 1123344544422 111111121


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          210 QAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                      ........... ......+   -....=.|+||+|.....+....|...
T Consensus       449 g~~~~~~~g~~-~~~~g~l---e~a~~GtL~Ldei~~L~~~~Q~~L~~~  493 (686)
T PRK15429        449 GHERGAFTGAS-AQRIGRF---ELADKSSLFLDEVGDMPLELQPKLLRV  493 (686)
T ss_pred             Ccccccccccc-cchhhHH---HhcCCCeEEEechhhCCHHHHHHHHHH
Confidence            11111111111 1111112   112335689999988876666666543

>PRK10536 hypothetical protein; Provisional

Probab=96.06  E-value=0.015  Score=48.69  Aligned_cols=44  Identities=18%  Similarity=0.221  Sum_probs=35.6

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.++......+..+|..        ..++.+.|+.|+|||+||..+..+
T Consensus        54 ~~~i~p~n~~Q~~~l~al~~--------~~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         54 TSPILARNEAQAHYLKAIES--------KQLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             CccccCCCHHHHHHHHHHhc--------CCeEEEECCCCCCHHHHHHHHHHH
Confidence            34467788888888888854        248999999999999999988764

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

Probab=96.04  E-value=0.048  Score=51.42  Aligned_cols=117  Identities=18%  Similarity=0.086  Sum_probs=73.2

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccc------cccccceeEEEeeCCCCCHH
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAG------VKKYFSFRACAYVSEDFDAV  202 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~------~~~~f~~~~wv~v~~~~~~~  202 (261)
                      +..+-+|+.+..+|-+++...=. ....-+++.|.|.+|+|||..+..|.+..+      .-..| +.+.|+.-.-....
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~-~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f-~yveINgm~l~~~~  472 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFIS-DQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKF-DYVEINGLRLASPR  472 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcC-CCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCc-cEEEEcceeecCHH
Confidence            34566799999999888866322 112345999999999999999999988532      11233 23344544445688


Q ss_pred             HHHHHHHHHhcCCCC--CCCHHHHHHHHH-HHhCCCeEEEEEeCCCCC
Q 041190          203 GVTKVILQAAAGSAD--VNDLNLLQLQLE-NQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       203 ~i~~~i~~~l~~~~~--~~~~~~~~~~l~-~~l~~kr~LiVlDdvw~~  247 (261)
                      +++..|...+.....  ...++.+..++. ..-+.+..+|++|++...
T Consensus       473 ~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~L  520 (767)
T KOG1514|consen  473 EIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDIL  520 (767)
T ss_pred             HHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHH
Confidence            889899888873322  223333333222 001245688898887654

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=96.04  E-value=0.012  Score=43.72  Aligned_cols=51  Identities=22%  Similarity=0.354  Sum_probs=35.3

Q ss_pred             CccccccchHHHHHHHhhCCCC-CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL-NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~-~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.+-..+.+++.|..--. ...+++=|++..|.+|+|||.+++.+.+.
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            3577876666666665544111 13456789999999999999988777655

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

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.03  E-value=0.017  Score=54.09  Aligned_cols=50  Identities=18%  Similarity=0.203  Sum_probs=39.6

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .....++|......++++.+..-.    ..-..|.|+|.+|+|||++|+.+++.
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a----~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVA----RSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHh----CcCCCEEEECCCCccHHHHHHHHHHh
Confidence            345679999999998888876532    12345789999999999999999876

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.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.03  E-value=0.049  Score=47.41  Aligned_cols=25  Identities=32%  Similarity=0.379  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++.++|++|+||||++..+...
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~  137 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHK  137 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4689999999999999999888654

>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=96.03  E-value=0.0052  Score=47.17  Aligned_cols=22  Identities=41%  Similarity=0.585  Sum_probs=19.7

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |.++|++|+||||+|+.+....
T Consensus         2 i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            6899999999999999998763

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.

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=96.02  E-value=0.014  Score=46.53  Aligned_cols=23  Identities=39%  Similarity=0.586  Sum_probs=20.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +|.|.|+.|+||||+++.+.+..
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l   24 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERL   24 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999998763

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.01  E-value=0.0093  Score=47.25  Aligned_cols=25  Identities=32%  Similarity=0.551  Sum_probs=22.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.++.|.|++|+|||||++.++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3678899999999999999999973

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=96.01  E-value=0.04  Score=46.81  Aligned_cols=93  Identities=24%  Similarity=0.239  Sum_probs=68.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEE-EeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCC
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRAC-AYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNK  235 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~w-v~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~k  235 (261)
                      -+...++|+.|+|||+-++.+++..       +..| +..++.++...+...+...+. .............+..++++.
T Consensus        94 g~l~~vyg~~g~gKt~a~~~y~~s~-------p~~~l~~~~p~~~a~~~i~~i~~~~~-~~~~~~~~d~~~~~~~~l~~~  165 (297)
T COG2842          94 GSLVVVYGYAGLGKTQAAKNYAPSN-------PNALLIEADPSYTALVLILIICAAAF-GATDGTINDLTERLMIRLRDT  165 (297)
T ss_pred             CceEEEeccccchhHHHHHhhcccC-------ccceeecCChhhHHHHHHHHHHHHHh-cccchhHHHHHHHHHHHHccC
Confidence            3488899999999999999998862       3455 456676776666666555444 223344556667777888999


Q ss_pred             eEEEEEeCCCCCChhhHHHhhc
Q 041190          236 KFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       236 r~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      .-+|+.|+-...-+..++.|+.
T Consensus       166 ~~~iivDEA~~L~~~ale~lr~  187 (297)
T COG2842         166 VRLIIVDEADRLPYRALEELRR  187 (297)
T ss_pred             cceeeeehhhccChHHHHHHHH
Confidence            9999999999988777777764

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=96.00  E-value=0.0063  Score=49.54  Aligned_cols=27  Identities=30%  Similarity=0.468  Sum_probs=24.1

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++++|+++|..|+|||||.+.+.+.
T Consensus        19 ~~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        19 KHGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             hcCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            447899999999999999999998775

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.00  E-value=0.015  Score=50.94  Aligned_cols=45  Identities=18%  Similarity=0.113  Sum_probs=33.1

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.......+.+.+..-.    ..-..|.|+|.+|+||+++|+.+++.
T Consensus         1 liG~S~~m~~~~~~~~~~a----~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLA----PLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHh----CCCCCEEEECCCCChHHHHHHHHHHh
Confidence            3566666677776665532    23356799999999999999999875

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

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.00  E-value=0.0054  Score=50.79  Aligned_cols=22  Identities=36%  Similarity=0.513  Sum_probs=19.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      --+++|+|++|+|||||.+.|.
T Consensus        29 GEfvsilGpSGcGKSTLLriiA   50 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIA   50 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHh
Confidence            3589999999999999999985

>PRK14737 gmk guanylate kinase; Provisional

Probab=96.00  E-value=0.0083  Score=48.04  Aligned_cols=25  Identities=24%  Similarity=0.425  Sum_probs=22.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.|+|++|+|||||++.+...
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3578999999999999999999875

>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=95.99  E-value=0.0064  Score=45.71  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|..|+|||||.+.+...
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEEccCCCccccceeeeccc
Confidence            58999999999999999998765

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 ....

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

Probab=95.99  E-value=0.0074  Score=50.39  Aligned_cols=57  Identities=26%  Similarity=0.325  Sum_probs=40.9

Q ss_pred             CCCCccccccchHH---HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc
Q 041190          127 VDEEEVYGREKDKE---VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV  183 (261)
Q Consensus       127 ~~~~~~~gr~~~~~---~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  183 (261)
                      ..-.+++|.++.+.   -|.+.|...+.=+.+.++.|..+|++|+|||-+|+.+.+..++
T Consensus       118 it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kv  177 (368)
T COG1223         118 ITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKV  177 (368)
T ss_pred             ccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCC
Confidence            33456888765553   3455565533224677899999999999999999999997543

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=95.99  E-value=0.0099  Score=50.53  Aligned_cols=64  Identities=20%  Similarity=0.134  Sum_probs=41.1

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      .+|+..|...    ..+..+|+|.|.||+||+||.-.+-.....+.+==.++=|.-|++++-..|+.+
T Consensus        38 ~~ll~~l~p~----tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLGD  101 (323)
T COG1703          38 RELLRALYPR----TGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGD  101 (323)
T ss_pred             HHHHHHHhhc----CCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCcccccc
Confidence            4555656553    346789999999999999998777665322222222344556666666555544

>PRK13947 shikimate kinase; Provisional

Probab=95.98  E-value=0.0055  Score=48.07  Aligned_cols=23  Identities=35%  Similarity=0.421  Sum_probs=20.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -|.|+|++|+||||+++.+.+..
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998763

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=95.97  E-value=0.041  Score=46.78  Aligned_cols=51  Identities=24%  Similarity=0.117  Sum_probs=37.0

Q ss_pred             CccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++-|.+.+..+|.+...-.-..       +-..++=+-+||.+|+|||.||+.|.|.
T Consensus       185 ~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANq  242 (440)
T KOG0726|consen  185 ADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQ  242 (440)
T ss_pred             cccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcc
Confidence            35667888888888765432110       2234556778999999999999999997

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.97  E-value=0.05  Score=43.40  Aligned_cols=41  Identities=24%  Similarity=0.233  Sum_probs=26.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcccccccc--------ceeEEEeeCCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYF--------SFRACAYVSED  198 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f--------~~~~wv~v~~~  198 (261)
                      .+..|+|++|+||||++..+....-....|        ..+.|++...+
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            488999999999999998887653222222        13567776554

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.97  E-value=0.052  Score=52.54  Aligned_cols=99  Identities=16%  Similarity=0.024  Sum_probs=62.8

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-.+|...   +-+.-+++-|+|++|+|||||+.+++...  ...=...+|+...+.++..     .+++++-.   
T Consensus        45 i~~LD~lLg~G---Gip~GsiteI~G~~GsGKTtLal~~~~~a--~~~G~~v~yId~E~t~~~~-----~A~~lGvDl~~  114 (790)
T PRK09519         45 SIALDVALGIG---GLPRGRVIEIYGPESSGKTTVALHAVANA--QAAGGVAAFIDAEHALDPD-----YAKKLGVDTDS  114 (790)
T ss_pred             cHHHHHhhcCC---CccCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEECCccchhHH-----HHHHcCCChhH
Confidence            44555666422   24567899999999999999997765432  1122346888888877743     45666511   


Q ss_pred             ---CCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          216 ---ADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       216 ---~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                         ..+...+.....+...++ ++--|||+|.|-..
T Consensus       115 llv~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~aL  150 (790)
T PRK09519        115 LLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAAL  150 (790)
T ss_pred             eEEecCCCHHHHHHHHHHHhhcCCCeEEEEcchhhh
Confidence               123344555555666554 46778999998744

>PRK13975 thymidylate kinase; Provisional

Probab=95.96  E-value=0.0063  Score=48.84  Aligned_cols=24  Identities=38%  Similarity=0.526  Sum_probs=21.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+|.|.|+.|+||||+++.+.+..
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l   26 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKL   26 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999998874

>PRK09087 hypothetical protein; Validated

Probab=95.96  E-value=0.0065  Score=50.26  Aligned_cols=24  Identities=33%  Similarity=0.391  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.+.|+|++|+|||+|++..++.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            467899999999999999998876

>PLN02200 adenylate kinase family protein

Probab=95.95  E-value=0.0073  Score=50.21  Aligned_cols=25  Identities=20%  Similarity=0.170  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.|.|++|+||||+|+.+.+.
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~   66 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVET   66 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999775

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.95  E-value=0.038  Score=49.80  Aligned_cols=86  Identities=19%  Similarity=0.222  Sum_probs=47.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHH-----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLN-----  222 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~-----  222 (261)
                      -..++|.|..|+|||||++.+.+..+    .+..+...+.+.. ...++...+...=. .       ..+.....     
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~~~----~~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~  212 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARYTE----ADVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAA  212 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCC----CCEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHH
Confidence            34689999999999999998887532    1233344454432 23444443332211 0       11111111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEeCCCC
Q 041190          223 LLQLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       223 ~~~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                      ...-.+-+++  +++++|+++||+-.
T Consensus       213 ~~a~tiAEyfr~~G~~Vll~~Dsltr  238 (411)
T TIGR03496       213 FYATAIAEYFRDQGKDVLLLMDSLTR  238 (411)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEeChHH
Confidence            1112233333  58999999999854

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=95.93  E-value=0.0085  Score=52.68  Aligned_cols=49  Identities=20%  Similarity=0.284  Sum_probs=38.1

Q ss_pred             CCCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          126 LVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       126 ~~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++-..++|.++-+..|...+..      +.++-+.|.|..|+||||+|+.+++-
T Consensus        13 ~~pf~~ivGq~~~k~al~~~~~~------p~~~~vli~G~~GtGKs~~ar~~~~~   61 (350)
T CHL00081         13 VFPFTAIVGQEEMKLALILNVID------PKIGGVMIMGDRGTGKSTTIRALVDL   61 (350)
T ss_pred             CCCHHHHhChHHHHHHHHHhccC------CCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence            34556799999888887776643      35566679999999999999999664

>PLN02348 phosphoribulokinase

Probab=95.93  E-value=0.011  Score=52.57  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=23.8

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++..+|+|.|.+|+||||+|+.+.+.
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L~~~   72 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRLTSV   72 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            346789999999999999999999875

>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=95.93  E-value=0.0072  Score=43.71  Aligned_cols=21  Identities=43%  Similarity=0.531  Sum_probs=19.4

Q ss_pred             eEEeEeecCCCChHHHHHHHh
Q 041190          158 SVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ..+.|.|++|+|||||++.+.
T Consensus        16 e~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          16 VGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             EEEEEEcCCCCCHHHHHHHhh
Confidence            678999999999999999976

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

>PRK08356 hypothetical protein; Provisional

Probab=95.93  E-value=0.0075  Score=48.59  Aligned_cols=20  Identities=30%  Similarity=0.483  Sum_probs=19.0

Q ss_pred             eEEeEeecCCCChHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLV  177 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v  177 (261)
                      .+|.|+|++|+||||+|+.+
T Consensus         6 ~~i~~~G~~gsGK~t~a~~l   25 (195)
T PRK08356          6 MIVGVVGKIAAGKTTVAKFF   25 (195)
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            67999999999999999999

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=95.93  E-value=0.044  Score=49.77  Aligned_cols=89  Identities=18%  Similarity=0.234  Sum_probs=53.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHHH-----
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLNL-----  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~~-----  223 (261)
                      .-++|.|.+|+|||||+..+...... ++=.+.+++-+++.. .+.+++.++...-. .       ..+......     
T Consensus       144 Qr~~If~~~G~GKt~L~~~~~~~~~~-~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~  222 (461)
T TIGR01039       144 GKIGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVAL  222 (461)
T ss_pred             CEEEeecCCCCChHHHHHHHHHHHHh-cCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            45899999999999999998766322 122356677776654 34555555543211 1       111111111     


Q ss_pred             HHHHHHHHh---CCCeEEEEEeCCCCC
Q 041190          224 LQLQLENQL---KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 ~~~~l~~~l---~~kr~LiVlDdvw~~  247 (261)
                      ..-.+-+++   +++++|+++||+-.-
T Consensus       223 ~a~tiAEyfrd~~G~~VLll~DslTR~  249 (461)
T TIGR01039       223 TGLTMAEYFRDEQGQDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHHHHHHHHhcCCeeEEEecchhHH
Confidence            222355555   468999999999653

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.91  E-value=0.028  Score=52.25  Aligned_cols=86  Identities=19%  Similarity=0.127  Sum_probs=48.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEE-EeeCCCCCHHHHHHHHHHHhc-----CCCCCCCH-----HHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRAC-AYVSEDFDAVGVTKVILQAAA-----GSADVNDL-----NLLQL  226 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~w-v~v~~~~~~~~i~~~i~~~l~-----~~~~~~~~-----~~~~~  226 (261)
                      .-..|+|++|+|||||++.|.+.... .+=++.++ +-|.+-+...   .++-..+.     ...+....     ..+.-
T Consensus       417 QR~LIvgpp~aGKTtLL~~IAn~i~~-n~~~~~~ivvLIgERpeEV---tdm~rsVkgeVVasT~D~p~~~~~~~a~~ai  492 (672)
T PRK12678        417 QRGLIVSPPKAGKTTILQNIANAITT-NNPECHLMVVLVDERPEEV---TDMQRSVKGEVIASTFDRPPSDHTTVAELAI  492 (672)
T ss_pred             CEeEEeCCCCCCHHHHHHHHHHHHhh-cCCCeEEEEEEEeCchhhH---HHHHHhccceEEEECCCCCHHHHHHHHHHHH
Confidence            35789999999999999999886321 23344443 3455533221   22333331     22222111     12223


Q ss_pred             HHHHHh--CCCeEEEEEeCCCCC
Q 041190          227 QLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       227 ~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      .+-++|  .++.+||+||++-..
T Consensus       493 ~~Ae~fre~G~dVlillDSlTR~  515 (672)
T PRK12678        493 ERAKRLVELGKDVVVLLDSITRL  515 (672)
T ss_pred             HHHHHHHHcCCCEEEEEeCchHH
Confidence            344444  689999999998543

>TIGR00416 sms DNA repair protein RadA

Probab=95.91  E-value=0.034  Score=50.88  Aligned_cols=100  Identities=17%  Similarity=0.038  Sum_probs=56.9

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS  215 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~  215 (261)
                      ......|-++|..    +-..-.++.|.|.+|+|||||+.++.....  ..-...+|++..+.  ..++... ...++..
T Consensus        77 ~TGi~~LD~vLgG----Gi~~GsvilI~G~pGsGKTTL~lq~a~~~a--~~g~kvlYvs~EEs--~~qi~~r-a~rlg~~  147 (454)
T TIGR00416        77 SSGFGELDRVLGG----GIVPGSLILIGGDPGIGKSTLLLQVACQLA--KNQMKVLYVSGEES--LQQIKMR-AIRLGLP  147 (454)
T ss_pred             ccCcHHHHHHhcC----CccCCeEEEEEcCCCCCHHHHHHHHHHHHH--hcCCcEEEEECcCC--HHHHHHH-HHHcCCC
Confidence            3345566666643    234567999999999999999998865521  11123567765443  3333221 2233311


Q ss_pred             ------CCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          216 ------ADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       216 ------~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                            ....+.+.+...+.+   .+.-++|+|.+-..
T Consensus       148 ~~~l~~~~e~~~~~I~~~i~~---~~~~~vVIDSIq~l  182 (454)
T TIGR00416       148 EPNLYVLSETNWEQICANIEE---ENPQACVIDSIQTL  182 (454)
T ss_pred             hHHeEEcCCCCHHHHHHHHHh---cCCcEEEEecchhh
Confidence                  123345555444433   35568999998643

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)).

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.90  E-value=0.0068  Score=47.89  Aligned_cols=23  Identities=26%  Similarity=0.361  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..|.|+|+.|+||||+++.+.+.
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHH
Confidence            46999999999999999999876

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.89  E-value=0.063  Score=45.51  Aligned_cols=92  Identities=16%  Similarity=0.163  Sum_probs=52.9

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhcccccccccee-EEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSFR-ACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~~-~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~----  222 (261)
                      .-++|.|..|+|||+|| ..+.+..    +-+.. +++-+.+... ..+++.++...=. .       ..+.....    
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            45899999999999995 6665541    22334 5666766543 4555555543211 1       11111111    


Q ss_pred             -----HHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          223 -----LLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       223 -----~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                           .+.+.++.  +++.+|+++||+-.-. ..|..+.
T Consensus       146 ~~~a~aiAE~fr~--~G~~Vlvl~DslTr~A-~A~rEis  181 (274)
T cd01132         146 PYTGCAMGEYFMD--NGKHALIIYDDLSKQA-VAYRQMS  181 (274)
T ss_pred             HHHHHHHHHHHHH--CCCCEEEEEcChHHHH-HHHHHHH
Confidence                 22333433  5899999999996652 4555543

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.

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=95.88  E-value=0.036  Score=47.23  Aligned_cols=114  Identities=16%  Similarity=0.219  Sum_probs=65.8

Q ss_pred             CccccccchHHHHHHHhhCC-CCCCCCCceEEeEeecCCCChHHHHHHHhhcc---ccccccc--eeEEEeeCCCCCHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGD-DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA---GVKKYFS--FRACAYVSEDFDAVG  203 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~-~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~---~~~~~f~--~~~wv~v~~~~~~~~  203 (261)
                      ..++|..--++.++..+..- ......++=+++.+|.+|+||..+++.+.++.   ..+..|=  .++-.+.++...++.
T Consensus        82 ~~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~  161 (344)
T KOG2170|consen   82 RALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIED  161 (344)
T ss_pred             HHhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHH
Confidence            34777665566666555431 00024567799999999999999999887763   1122220  011111222111111


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHHHHh-CCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          204 VTKVILQAAAGSADVNDLNLLQLQLENQL-KNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       204 i~~~i~~~l~~~~~~~~~~~~~~~l~~~l-~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      -                -+++...+++.+ .-+|.|+|+|+|...-++..+.|++-|
T Consensus       162 Y----------------k~eL~~~v~~~v~~C~rslFIFDE~DKmp~gLld~lkpfL  202 (344)
T KOG2170|consen  162 Y----------------KEELKNRVRGTVQACQRSLFIFDEVDKLPPGLLDVLKPFL  202 (344)
T ss_pred             H----------------HHHHHHHHHHHHHhcCCceEEechhhhcCHhHHHHHhhhh
Confidence            1                123344444444 347899999999998777777777654

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.88  E-value=0.0089  Score=46.95  Aligned_cols=26  Identities=35%  Similarity=0.419  Sum_probs=23.3

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++..+|...|.+|+||||+|..++..
T Consensus        21 ~~~~viW~TGLSGsGKSTiA~ale~~   46 (197)
T COG0529          21 QKGAVIWFTGLSGSGKSTIANALEEK   46 (197)
T ss_pred             CCCeEEEeecCCCCCHHHHHHHHHHH
Confidence            35679999999999999999999876

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.86  E-value=0.045  Score=43.12  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++.|.|.+|+||||+|..+...
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~   24 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQ   24 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHH
Confidence            36899999999999999998765

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.83  E-value=0.019  Score=50.59  Aligned_cols=85  Identities=15%  Similarity=0.138  Sum_probs=47.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeE
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKF  237 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~  237 (261)
                      ..+.|.|++|+||||+++.+.+.  +..+...+++. +.++..  ........-+.+.....+......-++..|+...=
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~--i~~~~~~~i~t-iEdp~E--~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr~~pd  197 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDY--INKNAAGHIIT-IEDPIE--YVHRNKRSLINQREVGLDTLSFANALRAALREDPD  197 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh--hCcCCCCEEEE-EcCChh--hhccCccceEEccccCCCCcCHHHHHHHhhccCCC
Confidence            68999999999999999998875  33333344432 222111  00000000000000111122344557778888888


Q ss_pred             EEEEeCCCCC
Q 041190          238 LLVLDDMWSE  247 (261)
Q Consensus       238 LiVlDdvw~~  247 (261)
                      .|++|++.+.
T Consensus       198 ~i~vgEird~  207 (343)
T TIGR01420       198 VILIGEMRDL  207 (343)
T ss_pred             EEEEeCCCCH
Confidence            9999999865

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.

>COG3899 Predicted ATPase [General function prediction only]

Probab=95.83  E-value=0.031  Score=55.05  Aligned_cols=46  Identities=26%  Similarity=0.398  Sum_probs=39.7

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++||+.+.+.|...+.+.   ....-.++.+.|..|+|||+|+++|..-
T Consensus         2 l~GRe~ev~~Ll~~f~~v---~~g~~~~~lv~G~sGIGKsalv~ev~~~   47 (849)
T COG3899           2 LYGRETELAQLLAAFDRV---SKGRGEVVLVAGESGIGKSALVNEVHKP   47 (849)
T ss_pred             CCchHhHHHHHHHHHHHH---hCCCeEEEEEeecCCCcHHHHHHHHHHH
Confidence            689999999999988774   2345569999999999999999999876

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.82  E-value=0.0067  Score=47.10  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |++|+|+.|+|||||+..+....
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l   23 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKAL   23 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            57899999999999999998863

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.82  E-value=0.02  Score=52.25  Aligned_cols=97  Identities=21%  Similarity=0.108  Sum_probs=57.1

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC--
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS--  215 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~--  215 (261)
                      ....|-++|..    +-..-.++.|.|.+|+|||||+.++.....  ..-...+|++..+.  ...+... .+.++..  
T Consensus        65 Gi~~LD~~LgG----Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a--~~g~~vlYvs~Ees--~~qi~~r-a~rlg~~~~  135 (446)
T PRK11823         65 GIGELDRVLGG----GLVPGSVVLIGGDPGIGKSTLLLQVAARLA--AAGGKVLYVSGEES--ASQIKLR-AERLGLPSD  135 (446)
T ss_pred             CcHHHHHHhcC----CccCCEEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEEcccc--HHHHHHH-HHHcCCChh
Confidence            44566666643    234567999999999999999999877532  11124567765543  3333222 3444411  


Q ss_pred             ----CCCCCHHHHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          216 ----ADVNDLNLLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       216 ----~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                          ....+.+.+...+.+   .+.-+||+|.+-.
T Consensus       136 ~l~~~~e~~l~~i~~~i~~---~~~~lVVIDSIq~  167 (446)
T PRK11823        136 NLYLLAETNLEAILATIEE---EKPDLVVIDSIQT  167 (446)
T ss_pred             cEEEeCCCCHHHHHHHHHh---hCCCEEEEechhh
Confidence                122345555554432   3566899999864

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=95.81  E-value=0.0077  Score=47.79  Aligned_cols=24  Identities=17%  Similarity=0.235  Sum_probs=21.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.|+|++|+|||||++.+....
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l   27 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALF   27 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            478999999999999999998753

>PRK13695 putative NTPase; Provisional

Probab=95.81  E-value=0.0094  Score=47.04  Aligned_cols=23  Identities=43%  Similarity=0.434  Sum_probs=20.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -+.|+|.+|+|||||++.+++..
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999988763

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.79  E-value=0.033  Score=50.79  Aligned_cols=89  Identities=25%  Similarity=0.227  Sum_probs=51.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccc--eeEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFS--FRACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~--~~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~----  222 (261)
                      .-++|.|-.|+|||||+..+.+.......+.  ..+++-+++..+ ..+++.++...=. .       ..+.....    
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            3578899999999999999988643321111  456677766543 4455555543211 1       11111111    


Q ss_pred             -HHHHHHHHHh---CCCeEEEEEeCCCC
Q 041190          223 -LLQLQLENQL---KNKKFLLVLDDMWS  246 (261)
Q Consensus       223 -~~~~~l~~~l---~~kr~LiVlDdvw~  246 (261)
                       ...-.+-+++   +++++|+++||+-.
T Consensus       222 ~~~a~tiAEyfr~d~G~~VLli~DslTR  249 (458)
T TIGR01041       222 PRMALTAAEYLAFEKDMHVLVILTDMTN  249 (458)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcChhH
Confidence             1122245555   47899999999954

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK04182 cytidylate kinase; Provisional

Probab=95.79  E-value=0.0079  Score=47.40  Aligned_cols=23  Identities=43%  Similarity=0.638  Sum_probs=21.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +|.|.|+.|+||||+++.+.+..
T Consensus         2 ~I~i~G~~GsGKstia~~la~~l   24 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68999999999999999998763

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.78  E-value=0.011  Score=50.33  Aligned_cols=51  Identities=27%  Similarity=0.277  Sum_probs=35.4

Q ss_pred             CccccccchHHHHHHHhhCC-------CCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGD-------DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +++-|.+..++.|.+...-.       .. ....-+-|.++|++|+||+.||+.|....
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtG-kR~PwrgiLLyGPPGTGKSYLAKAVATEA  190 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTG-KRKPWRGILLYGPPGTGKSYLAKAVATEA  190 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcC-CCCcceeEEEeCCCCCcHHHHHHHHHhhc
Confidence            34667777777777643221       00 12235678899999999999999998863

>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=95.76  E-value=0.02  Score=45.36  Aligned_cols=36  Identities=22%  Similarity=0.155  Sum_probs=25.0

Q ss_pred             EeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          160 IPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      +.|.|++|+|||+|+.++....- +.. ....|++...
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~g-~~v~~~s~e~   37 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-ARG-EPGLYVTLEE   37 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HCC-CcEEEEECCC
Confidence            57899999999999988765421 111 2356777655

A related protein is found in archaea.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=95.76  E-value=0.024  Score=45.44  Aligned_cols=24  Identities=42%  Similarity=0.470  Sum_probs=21.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+|.|.|..|+||||+++.+.+..
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l   27 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLL   27 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            579999999999999999998763

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=95.76  E-value=0.018  Score=54.96  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-+.++|++|+|||++|+.+.+.
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~  208 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGE  208 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Confidence            34889999999999999999876

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=95.76  E-value=0.027  Score=52.37  Aligned_cols=49  Identities=18%  Similarity=0.188  Sum_probs=40.0

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....++|.......+.+.+..-.    ..-..|.|+|.+|+|||++|+.+++.
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a----~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVA----ASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHh----CCCCcEEEECCCCccHHHHHHHHHHh
Confidence            34568999999999888887643    23457899999999999999999876

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=95.76  E-value=0.052  Score=45.20  Aligned_cols=59  Identities=22%  Similarity=0.103  Sum_probs=39.8

Q ss_pred             ccc-ccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          132 VYG-REKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       132 ~~g-r~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      ++| .+.+..+|.+.+.-.-..       +-.+++=+.++|++|.|||.||+.|+++.       +.-++.||+
T Consensus       148 MiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht-------~c~firvsg  214 (404)
T KOG0728|consen  148 MIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT-------DCTFIRVSG  214 (404)
T ss_pred             HhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc-------ceEEEEech
Confidence            444 577777777665432100       22356678899999999999999999872       234567776

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.74  E-value=0.048  Score=49.48  Aligned_cols=86  Identities=16%  Similarity=0.259  Sum_probs=47.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHHH----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLNL----  223 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~~----  223 (261)
                      -..++|.|..|+|||||++.+......    +....+-+.+.. ...++...+...-+ .       ..+......    
T Consensus       163 Gq~~~I~G~sG~GKTtLl~~ia~~~~~----d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~  238 (441)
T PRK09099        163 GQRMGIFAPAGVGKSTLMGMFARGTQC----DVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAA  238 (441)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHH
Confidence            457899999999999999999875322    223333344322 33444444433211 0       111111111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCCC
Q 041190          224 -LQLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 -~~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                       ..-.+-+++  +++++|+++||+-.
T Consensus       239 ~~a~tiAEyfrd~G~~VLl~~DslTr  264 (441)
T PRK09099        239 YVATAIAEYFRDRGLRVLLMMDSLTR  264 (441)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchhH
Confidence             112233444  58999999999854

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.73  E-value=0.0086  Score=48.63  Aligned_cols=24  Identities=33%  Similarity=0.333  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.|+.|+|++|+|||||.+.+..=
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~L   51 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGL   51 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            458999999999999999998653

>PLN02796 D-glycerate 3-kinase

Probab=95.73  E-value=0.0095  Score=52.05  Aligned_cols=25  Identities=36%  Similarity=0.236  Sum_probs=22.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.-+|+|.|..|+|||||++.+..-
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~l  123 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYL  123 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            5678999999999999999999876

>TIGR00017 cmk cytidylate kinase

Probab=95.72  E-value=0.033  Score=45.78  Aligned_cols=23  Identities=39%  Similarity=0.592  Sum_probs=21.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|+|.|+.|+||||+++.+...
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~   25 (217)
T TIGR00017         3 MIIAIDGPSGAGKSTVAKAVAEK   25 (217)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999999875

This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.70  E-value=0.13  Score=43.52  Aligned_cols=50  Identities=22%  Similarity=0.105  Sum_probs=31.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      -.++.|.|.+|+||||++.++....- ..+=..+.|++...  +..++...+.
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~-~~~g~~vl~iS~E~--~~~~~~~r~~   79 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLI-TQHGVRVGTISLEE--PVVRTARRLL   79 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH-HhcCceEEEEEccc--CHHHHHHHHH
Confidence            45888999999999999998866521 11112466777655  3334444443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=95.69  E-value=0.0087  Score=49.21  Aligned_cols=22  Identities=36%  Similarity=0.532  Sum_probs=19.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|++|+|||||...+..
T Consensus        32 e~vaI~GpSGSGKSTLLniig~   53 (226)
T COG1136          32 EFVAIVGPSGSGKSTLLNLLGG   53 (226)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999998853

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.68  E-value=0.014  Score=54.41  Aligned_cols=26  Identities=31%  Similarity=0.530  Sum_probs=23.3

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|+|.|++|+||||||+.+...
T Consensus        63 ~~riIIGIaGpSGSGKTTLAk~Lagl   88 (656)
T PLN02318         63 DGIILVGVAGPSGAGKTVFTEKVLNF   88 (656)
T ss_pred             CCeEEEEEECCCCCcHHHHHHHHHhh
Confidence            35789999999999999999999765

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=95.67  E-value=0.0084  Score=47.92  Aligned_cols=21  Identities=33%  Similarity=0.360  Sum_probs=19.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            689999999999999999876

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.66  E-value=0.0074  Score=47.02  Aligned_cols=21  Identities=43%  Similarity=0.425  Sum_probs=17.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|..|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999865

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=95.66  E-value=0.0089  Score=46.56  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=21.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++++|+|..++|||||...+....
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L   26 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKL   26 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHH
Confidence            4799999999999999999996653

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.66  E-value=0.11  Score=45.44  Aligned_cols=26  Identities=31%  Similarity=0.342  Sum_probs=22.8

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|+|.|.+|+|||||+..+...
T Consensus        54 ~~~~~igi~G~~GaGKSTl~~~l~~~   79 (332)
T PRK09435         54 GNALRIGITGVPGVGKSTFIEALGMH   79 (332)
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            35789999999999999999987665

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.66  E-value=0.032  Score=49.58  Aligned_cols=100  Identities=22%  Similarity=0.143  Sum_probs=61.0

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc-
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA-  213 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~-  213 (261)
                      ......++-..|...    --.-+++.|-|-+|+|||||.-++..+...+  - ...+|+-.+.....++   -.++++ 
T Consensus        75 i~tg~~EldRVLGGG----~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~--~-~vLYVsGEES~~Qikl---RA~RL~~  144 (456)
T COG1066          75 ISTGIEELDRVLGGG----LVPGSVILIGGDPGIGKSTLLLQVAARLAKR--G-KVLYVSGEESLQQIKL---RADRLGL  144 (456)
T ss_pred             ccCChHHHHhhhcCC----cccccEEEEccCCCCCHHHHHHHHHHHHHhc--C-cEEEEeCCcCHHHHHH---HHHHhCC
Confidence            344566666666542    2245799999999999999999998873222  2 4555554443332222   244555 


Q ss_pred             CCC-----CCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          214 GSA-----DVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       214 ~~~-----~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      ...     ...+.+.+.+.+.+   .+.-|+|+|.+...
T Consensus       145 ~~~~l~l~aEt~~e~I~~~l~~---~~p~lvVIDSIQT~  180 (456)
T COG1066         145 PTNNLYLLAETNLEDIIAELEQ---EKPDLVVIDSIQTL  180 (456)
T ss_pred             CccceEEehhcCHHHHHHHHHh---cCCCEEEEecccee
Confidence            221     23455555554443   68899999998654

>cd04155 Arl3 Arl3 subfamily

Probab=95.65  E-value=0.01  Score=46.39  Aligned_cols=24  Identities=29%  Similarity=0.376  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.|+|++|+|||||.+.+...
T Consensus        14 ~~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          14 EPRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             ccEEEEEccCCCCHHHHHHHHhcC
Confidence            456899999999999999999875

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.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=95.65  E-value=0.0099  Score=46.45  Aligned_cols=22  Identities=41%  Similarity=0.667  Sum_probs=20.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|.|.|+.|+||||+|+.+.+.
T Consensus         2 iI~i~G~~GSGKstia~~la~~   23 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEK   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            7899999999999999999775

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.

>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=95.65  E-value=0.011  Score=44.08  Aligned_cols=26  Identities=35%  Similarity=0.565  Sum_probs=17.8

Q ss_pred             EeEeecCCCChHHHHHHHhhcccccccc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDAGVKKYF  187 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~~~~~~f  187 (261)
                      +-+.|.+|+||||+|+.+...  ....|
T Consensus         2 vLleg~PG~GKT~la~~lA~~--~~~~f   27 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS--LGLSF   27 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH--TT--E
T ss_pred             EeeECCCccHHHHHHHHHHHH--cCCce
Confidence            578999999999999999887  44445

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.

>PRK15453 phosphoribulokinase; Provisional

Probab=95.64  E-value=0.011  Score=50.16  Aligned_cols=25  Identities=28%  Similarity=0.399  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..+|+|.|.+|+||||+++.+.+.
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~i   28 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKI   28 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999988753

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.63  E-value=0.054  Score=51.92  Aligned_cols=97  Identities=23%  Similarity=0.227  Sum_probs=54.1

Q ss_pred             ccccccc---hHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHH
Q 041190          131 EVYGREK---DKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGV  204 (261)
Q Consensus       131 ~~~gr~~---~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i  204 (261)
                      ++-|-++   ++++++++|.+.+.   -+-.-++=+-++|++|+|||-||+.+.-...+       -++++|.+      
T Consensus       312 DVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgV-------PF~svSGS------  378 (774)
T KOG0731|consen  312 DVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGV-------PFFSVSGS------  378 (774)
T ss_pred             cccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCC-------ceeeechH------
Confidence            4666654   45555566655320   01223455789999999999999999986443       34555552      


Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHH-HHHhCCCeEEEEEeCCCCC
Q 041190          205 TKVILQAAAGSADVNDLNLLQLQL-ENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       205 ~~~i~~~l~~~~~~~~~~~~~~~l-~~~l~~kr~LiVlDdvw~~  247 (261)
                        +..+.+..   ..  ....+.+ ...=.+..++|.+|++..-
T Consensus       379 --EFvE~~~g---~~--asrvr~lf~~ar~~aP~iifideida~  415 (774)
T KOG0731|consen  379 --EFVEMFVG---VG--ASRVRDLFPLARKNAPSIIFIDEIDAV  415 (774)
T ss_pred             --HHHHHhcc---cc--hHHHHHHHHHhhccCCeEEEecccccc
Confidence              22222220   00  1111122 2222456789999988654

>PRK06761 hypothetical protein; Provisional

Probab=95.63  E-value=0.021  Score=48.65  Aligned_cols=24  Identities=33%  Similarity=0.538  Sum_probs=22.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ++|.|.|++|+||||+++.+.+..
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L   27 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDIL   27 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            579999999999999999999874

>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=95.62  E-value=0.011  Score=43.07  Aligned_cols=21  Identities=29%  Similarity=0.466  Sum_probs=19.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |+|.|++|+|||||.+.+.+.
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            689999999999999999974

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 ....

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.62  E-value=0.022  Score=48.69  Aligned_cols=26  Identities=27%  Similarity=0.228  Sum_probs=23.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..++.|.|.+|+|||||...+.+.
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~  127 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMR  127 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999999886

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=95.61  E-value=0.064  Score=48.55  Aligned_cols=24  Identities=25%  Similarity=0.350  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -..++|.|..|+|||||++.+...
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~  180 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKG  180 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhc
Confidence            458899999999999999999875

>PRK14532 adenylate kinase; Provisional

Probab=95.61  E-value=0.0091  Score=47.66  Aligned_cols=21  Identities=24%  Similarity=0.311  Sum_probs=19.2

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.+.|++|+||||+|+.+.+.
T Consensus         3 i~~~G~pGsGKsT~a~~la~~   23 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEE   23 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            778999999999999999775

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.60  E-value=0.011  Score=46.04  Aligned_cols=24  Identities=38%  Similarity=0.672  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++.|+|.+|+||||+.+.+-..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~   27 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKE   27 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHH
Confidence            579999999999999999877665

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=95.60  E-value=0.011  Score=49.69  Aligned_cols=24  Identities=29%  Similarity=0.322  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .-.+++|.|+.|+|||||.+.++.
T Consensus        27 ~G~i~~iiGpNG~GKSTLLk~l~g   50 (258)
T COG1120          27 KGEITGILGPNGSGKSTLLKCLAG   50 (258)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999999976

>PRK06820 type III secretion system ATPase; Validated

Probab=95.60  E-value=0.08  Score=48.01  Aligned_cols=83  Identities=22%  Similarity=0.262  Sum_probs=47.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc--C----------CCCCCCHHH--
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA--G----------SADVNDLNL--  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~--~----------~~~~~~~~~--  223 (261)
                      ..++|+|.+|+|||||++.+....    +-+..+..-+.....  + ...+.+...  .          ..+......  
T Consensus       164 qri~I~G~sG~GKStLl~~I~~~~----~~dv~V~~~iGergr--E-v~ef~e~~l~~~~~~rtvvv~atsd~p~~~r~~  236 (440)
T PRK06820        164 QRIGIFAAAGVGKSTLLGMLCADS----AADVMVLALIGERGR--E-VREFLEQVLTPEARARTVVVVATSDRPALERLK  236 (440)
T ss_pred             CEEEEECCCCCChHHHHHHHhccC----CCCEEEEEEEccChH--H-HHHHHHHhhccCCceeEEEEEeCCCCCHHHHHH
Confidence            468999999999999999988752    223344455555422  2 333333322  1          111111111  


Q ss_pred             ---HHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          224 ---LQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 ---~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                         ..-.+-+++  +++++|+++||+-.-
T Consensus       237 a~~~a~tiAEyfrd~G~~VLl~~Dsltr~  265 (440)
T PRK06820        237 GLSTATTIAEYFRDRGKKVLLMADSLTRY  265 (440)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEccchhHH
Confidence               112234444  589999999999553

>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=95.59  E-value=0.01  Score=48.59  Aligned_cols=24  Identities=29%  Similarity=0.344  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            358999999999999999999754

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.59  E-value=0.017  Score=47.17  Aligned_cols=52  Identities=13%  Similarity=0.063  Sum_probs=29.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhccc-----cccccceeEEEeeCCCCCHHHHHHHHHH
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAG-----VKKYFSFRACAYVSEDFDAVGVTKVILQ  210 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~-----~~~~f~~~~wv~v~~~~~~~~i~~~i~~  210 (261)
                      +..|.|++|+||||++..+....-     ....-...+-+.......+..++..+.+
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            788999999999986666655420     0122233444444444566666666665

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

Probab=95.58  E-value=0.02  Score=46.52  Aligned_cols=116  Identities=16%  Similarity=0.145  Sum_probs=56.1

Q ss_pred             ccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEe--e--CCC--CCHHH---
Q 041190          133 YGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAY--V--SED--FDAVG---  203 (261)
Q Consensus       133 ~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~--v--~~~--~~~~~---  203 (261)
                      .++..+....++.|..        ..++.+.|+.|+|||.||-...-+.-....|+..+++.  +  .+.  +-...   
T Consensus         3 ~p~~~~Q~~~~~al~~--------~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~e   74 (205)
T PF02562_consen    3 KPKNEEQKFALDALLN--------NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEE   74 (205)
T ss_dssp             ---SHHHHHHHHHHHH---------SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS------
T ss_pred             cCCCHHHHHHHHHHHh--------CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHH
Confidence            3455666667777763        35899999999999999987765543345676666553  1  111  00011   


Q ss_pred             ----HHHHHHHHhcCCCCCCCHHHHHHH------HHHHhCCC---eEEEEEeCCCCCChhhHHHhh
Q 041190          204 ----VTKVILQAAAGSADVNDLNLLQLQ------LENQLKNK---KFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       204 ----i~~~i~~~l~~~~~~~~~~~~~~~------l~~~l~~k---r~LiVlDdvw~~~~~~w~~l~  256 (261)
                          .+.-+.+.+..-......+.+...      --.+++|.   ..+|++|+..|.+++.+..+.
T Consensus        75 K~~p~~~p~~d~l~~~~~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~il  140 (205)
T PF02562_consen   75 KMEPYLRPIYDALEELFGKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMIL  140 (205)
T ss_dssp             ---TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHH
Confidence                111122222211122233332211      12234454   479999999999888887654

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

>PRK13948 shikimate kinase; Provisional

Probab=95.58  E-value=0.013  Score=46.77  Aligned_cols=25  Identities=16%  Similarity=0.296  Sum_probs=22.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....|.++|+.|+||||+++.+.+.
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~   33 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRA   33 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4578899999999999999999876

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=95.56  E-value=0.0088  Score=50.13  Aligned_cols=22  Identities=32%  Similarity=0.623  Sum_probs=19.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.++|++|+||||+|+.+...
T Consensus         1 LIvl~G~pGSGKST~a~~La~~   22 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKK   22 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            3689999999999999999765

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.56  E-value=0.1  Score=43.24  Aligned_cols=41  Identities=17%  Similarity=0.045  Sum_probs=27.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      .-.++.|.|.+|+|||+++.++..+.-.... ....|++...
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g-~~vly~s~E~   52 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQG-KPVLFFSLEM   52 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCC-CceEEEeCCC
Confidence            3468999999999999999887655221111 2355665443

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.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=95.56  E-value=0.011  Score=47.81  Aligned_cols=23  Identities=35%  Similarity=0.524  Sum_probs=20.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ..+|+++|+.|+||||+|+..-+
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            46899999999999999997755

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=95.56  E-value=0.072  Score=48.41  Aligned_cols=25  Identities=24%  Similarity=0.311  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-..++|+|..|+|||||++.+...
T Consensus       157 ~Gq~i~I~G~sG~GKStLl~~I~~~  181 (438)
T PRK07721        157 KGQRVGIFAGSGVGKSTLMGMIARN  181 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc
Confidence            3468999999999999999988875

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=95.55  E-value=0.077  Score=48.18  Aligned_cols=89  Identities=24%  Similarity=0.278  Sum_probs=52.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccc------------cccceeEEEeeCCCCCHHHHHHHHHHHhc-C--------CC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVK------------KYFSFRACAYVSEDFDAVGVTKVILQAAA-G--------SA  216 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~------------~~f~~~~wv~v~~~~~~~~i~~~i~~~l~-~--------~~  216 (261)
                      .-++|.|-+|+|||||+..+.+..+..            +.| ..+++-+++.....+.+.+.+...+ -        ..
T Consensus       142 QRigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~-v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~ats  220 (466)
T TIGR01040       142 QKIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNF-AIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLA  220 (466)
T ss_pred             CeeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCce-EEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECC
Confidence            357889999999999999988764310            111 4566677776555554444444433 1        11


Q ss_pred             CCCCHHH-----HHHHHHHHhC---CCeEEEEEeCCCCC
Q 041190          217 DVNDLNL-----LQLQLENQLK---NKKFLLVLDDMWSE  247 (261)
Q Consensus       217 ~~~~~~~-----~~~~l~~~l~---~kr~LiVlDdvw~~  247 (261)
                      +......     ..-.+-++++   ++++|+++||+-.-
T Consensus       221 d~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslTr~  259 (466)
T TIGR01040       221 NDPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMSSY  259 (466)
T ss_pred             CCCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChHHH
Confidence            1111111     1222455554   69999999999553

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=95.55  E-value=0.011  Score=50.87  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.++|++|+||||+|+.+.+.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~   25 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAK   25 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHH
Confidence            57888999999999999998775

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=95.55  E-value=0.073  Score=47.98  Aligned_cols=87  Identities=18%  Similarity=0.219  Sum_probs=48.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc--------CCCCCCCHH-----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA--------GSADVNDLN-----  222 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~--------~~~~~~~~~-----  222 (261)
                      -..++|+|..|+|||||++.+.+..+.    +.....-+.+.. ...++..+.+.+-+        ...+.....     
T Consensus       137 Gqri~I~G~sG~GKTtLl~~i~~~~~~----~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~~  212 (413)
T TIGR03497       137 GQRVGIFAGSGVGKSTLLGMIARNAKA----DINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKAA  212 (413)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHH
Confidence            457999999999999999988875321    222223344332 33444444333211        111211111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          223 LLQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ~~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      ...-.+-+++  +++++|+++||+-.-
T Consensus       213 ~~a~tiAEyfr~~G~~Vll~~Dsltr~  239 (413)
T TIGR03497       213 FTATAIAEYFRDQGKDVLLMMDSVTRF  239 (413)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEcCcHHH
Confidence            1112233444  589999999999654

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.

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=95.54  E-value=0.012  Score=45.79  Aligned_cols=23  Identities=39%  Similarity=0.537  Sum_probs=21.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++.|+|..|+|||||+..+...
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~   24 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPA   24 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999875

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.

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.54  E-value=0.073  Score=48.14  Aligned_cols=87  Identities=20%  Similarity=0.248  Sum_probs=49.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc-C-------CCCCCCH-----H
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA-G-------SADVNDL-----N  222 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~-~-------~~~~~~~-----~  222 (261)
                      -..++|+|..|+|||||++.++...+.    +.....-+.+. ....+++...+..-+ .       ..+....     .
T Consensus       156 Gqri~I~G~sG~GKTtLl~~Ia~~~~~----~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~  231 (432)
T PRK06793        156 GQKIGIFAGSGVGKSTLLGMIAKNAKA----DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAA  231 (432)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCCC----CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHH
Confidence            357899999999999999999876322    11222223332 455556555544422 1       1111111     1


Q ss_pred             HHHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          223 LLQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ~~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      .....+-+++  +++..||++||+-+-
T Consensus       232 ~~a~~iAEyfr~~G~~VLlilDslTr~  258 (432)
T PRK06793        232 KLATSIAEYFRDQGNNVLLMMDSVTRF  258 (432)
T ss_pred             HHHHHHHHHHHHcCCcEEEEecchHHH
Confidence            1122233333  589999999999665

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.54  E-value=0.037  Score=52.48  Aligned_cols=73  Identities=16%  Similarity=0.121  Sum_probs=45.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc-ccceeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK-YFSFRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~-~f~~~~wv~v~~~~~~~~i~~~i  208 (261)
                      ..++|.++.++.+...+...        ..+-++|++|+||||+++.+.+.  ... .|...+++.=+. .+...+++.+
T Consensus        18 ~~viG~~~a~~~l~~a~~~~--------~~~ll~G~pG~GKT~la~~la~~--l~~~~~~~~~~~~n~~-~~~~~~~~~v   86 (608)
T TIGR00764        18 DQVIGQEEAVEIIKKAAKQK--------RNVLLIGEPGVGKSMLAKAMAEL--LPDEELEDILVYPNPE-DPNMPRIVEV   86 (608)
T ss_pred             hhccCHHHHHHHHHHHHHcC--------CCEEEECCCCCCHHHHHHHHHHH--cCchhheeEEEEeCCC-CCchHHHHHH
Confidence            45788887777777766542        24458999999999999999876  332 233233222221 2344556666


Q ss_pred             HHHhc
Q 041190          209 LQAAA  213 (261)
Q Consensus       209 ~~~l~  213 (261)
                      ...++
T Consensus        87 ~~~~g   91 (608)
T TIGR00764        87 PAGEG   91 (608)
T ss_pred             HHhhc
Confidence            65554

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=95.54  E-value=0.011  Score=48.14  Aligned_cols=24  Identities=33%  Similarity=0.365  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G~   50 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNGL   50 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999754

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.

>PRK13946 shikimate kinase; Provisional

Probab=95.53  E-value=0.01  Score=47.29  Aligned_cols=25  Identities=20%  Similarity=0.309  Sum_probs=22.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+.|.+.|++|+||||+++.+.+..
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~L   34 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATML   34 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc
Confidence            4579999999999999999998763

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.52  E-value=0.019  Score=45.82  Aligned_cols=23  Identities=39%  Similarity=0.403  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+.|+|++|+||||+++.+..-
T Consensus        26 ~~i~I~G~tGSGKTTll~aL~~~   48 (186)
T cd01130          26 KNILISGGTGSGKTTLLNALLAF   48 (186)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            58999999999999999998765

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.

>PRK01184 hypothetical protein; Provisional

Probab=95.52  E-value=0.0097  Score=47.32  Aligned_cols=22  Identities=27%  Similarity=0.599  Sum_probs=18.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.++|++|+||||+++ +...
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~~   23 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IARE   23 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHHH
Confidence            479999999999999987 4443

>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=95.52  E-value=0.061  Score=45.43  Aligned_cols=22  Identities=36%  Similarity=0.475  Sum_probs=19.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|+|.|.+|+||||+++.+.+.
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~   22 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHI   22 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999988754

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.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=95.50  E-value=0.011  Score=48.25  Aligned_cols=24  Identities=25%  Similarity=0.440  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl   52 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGI   52 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999764

>PLN02165 adenylate isopentenyltransferase

Probab=95.48  E-value=0.012  Score=51.11  Aligned_cols=25  Identities=28%  Similarity=0.299  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.++.|+|++|+||||||..+...
T Consensus        42 ~g~iivIiGPTGSGKStLA~~LA~~   66 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSVDLATR   66 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHH
Confidence            4458999999999999999998776

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=95.47  E-value=0.033  Score=49.87  Aligned_cols=67  Identities=18%  Similarity=0.174  Sum_probs=45.7

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHH-HHHhhccccccccceeEEEeeCC---CCCHHHHHHHHHH
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSFRACAYVSE---DFDAVGVTKVILQ  210 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~~~wv~v~~---~~~~~~i~~~i~~  210 (261)
                      |.+..++|..||...      .-.+|.|.||.|+||+.|+ .++.++.+-      +..+.|.+   ..+-..++..+..
T Consensus         1 R~e~~~~L~~wL~e~------~~TFIvV~GPrGSGK~elV~d~~L~~r~~------vL~IDC~~i~~ar~D~~~I~~lA~   68 (431)
T PF10443_consen    1 RKEAIEQLKSWLNEN------PNTFIVVQGPRGSGKRELVMDHVLKDRKN------VLVIDCDQIVKARGDAAFIKNLAS   68 (431)
T ss_pred             CchHHHHHHHHHhcC------CCeEEEEECCCCCCccHHHHHHHHhCCCC------EEEEEChHhhhccChHHHHHHHHH
Confidence            456789999999764      3469999999999999999 888876332      33343322   2334555666666


Q ss_pred             Hhc
Q 041190          211 AAA  213 (261)
Q Consensus       211 ~l~  213 (261)
                      ++|
T Consensus        69 qvG   71 (431)
T PF10443_consen   69 QVG   71 (431)
T ss_pred             hcC
Confidence            655

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PF13245 AAA_19: Part of AAA domain

Probab=95.47  E-value=0.014  Score=39.45  Aligned_cols=23  Identities=35%  Similarity=0.420  Sum_probs=16.9

Q ss_pred             eEEeEeecCCCChHH-HHHHHhhc
Q 041190          158 SVIPITGMGGLGKTT-LAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTt-La~~v~~~  180 (261)
                      +++.|.|++|+|||+ +++.+..-
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l   34 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAEL   34 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            577889999999995 55554443

>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=95.47  E-value=0.012  Score=46.70  Aligned_cols=23  Identities=30%  Similarity=0.447  Sum_probs=20.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhh
Confidence            35899999999999999999864

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.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=95.46  E-value=0.012  Score=47.09  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.|+.|+|||||.+.+..-
T Consensus        19 e~~~i~G~nGsGKSTLl~~i~G~   41 (190)
T TIGR01166        19 EVLALLGANGAGKSTLLLHLNGL   41 (190)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999998754

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.

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.46  E-value=0.015  Score=48.46  Aligned_cols=20  Identities=30%  Similarity=0.328  Sum_probs=17.3

Q ss_pred             EeecCCCChHHHHHHHhhcc
Q 041190          162 ITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       162 I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |+||+|+||||+++.+.+..
T Consensus         1 ViGpaGSGKTT~~~~~~~~~   20 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWL   20 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            68999999999999998764

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=95.44  E-value=0.013  Score=47.76  Aligned_cols=25  Identities=32%  Similarity=0.361  Sum_probs=22.1

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .. .+++|+|+.|+|||||++.+..-
T Consensus        22 ~~-e~~~i~G~nGsGKSTLl~~l~G~   46 (214)
T cd03297          22 NE-EVTGIFGASGAGKSTLLRCIAGL   46 (214)
T ss_pred             cc-eeEEEECCCCCCHHHHHHHHhCC
Confidence            35 89999999999999999999754

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.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.44  E-value=0.024  Score=45.74  Aligned_cols=23  Identities=35%  Similarity=0.442  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++..|.|++|+||||+++.+...
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~   41 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEA   41 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCHHHHHHHHHHH
Confidence            57888999999999999998765

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=95.43  E-value=0.012  Score=46.10  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|+|++|+||||+++.+.+.
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~   25 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQA   25 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5788999999999999999775

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

Probab=95.43  E-value=0.0083  Score=45.46  Aligned_cols=45  Identities=24%  Similarity=0.214  Sum_probs=29.6

Q ss_pred             ccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          133 YGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       133 ~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +|.-....++.+.+..-.    ..-..|.|+|.+|+||+++|+.++...
T Consensus         1 vG~S~~~~~l~~~l~~~a----~~~~pvli~GE~GtGK~~~A~~lh~~~   45 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLA----KSSSPVLITGEPGTGKSLLARALHRYS   45 (138)
T ss_dssp             --SCHHHHHHHHHHHHHH----CSSS-EEEECCTTSSHHHHHHCCHHTT
T ss_pred             CCCCHHHHHHHHHHHHHh----CCCCcEEEEcCCCCCHHHHHHHHHhhc
Confidence            355555556665554421    123567999999999999999998863

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=95.42  E-value=0.011  Score=46.94  Aligned_cols=21  Identities=43%  Similarity=0.585  Sum_probs=19.2

Q ss_pred             EEeEeecCCCChHHHHHHHhh
Q 041190          159 VIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      +|+|+|..|+||||+++.+.+
T Consensus         1 ii~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999866

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK14531 adenylate kinase; Provisional

Probab=95.42  E-value=0.013  Score=46.72  Aligned_cols=22  Identities=27%  Similarity=0.247  Sum_probs=20.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|+|++|+||||+++.+...
T Consensus         4 ~i~i~G~pGsGKsT~~~~la~~   25 (183)
T PRK14531          4 RLLFLGPPGAGKGTQAARLCAA   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999776

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=95.40  E-value=0.013  Score=48.65  Aligned_cols=23  Identities=35%  Similarity=0.589  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus        27 e~~~l~G~nGsGKSTLl~~l~G~   49 (235)
T cd03261          27 EILAIIGPSGSGKSTLLRLIVGL   49 (235)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999754

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.

>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=95.40  E-value=0.013  Score=46.36  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.|+.|+|||||++.+..-
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGL   49 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999754

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.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=95.39  E-value=0.061  Score=48.70  Aligned_cols=24  Identities=17%  Similarity=0.235  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -..++|.|..|+|||||++.+...
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~  178 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRY  178 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhcc
Confidence            457999999999999999998875

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=95.36  E-value=0.013  Score=47.96  Aligned_cols=23  Identities=26%  Similarity=0.498  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus        31 ~~~~i~G~nGsGKSTLl~~l~Gl   53 (220)
T cd03293          31 EFVALVGPSGCGKSTLLRIIAGL   53 (220)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999764

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.

>COG4240 Predicted kinase [General function prediction only]

Probab=95.36  E-value=0.071  Score=43.76  Aligned_cols=79  Identities=18%  Similarity=0.141  Sum_probs=44.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc------CCCCCCCHHHHHHHHH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA------GSADVNDLNLLQLQLE  229 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~------~~~~~~~~~~~~~~l~  229 (261)
                      ++-+++|+|+.|+||||++-.+++...-+.. ......++..-+-...=.-.++++..      +....+|..-....+.
T Consensus        49 rPli~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnVLn  127 (300)
T COG4240          49 RPLIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNVLN  127 (300)
T ss_pred             CceEEEeecCCCCchhhHHHHHHHHHHHhcc-cceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHHHH
Confidence            4779999999999999999999987433322 23344443332111111122333321      2234556655556666


Q ss_pred             HHhCCC
Q 041190          230 NQLKNK  235 (261)
Q Consensus       230 ~~l~~k  235 (261)
                      ...+++
T Consensus       128 ai~~g~  133 (300)
T COG4240         128 AIARGG  133 (300)
T ss_pred             HHhcCC
Confidence            555555

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=95.35  E-value=0.11  Score=47.49  Aligned_cols=92  Identities=16%  Similarity=0.202  Sum_probs=52.8

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhcccccccccee-EEEeeCCCC-CHHHHHHHHHHHhc-C-------CCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSFR-ACAYVSEDF-DAVGVTKVILQAAA-G-------SADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~~-~wv~v~~~~-~~~~i~~~i~~~l~-~-------~~~~~~~~----  222 (261)
                      .-++|.|..|+|||+|| ..+.+..    .-+.. +++-+++.. ...++...+...=. .       ..+.....    
T Consensus       142 QR~~I~g~~g~GKt~Lal~~I~~q~----~~dv~cV~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r~~a  217 (485)
T CHL00059        142 QRELIIGDRQTGKTAVATDTILNQK----GQNVICVYVAIGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLA  217 (485)
T ss_pred             CEEEeecCCCCCHHHHHHHHHHhcc----cCCeEEEEEEecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHHHHH
Confidence            35789999999999995 5555542    23334 677777654 34455555443211 1       11111111    


Q ss_pred             -----HHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          223 -----LLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       223 -----~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                           .+...++.  +++++|+|+||+-.-. ..|.++.
T Consensus       218 p~~a~aiAEyfr~--~G~~VLlv~DdlTr~A-~A~REis  253 (485)
T CHL00059        218 PYTGAALAEYFMY--RGRHTLIIYDDLSKQA-QAYRQMS  253 (485)
T ss_pred             HHHHhhHHHHHHH--cCCCEEEEEcChhHHH-HHHHHHH
Confidence                 12333333  5899999999997653 4555543

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.35  E-value=0.018  Score=45.85  Aligned_cols=25  Identities=36%  Similarity=0.434  Sum_probs=22.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.+.|.+|+||||+|+.+...
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~   41 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKK   41 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999999875

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=95.35  E-value=0.012  Score=50.20  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=19.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++|.|.+|+|||||++.+..-
T Consensus         1 iigI~G~sGsGKSTl~~~L~~l   22 (273)
T cd02026           1 IIGVAGDSGCGKSTFLRRLTSL   22 (273)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh
Confidence            5899999999999999999854

This enzyme 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.

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=95.34  E-value=0.012  Score=47.85  Aligned_cols=24  Identities=42%  Similarity=0.573  Sum_probs=21.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .-|.|+|++|+|||||+..+.++.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCc
Confidence            468899999999999999998764

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=95.34  E-value=0.014  Score=44.94  Aligned_cols=22  Identities=32%  Similarity=0.623  Sum_probs=19.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||++.+.+.
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~   23 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYD   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999999765

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

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=95.34  E-value=0.014  Score=49.66  Aligned_cols=25  Identities=32%  Similarity=0.489  Sum_probs=22.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      ++|+|+|.+|+|||||+..+....+
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L~   26 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRLS   26 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5899999999999999999988743

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=95.34  E-value=0.014  Score=47.47  Aligned_cols=24  Identities=25%  Similarity=0.386  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          26 GEIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999764

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.

>cd04163 Era Era subfamily

Probab=95.33  E-value=0.016  Score=44.30  Aligned_cols=24  Identities=25%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|+++|.+|+|||||.+.+...
T Consensus         3 ~~~i~~~G~~g~GKttl~~~l~~~   26 (168)
T cd04163           3 SGFVAIVGRPNVGKSTLLNALVGQ   26 (168)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            357999999999999999998654

Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=95.33  E-value=0.014  Score=47.82  Aligned_cols=23  Identities=26%  Similarity=0.502  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.++.-
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~Gl   51 (220)
T cd03263          29 EIFGLLGHNGAGKTTTLKMLTGE   51 (220)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999764

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>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=95.33  E-value=0.013  Score=46.46  Aligned_cols=24  Identities=38%  Similarity=0.466  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl   48 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQ   48 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC
Confidence            358999999999999999999764

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.

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=95.33  E-value=0.014  Score=48.65  Aligned_cols=24  Identities=29%  Similarity=0.346  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        28 Ge~~~l~G~nGsGKSTLl~~l~Gl   51 (243)
T TIGR02315        28 GEFVAIIGPSGAGKSTLLRCINRL   51 (243)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998753

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=95.33  E-value=0.026  Score=53.02  Aligned_cols=46  Identities=15%  Similarity=0.112  Sum_probs=31.7

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+.|.+-.+.|.+..-.    ...+..+|.++|++|+||||+|+.+....
T Consensus       371 ~f~rpeV~~iL~~~~~~----r~~~g~~Ivl~Gl~GSGKSTia~~La~~L  416 (568)
T PRK05537        371 WFSFPEVVAELRRTYPP----RHKQGFTVFFTGLSGAGKSTIAKALMVKL  416 (568)
T ss_pred             hhcHHHHHHHHHHHhcc----ccCCCeEEEEECCCCChHHHHHHHHHHHh
Confidence            33455545544444332    33455689999999999999999998763

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=95.32  E-value=0.014  Score=48.53  Aligned_cols=24  Identities=25%  Similarity=0.313  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (241)
T cd03256          27 GEFVALIGPSGAGKSTLLRCLNGL   50 (241)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999753

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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.

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=95.32  E-value=0.16  Score=46.07  Aligned_cols=87  Identities=20%  Similarity=0.230  Sum_probs=48.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc-C-------CCCCCCHH-----
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA-G-------SADVNDLN-----  222 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~-~-------~~~~~~~~-----  222 (261)
                      -..++|.|.+|+|||||.+.+.....    -+....+.+... .....+......... .       ..+.....     
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            45789999999999999999987532    223333344432 234444433332211 0       11111111     


Q ss_pred             HHHHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          223 LLQLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ~~~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      .....+-+++  .+++.|+++|++-.-
T Consensus       221 ~~a~~~AE~f~~~g~~Vl~~~Dsltr~  247 (422)
T TIGR02546       221 YTATAIAEYFRDQGKRVLLMMDSLTRF  247 (422)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCchHH
Confidence            1122234444  578999999999653

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=95.31  E-value=0.047  Score=48.51  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=22.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....+.|.|.+|+|||+|.+.+.+..
T Consensus        21 ~~~~~fv~G~~GtGKs~l~~~i~~~~   46 (364)
T PF05970_consen   21 EGLNFFVTGPAGTGKSFLIKAIIDYL   46 (364)
T ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHh
Confidence            34688999999999999999998873

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.29  E-value=0.1  Score=51.10  Aligned_cols=117  Identities=16%  Similarity=0.079  Sum_probs=66.7

Q ss_pred             cccccchHHHHHHHhhCCCCC-CC-CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          132 VYGREKDKEVIVGLLLGDDLN-SG-PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~-~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      ++|.++.+..|.+.+...... .+ ...-.+.+.|+.|+|||.||+.+..-  +-+.++.-+-+..|+-      . ++.
T Consensus       564 V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~--~Fgse~~~IriDmse~------~-evs  634 (898)
T KOG1051|consen  564 VIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEY--VFGSEENFIRLDMSEF------Q-EVS  634 (898)
T ss_pred             ccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHH--HcCCccceEEechhhh------h-hhh
Confidence            566677777777776654310 11 25667888999999999999988765  3222333344444441      1 122


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHhCCCe-EEEEEeCCCCCChhhHHHhhcc
Q 041190          210 QAAAGSADVNDLNLLQLQLENQLKNKK-FLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l~~kr-~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                      +.++.++. ---.+--..|.+.++.+. .+|+||||....+.....|..+
T Consensus       635 kligsp~g-yvG~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~  683 (898)
T KOG1051|consen  635 KLIGSPPG-YVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQL  683 (898)
T ss_pred             hccCCCcc-cccchhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHHH
Confidence            23331110 000111235666676654 5778899998877666655443

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=95.29  E-value=0.015  Score=47.20  Aligned_cols=24  Identities=42%  Similarity=0.558  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~Gl   49 (205)
T cd03226          26 GEIIALTGKNGAGKTTLAKILAGL   49 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999764

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most 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.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=95.29  E-value=0.012  Score=48.21  Aligned_cols=23  Identities=30%  Similarity=0.287  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            47889999999999999999874

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

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=95.29  E-value=0.015  Score=47.46  Aligned_cols=23  Identities=39%  Similarity=0.648  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus        29 ~~~~l~G~nGsGKSTLl~~i~Gl   51 (214)
T TIGR02673        29 EFLFLTGPSGAGKTTLLKLLYGA   51 (214)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999654

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=95.28  E-value=0.014  Score=47.57  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~G~   48 (213)
T cd03235          25 GEFLAIVGPNGAGKSTLLKAILGL   48 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            358999999999999999999764

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>PLN03046 D-glycerate 3-kinase; Provisional

Probab=95.28  E-value=0.019  Score=51.49  Aligned_cols=26  Identities=31%  Similarity=0.097  Sum_probs=22.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+-+|+|.|..|+|||||++.+..-
T Consensus       210 ~~PlIIGIsG~qGSGKSTLa~~L~~l  235 (460)
T PLN03046        210 IPPLVIGFSAPQGCGKTTLVFALDYL  235 (460)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999999643

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=95.26  E-value=0.015  Score=47.88  Aligned_cols=24  Identities=29%  Similarity=0.373  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G~   49 (227)
T cd03260          26 GEITALIGPSGCGKSTLLRLLNRL   49 (227)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999999754

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=95.26  E-value=0.015  Score=47.34  Aligned_cols=24  Identities=29%  Similarity=0.570  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        27 G~~~~i~G~nGsGKSTLl~~l~G~   50 (214)
T cd03292          27 GEFVFLVGPSGAGKSTLLKLIYKE   50 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999764

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=95.26  E-value=0.014  Score=47.58  Aligned_cols=22  Identities=32%  Similarity=0.443  Sum_probs=20.3

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++|+|+.|+|||||++.++.-
T Consensus        27 ~~~i~G~nGsGKSTLl~~l~Gl   48 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILATL   48 (211)
T ss_pred             cEEEECCCCCCHHHHHHHHhCC
Confidence            8999999999999999999853

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. 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.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.25  E-value=0.015  Score=44.40  Aligned_cols=24  Identities=38%  Similarity=0.454  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+-|-|.|.+|+|||||+..+...
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~   30 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEK   30 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHH
Confidence            456889999999999999999865

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=95.24  E-value=0.015  Score=47.87  Aligned_cols=24  Identities=29%  Similarity=0.364  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.++.-
T Consensus        36 Ge~~~i~G~nGsGKSTLl~~i~Gl   59 (228)
T PRK10584         36 GETIALIGESGSGKSTLLAILAGL   59 (228)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC
Confidence            368999999999999999999754

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=95.24  E-value=0.015  Score=47.31  Aligned_cols=24  Identities=33%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G~   49 (213)
T cd03259          26 GEFLALLGPSGCGKTTLLRLIAGL   49 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999753

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. 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.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=95.24  E-value=0.014  Score=44.86  Aligned_cols=19  Identities=37%  Similarity=0.371  Sum_probs=17.8

Q ss_pred             EeecCCCChHHHHHHHhhc
Q 041190          162 ITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       162 I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|++|+||||+|+.+...
T Consensus         1 i~G~PgsGK~t~~~~la~~   19 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKR   19 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHh
Confidence            6899999999999999886

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>PRK14528 adenylate kinase; Provisional

Probab=95.23  E-value=0.016  Score=46.33  Aligned_cols=23  Identities=30%  Similarity=0.372  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|.|++|+||||+++.+...
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~   24 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCER   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            45889999999999999999765

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

Probab=95.23  E-value=0.017  Score=55.45  Aligned_cols=43  Identities=21%  Similarity=0.332  Sum_probs=33.0

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhh
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -++||+++++.++..|.+...    +.+  -.+|.+|+|||+++.-+..
T Consensus       171 PvIGRd~EI~r~iqIL~RR~K----NNP--vLiGEpGVGKTAIvEGLA~  213 (786)
T COG0542         171 PVIGRDEEIRRTIQILSRRTK----NNP--VLVGEPGVGKTAIVEGLAQ  213 (786)
T ss_pred             CCcChHHHHHHHHHHHhccCC----CCC--eEecCCCCCHHHHHHHHHH
Confidence            389999999999999988642    222  3579999999997655544

>smart00072 GuKc Guanylate kinase homologues

Probab=95.23  E-value=0.022  Score=45.42  Aligned_cols=23  Identities=30%  Similarity=0.504  Sum_probs=21.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++.++|++|+||+||++.+...
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~   25 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQE   25 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhc
Confidence            67899999999999999999876

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=95.22  E-value=0.072  Score=48.79  Aligned_cols=89  Identities=20%  Similarity=0.244  Sum_probs=53.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc---------------CCCCCCCH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA---------------GSADVNDL  221 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~---------------~~~~~~~~  221 (261)
                      .-++|.|-+|+|||+|+..+....... +=+..+++-+++... ..+++.+++..-.               ...+....
T Consensus       162 QR~gIfgg~GvGKs~L~~~~~~~~~~~-~~dv~V~~lIGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p~~  240 (494)
T CHL00060        162 GKIGLFGGAGVGKTVLIMELINNIAKA-HGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPG  240 (494)
T ss_pred             CEEeeecCCCCChhHHHHHHHHHHHHh-cCCeEEEEEeccCchHHHHHHHHHHhcCccccCcccccceEEEEECCCCCHH
Confidence            458999999999999999887662111 115677888877543 4566666555110               01111111


Q ss_pred             H-----HHHHHHHHHhC--CC-eEEEEEeCCCCC
Q 041190          222 N-----LLQLQLENQLK--NK-KFLLVLDDMWSE  247 (261)
Q Consensus       222 ~-----~~~~~l~~~l~--~k-r~LiVlDdvw~~  247 (261)
                      .     ...-.+-++++  ++ ++||++||+-.-
T Consensus       241 ~R~~a~~~A~tiAEyfrd~g~~~VLll~DslTR~  274 (494)
T CHL00060        241 ARMRVGLTALTMAEYFRDVNKQDVLLFIDNIFRF  274 (494)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCEEEEcccchHH
Confidence            1     22333666663  44 999999999654

>PRK00698 tmk thymidylate kinase; Validated

Probab=95.22  E-value=0.017  Score=46.55  Aligned_cols=23  Identities=35%  Similarity=0.491  Sum_probs=21.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|+.|+||||+++.+.+.
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~   26 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKEL   26 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999875

>PLN02674 adenylate kinase

Probab=95.22  E-value=0.07  Score=44.58  Aligned_cols=25  Identities=20%  Similarity=0.254  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...|.|.|++|+||||+++.+..+.
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~   55 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEY   55 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHc
Confidence            3557899999999999999998763

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=95.21  E-value=0.016  Score=48.24  Aligned_cols=24  Identities=33%  Similarity=0.433  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (239)
T cd03296          28 GELVALLGPSGSGKTTLLRLIAGL   51 (239)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999764

Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). 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.

>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=95.20  E-value=0.016  Score=47.48  Aligned_cols=24  Identities=25%  Similarity=0.308  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G~   49 (220)
T cd03265          26 GEIFGLLGPNGAGKTTTIKMLTTL   49 (220)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999764

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.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=95.20  E-value=0.016  Score=47.45  Aligned_cols=24  Identities=33%  Similarity=0.423  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.|+.|+|||||.+.+..-
T Consensus        31 G~~~~i~G~nGsGKSTLl~~i~G~   54 (221)
T TIGR02211        31 GEIVAIVGSSGSGKSTLLHLLGGL   54 (221)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999754

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.20  E-value=0.017  Score=46.53  Aligned_cols=23  Identities=26%  Similarity=0.483  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|..|+|||||++.+..-
T Consensus        27 e~~~l~G~nGsGKSTLl~~l~G~   49 (195)
T PRK13541         27 AITYIKGANGCGKSSLLRMIAGI   49 (195)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999765

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=95.18  E-value=0.19  Score=42.66  Aligned_cols=94  Identities=16%  Similarity=0.189  Sum_probs=51.8

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCC
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSAD  217 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~  217 (261)
                      ++..|...|...       -+-.-++|.+|+||+|+++.+..=..    ++ ..-+.+++.++..+...++-.-      
T Consensus        19 hi~ri~RvL~~~-------~Gh~LLvG~~GsGr~sl~rLaa~i~~----~~-~~~i~~~~~y~~~~f~~dLk~~------   80 (268)
T PF12780_consen   19 HIARISRVLSQP-------RGHALLVGVGGSGRQSLARLAAFICG----YE-VFQIEITKGYSIKDFKEDLKKA------   80 (268)
T ss_dssp             HHHHHHHHHCST-------TEEEEEECTTTSCHHHHHHHHHHHTT----EE-EE-TTTSTTTHHHHHHHHHHHH------
T ss_pred             HHHHHHHHHcCC-------CCCeEEecCCCccHHHHHHHHHHHhc----cc-eEEEEeeCCcCHHHHHHHHHHH------
Confidence            344555556432       24456999999999999998765311    10 1123455656655543322211      


Q ss_pred             CCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          218 VNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       218 ~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                               ..+..+++++..+++.|-+-.++...+.|...
T Consensus        81 ---------~~~ag~~~~~~vfll~d~qi~~~~fLe~in~L  112 (268)
T PF12780_consen   81 ---------LQKAGIKGKPTVFLLTDSQIVDESFLEDINSL  112 (268)
T ss_dssp             ---------HHHHHCS-S-EEEEEECCCSSSCHHHHHHHHH
T ss_pred             ---------HHHHhccCCCeEEEecCcccchHhHHHHHHHH
Confidence                     12334568888888888776654455655443

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=95.18  E-value=0.017  Score=47.17  Aligned_cols=24  Identities=38%  Similarity=0.393  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        13 Ge~~~l~G~NGsGKSTLlk~i~Gl   36 (213)
T PRK15177         13 HEHIGILAAPGSGKTTLTRLLCGL   36 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            368999999999999999999864

>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=95.18  E-value=0.49  Score=36.31  Aligned_cols=84  Identities=13%  Similarity=0.181  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhcc-ccChhHHHHHHHHHHHHhhhHhHHH
Q 041190            6 EAILTVTVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQ-ITKPLTKKWLGKLQNLAYDAEDMLD   84 (261)
Q Consensus         6 ~~~~~~~v~~l~~~l~~~~~~~~~~~~~v~~~i~~L~~~l~~i~~~l~~a~~~~-~~~~~~~~wl~~lr~~ayd~ed~ld   84 (261)
                      +-+.+++++.+++.+...+....+.....+.-+++|...++.|..++.+-+... .-+..-+.=+.++.+...++++++.
T Consensus         4 eL~~gaalG~~~~eLlk~v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L~~~L~~g~~LV~   83 (147)
T PF05659_consen    4 ELVGGAALGAVFGELLKAVIDASKKSLSFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERLKELLEKGKELVE   83 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHHHHHHHHHHHHHH
Confidence            334444444455555555555556666677789999999999999999877754 1222225667888888889999998


Q ss_pred             HHHHH
Q 041190           85 EFATE   89 (261)
Q Consensus        85 ~~~~~   89 (261)
                      .|..-
T Consensus        84 k~sk~   88 (147)
T PF05659_consen   84 KCSKV   88 (147)
T ss_pred             Hhccc
Confidence            88543

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 [].

>cd01862 Rab7 Rab7 subfamily

Probab=95.18  E-value=0.016  Score=45.02  Aligned_cols=21  Identities=38%  Similarity=0.558  Sum_probs=18.9

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 i~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           3 VIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999988765

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=95.17  E-value=0.016  Score=48.00  Aligned_cols=24  Identities=29%  Similarity=0.357  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~   50 (236)
T TIGR03864        27 GEFVALLGPNGAGKSTLFSLLTRL   50 (236)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999754

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=95.17  E-value=0.017  Score=46.77  Aligned_cols=23  Identities=30%  Similarity=0.367  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        25 e~~~i~G~nGsGKSTLl~~l~G~   47 (206)
T TIGR03608        25 KMYAIIGESGSGKSTLLNIIGLL   47 (206)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999754

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=95.17  E-value=0.017  Score=47.30  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~Gl   49 (222)
T cd03224          26 GEIVALLGRNGAGKTTLLKTIMGL   49 (222)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999998653

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). 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.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=95.17  E-value=0.017  Score=47.53  Aligned_cols=22  Identities=27%  Similarity=0.273  Sum_probs=19.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ...+.|||.+|+||||+|+.+-
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~   33 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLP   33 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcC
Confidence            4569999999999999999874

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>PRK02496 adk adenylate kinase; Provisional

Probab=95.16  E-value=0.019  Score=45.68  Aligned_cols=22  Identities=27%  Similarity=0.289  Sum_probs=19.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -+.|.|++|+||||+++.+...
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~   24 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEH   24 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999765

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=95.16  E-value=0.017  Score=47.86  Aligned_cols=23  Identities=35%  Similarity=0.486  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus        36 e~~~l~G~nGsGKSTLl~~l~Gl   58 (233)
T PRK11629         36 EMMAIVGSSGSGKSTLLHLLGGL   58 (233)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999754

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=95.16  E-value=0.017  Score=47.81  Aligned_cols=24  Identities=29%  Similarity=0.349  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~G~   54 (233)
T cd03258          31 GEIFGIIGRSGAGKSTLIRCINGL   54 (233)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999654

Other members of this system include the MetP permease and the MetQ substrate binding protein. 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.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=95.16  E-value=0.017  Score=44.60  Aligned_cols=22  Identities=27%  Similarity=0.536  Sum_probs=19.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||||++.+.+.
T Consensus         2 ki~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3688999999999999988754

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK00023 cmk cytidylate kinase; Provisional

Probab=95.15  E-value=0.069  Score=44.11  Aligned_cols=24  Identities=38%  Similarity=0.534  Sum_probs=22.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+|+|.|++|+||||+++.+.+..
T Consensus         5 ~~i~i~g~~gsGksti~~~la~~~   28 (225)
T PRK00023          5 IVIAIDGPAGSGKGTVAKILAKKL   28 (225)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            689999999999999999998764

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=95.15  E-value=0.17  Score=44.24  Aligned_cols=45  Identities=11%  Similarity=0.090  Sum_probs=32.3

Q ss_pred             cccc-ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYG-REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~g-r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++| .+.-++.|...+..+     .-.+..-++|+.|+||||+|+.+.+.
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~-----~l~ha~Lf~G~~G~gk~~~a~~la~~   51 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKN-----RLSHAYLFEGAKGTGKKATALWLAKS   51 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcC-----CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3556 555667777777543     23567789999999999999887544

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.14  E-value=0.017  Score=46.75  Aligned_cols=24  Identities=29%  Similarity=0.423  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        27 Ge~~~l~G~nGsGKSTLl~~l~G~   50 (204)
T PRK13538         27 GELVQIEGPNGAGKTSLLRILAGL   50 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999764

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.12  E-value=0.076  Score=45.00  Aligned_cols=79  Identities=15%  Similarity=0.227  Sum_probs=42.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC--CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED--FDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNK  235 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~k  235 (261)
                      .++.|.|+.|+||||+++.+.+.  +.. ...++ +.+.++  +....+     .++.  ...........-++..|+..
T Consensus        81 GlilisG~tGSGKTT~l~all~~--i~~-~~~~i-itiEdp~E~~~~~~-----~q~~--v~~~~~~~~~~~l~~~lR~~  149 (264)
T cd01129          81 GIILVTGPTGSGKTTTLYSALSE--LNT-PEKNI-ITVEDPVEYQIPGI-----NQVQ--VNEKAGLTFARGLRAILRQD  149 (264)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhh--hCC-CCCeE-EEECCCceecCCCc-----eEEE--eCCcCCcCHHHHHHHHhccC
Confidence            58999999999999999988654  211 11111 222221  111100     0111  00110112344566777777


Q ss_pred             eEEEEEeCCCCC
Q 041190          236 KFLLVLDDMWSE  247 (261)
Q Consensus       236 r~LiVlDdvw~~  247 (261)
                      .=.|+++++.+.
T Consensus       150 PD~i~vgEiR~~  161 (264)
T cd01129         150 PDIIMVGEIRDA  161 (264)
T ss_pred             CCEEEeccCCCH
Confidence            778888888886

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.

>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=95.12  E-value=0.034  Score=45.08  Aligned_cols=42  Identities=26%  Similarity=0.320  Sum_probs=28.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhh
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.+..+..|.-....        ..-+.++|++|+|||++|+.+-.
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            4577777666665544432        24789999999999999998853

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.12  E-value=0.14  Score=47.54  Aligned_cols=100  Identities=16%  Similarity=0.063  Sum_probs=58.2

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC---
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG---  214 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~---  214 (261)
                      ....|-++|..    +-+.-.++.|.|.+|+|||+|+.++....  ...-...+|++...+  ...+...+ ..++.   
T Consensus       258 Gi~~lD~~l~G----G~~~g~~~li~G~~G~GKT~l~~~~~~~~--~~~g~~~~yis~e~~--~~~i~~~~-~~~g~~~~  328 (509)
T PRK09302        258 GVPDLDEMLGG----GFFRGSIILVSGATGTGKTLLASKFAEAA--CRRGERCLLFAFEES--RAQLIRNA-RSWGIDLE  328 (509)
T ss_pred             CcHHHHHhhcC----CCCCCcEEEEEcCCCCCHHHHHHHHHHHH--HhCCCcEEEEEecCC--HHHHHHHH-HHcCCChH
Confidence            34555555532    23456788999999999999998887652  122345777776653  44444332 23331   


Q ss_pred             -------------CCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCC
Q 041190          215 -------------SADVNDLNLLQLQLENQLK-NKKFLLVLDDMWS  246 (261)
Q Consensus       215 -------------~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~  246 (261)
                                   .+.....+.....+.+.+. .+.-++|+|.+-.
T Consensus       329 ~~~~~g~l~i~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDslt~  374 (509)
T PRK09302        329 KMEEKGLLKIICARPESYGLEDHLIIIKREIEEFKPSRVAIDPLSA  374 (509)
T ss_pred             HHhhcCCceeecCCcccCCHHHHHHHHHHHHHHcCCCEEEEcCHHH
Confidence                         0112233455555655553 3445899999843

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=95.12  E-value=0.017  Score=47.48  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~G~   54 (228)
T cd03257          31 GETLGLVGESGSGKSTLARAILGL   54 (228)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999754

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=95.12  E-value=0.017  Score=48.58  Aligned_cols=24  Identities=33%  Similarity=0.394  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (255)
T PRK11248         27 GELLVVLGPSGCGKTTLLNLIAGF   50 (255)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999754

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=95.11  E-value=0.018  Score=39.96  Aligned_cols=23  Identities=52%  Similarity=0.683  Sum_probs=19.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ++.+.|.+|+||||++..+....
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l   23 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAAL   23 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            46789999999999999887763

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

---

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	261
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	7e-38
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	9e-33
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-24
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	6e-08
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	7e-07

>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 =  138 bits (350), Expect = 7e-38
 Identities = 33/245 (13%), Positives = 65/245 (26%), Gaps = 37/245 (15%)

Query: 38  LKKWEELL--VIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDMLDEFAT------E 89
           L+  E L   +    ++D            ++ +         A  ++            
Sbjct: 10  LQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYV 69

Query: 90  AFRRKLL-------------LLEQADRQPTATARLRYGRVQERPLSTPSLVDEEEVY-GR 135
           +F   LL              +          +           L    +     V+  R
Sbjct: 70  SFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTR 129

Query: 136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACA-- 193
           +K    I   L             + I GM G GK+ LA     D  + +          
Sbjct: 130 KKLVNAIQQKLSKLKGEP----GWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185

Query: 194 YVSEDFDAVGVTKVILQAAA-------GSADVNDLNLLQLQLENQL--KNKKFLLVLDDM 244
            V +   +  + K+                   ++   + +L   +  K+ + LL+LDD+
Sbjct: 186 SVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDV 245

Query: 245 WSENY 249
           W    
Sbjct: 246 WDSWV 250

>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 =  124 bits (312), Expect = 9e-33
 Identities = 40/269 (14%), Positives = 74/269 (27%), Gaps = 36/269 (13%)

Query: 15  MLVEK--LALEVIQLFARQEQIE-ADLKKWEELLVIIKVVLDDAEEKQITKPLTK----K 67
           ML E    AL      A    I   + +     L    +  +D  E              
Sbjct: 1   MLCEIECRALST----AHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIAN 56

Query: 68  WLGKLQNLAYDAEDMLDEFATEAFRRKLLLLE--------QADRQPTATARLRYGRVQ-E 118
           +L   +  A +   ++D F           LE        + D         ++ R   +
Sbjct: 57  FLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLD 116

Query: 119 RPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVF 178
           R L   ++  +   Y RE   + ++  L  D++        + + G  G GK+ +A    
Sbjct: 117 RKLLLGNVPKQMTCYIREYHVDRVIKKL--DEMCDLDS-FFLFLHGRAGSGKSVIASQAL 173

Query: 179 NDAG--VKKYFSFRACAYVSEDFDAVGVTKVI-----------LQAAAGSADVNDLNLLQ 225
           + +   +   +        S                       L        V  + L +
Sbjct: 174 SKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKR 233

Query: 226 LQLENQLKNKKFLLVLDDMWSENYDVWTN 254
           +     +     L V DD+  E    W  
Sbjct: 234 MICNALIDRPNTLFVFDDVVQEETIRWAQ 262

>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 =  101 bits (252), Expect = 2e-24
 Identities = 52/272 (19%), Positives = 97/272 (35%), Gaps = 61/272 (22%)

Query: 23  EVIQLFARQEQIEADL--KKWEELLVIIKVVLDDAEEKQITKPLTKK-------W--LGK 71
           +++ +F  ++    +   K  +++    K +L   E   I              W  L K
Sbjct: 20  DILSVF--EDAFVDNFDCKDVQDMP---KSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74

Query: 72  LQNLAYDA-EDMLD---EFATEAFRRKLLLLEQADRQPTATARLRYGRVQERPLSTPSLV 127
            + +     E++L    +F     + +        RQP+   R  Y   ++R  +   + 
Sbjct: 75  QEEMVQKFVEEVLRINYKFLMSPIKTE-------QRQPSMMTR-MYIEQRDRLYNDNQVF 126

Query: 128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF 187
            +  V  R +    +   LL  +L        + I G+ G GKT +A  V     V+   
Sbjct: 127 AKYNVS-RLQPYLKLRQALL--ELRPAKN---VLIDGVLGSGKTWVALDVCLSYKVQCKM 180

Query: 188 SFRACAY---VSEDFDAVGVTKVILQAAAGSADVN-------------DLNLLQLQLENQ 231
            F+   +   +        V + +LQ      D N              ++ +Q +L   
Sbjct: 181 DFK--IFWLNLKNCNSPETVLE-MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237

Query: 232 LKNKKF---LLVLDDMWSENYDVWT--NL-CK 257
           LK+K +   LLVL ++ +     W   NL CK
Sbjct: 238 LKSKPYENCLLVLLNVQNAK--AWNAFNLSCK 267

>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 = 52.5 bits (126), Expect = 6e-08
 Identities = 50/249 (20%), Positives = 85/249 (34%), Gaps = 41/249 (16%)

Query: 31  QEQIEADLKKWEELL--VIIKVVLDDAEEKQITKPLTKKWLGKLQNLAYDAEDML---DE 85
           +E +E D+K    ++  +I   VL   EE+++    T+         A     M+   D 
Sbjct: 13  REALEKDIKT-SYIMDHMISNGVLSVIEEEKVKSQATQY------QRAAALIKMILNKDN 65

Query: 86  FATEAFRRKLL------LLEQADRQPTATARLRYGRVQERPLSTP-SLVDEEEV------ 132
            A  +F   LL      L           +            S   +++ E  V      
Sbjct: 66  CAYISFYNALLHEGYKDLAALLQSGLPLVSSSSGKDTDGGITSFVRTVLCEGGVPQRPVI 125

Query: 133 -YGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK------ 185
              R+K    I   L    LN  PG+  + I GM G GK+ LA     D  + +      
Sbjct: 126 FVTRKKLVHAIQQKLW--KLNGEPGW--VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGG 181

Query: 186 -YFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQ----LQLENQLKNKKFLLV 240
            ++        S     +    + L      +    LN+ +    L++    K+ + LL+
Sbjct: 182 VHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLI 241

Query: 241 LDDMWSENY 249
           LDD+W    
Sbjct: 242 LDDVWDPWV 250

>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 = 46.0 bits (109), Expect = 7e-07
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 13 VEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEKQI--TKPLTKKWLG 70
          +  L+ KL   + + F   + ++ +++   + L  +   L    E          K W  
Sbjct: 3  ISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWAD 62

Query: 71 KLQNLAYDAEDMLDEF 86
          +++ L+Y  ED++D+F
Sbjct: 63 EVRELSYVIEDVVDKF 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	261
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.85
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.73
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.7
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.65
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.6
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.22
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.12
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.1
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.06
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.99
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.93
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.84
2fna_A	357	Conserved hypothetical protein; structural genomic	98.75
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.67
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.6
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.49
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.44
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.28
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.24
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.24
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.11
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.1
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.07
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.06
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.03
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.98
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.98
3pvs_A	447	Replication-associated recombination protein A; ma	97.98
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.97
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.96
3co5_A	143	Putative two-component system transcriptional RES	97.94
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.92
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.92
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.86
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.84
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.83
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.83
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.8
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.78
3bos_A	242	Putative DNA replication factor; P-loop containing	97.73
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.73
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.7
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.69
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.67
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.66
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.63
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.6
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.6
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.59
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.56
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.55
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.54
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.53
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.53
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.51
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.51
2qgz_A	308	Helicase loader, putative primosome component; str	97.51
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.47
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.46
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.45
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.43
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.42
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.38
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.37
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.35
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.35
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.33
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.3
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.28
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.26
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.25
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.22
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.17
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.15
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.15
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.12
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.12
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.12
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.11
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.05
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.05
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.99
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.94
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.93
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	96.92
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.92
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.92
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.91
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.91
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.91
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.9
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.88
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.87
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.83
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	96.81
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.81
3io5_A	333	Recombination and repair protein; storage dimer, i	96.8
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.79
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.79
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.79
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	96.75
2xxa_A	433	Signal recognition particle protein; protein trans	96.73
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.73
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.71
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.71
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.71
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.7
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.7
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.66
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.64
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.63
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.62
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.62
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.62
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.58
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.58
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.58
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.56
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.56
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.55
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.55
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.54
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.54
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.53
3ice_A	422	Transcription termination factor RHO; transcriptio	96.52
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.52
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	96.52
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.51
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.51
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.49
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.49
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.48
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.48
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.48
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.47
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.46
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.46
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.45
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.44
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.44
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.44
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.42
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.4
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.4
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	96.39
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.39
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.38
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.38
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.36
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.36
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.35
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.35
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.34
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.34
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.32
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.32
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.31
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.3
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.3
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.29
1via_A	175	Shikimate kinase; structural genomics, transferase	96.28
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.28
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.28
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.27
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.26
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	96.26
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	96.25
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.25
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	96.25
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.25
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.24
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.23
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.23
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.22
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.22
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.21
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.2
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.18
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.17
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.17
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.15
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.15
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	96.15
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.14
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.13
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.13
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.13
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.1
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.09
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.08
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.08
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	96.05
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.05
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.04
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.03
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	96.02
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	96.02
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	96.01
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.01
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.0
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.99
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.98
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.97
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.97
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.95
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	95.95
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	95.95
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.93
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	95.93
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.92
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.91
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.9
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.87
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.87
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.86
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.85
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.85
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.84
2og2_A	359	Putative signal recognition particle receptor; nuc	95.84
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.82
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	95.8
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	95.78
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.77
1b0u_A	262	Histidine permease; ABC transporter, transport pro	95.76
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.75
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	95.73
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.73
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.72
1ji0_A	240	ABC transporter; ATP binding protein, structural g	95.71
1g6h_A	257	High-affinity branched-chain amino acid transport	95.7
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.69
2ged_A	193	SR-beta, signal recognition particle receptor beta	95.68
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.66
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.66
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	95.66
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.65
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	95.65
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	95.64
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	95.64
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	95.63
1sgw_A	214	Putative ABC transporter; structural genomics, P p	95.62
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	95.62
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.61
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	95.61
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.6
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	95.57
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.57
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.56
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	95.55
2ghi_A	260	Transport protein; multidrug resistance protein, M	95.54
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.53
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.52
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.51
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.5
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.5
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	95.5
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	95.49
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	95.49
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	95.49
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	95.48
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	95.48
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.48
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	95.48
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.47
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	95.46
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	95.46
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.45
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.45
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	95.44
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.4
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.4
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.38
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.35
3end_A	307	Light-independent protochlorophyllide reductase ir	95.34
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.33
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.32
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.31
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	95.3
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.29
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.27
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	95.26
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	95.22
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	95.15
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	95.15
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	95.15
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	95.14
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.13
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	95.13
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	95.09
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	95.09
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	95.08
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.08
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	95.07
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.07
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	95.06
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	95.06
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.02
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.01
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	95.0
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.0
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.99
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	94.98
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.96
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	94.93
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.93
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	94.93
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.93
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	94.91
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.88
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.87
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	94.86
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	94.84
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	94.81
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.79
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	94.78
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.77
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	94.77
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	94.72
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.7
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	94.67
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	94.63
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.63
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.61
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	94.6
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.59
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	94.58
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.57
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	94.56
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.55
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	94.55
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	94.54
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	94.54
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	94.54
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	94.53
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	94.52
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.49
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	94.49
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	94.49
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.48
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	94.48
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	94.47
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	94.47
1nrj_B	218	SR-beta, signal recognition particle receptor beta	94.47
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	94.46
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	94.46
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.45
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	94.44
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	94.43
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	94.43
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	94.41
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	94.4
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	94.4
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	94.39
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	94.39
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.37
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.37
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	94.36
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	94.35
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	94.35
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.33
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.33
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.32
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	94.32
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	94.3
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	94.3
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	94.29
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	94.28
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	94.23
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.22
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	94.21
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	94.21
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	94.2
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	94.2
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.19
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	94.19
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	94.18
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.17
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	94.12
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	94.11
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	94.11
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	94.11
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	94.1
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.09
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	94.09
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	94.07
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	94.06
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	94.03
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	94.0
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	93.99
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.97
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.96
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.96
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.96
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	93.94
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	93.94
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	93.93
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	93.93
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	93.92
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	93.92
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.9
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	93.9
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	93.89
1p9r_A	418	General secretion pathway protein E; bacterial typ	93.89
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	93.88
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.88
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	93.83
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	93.83
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	93.83
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	93.8
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	93.79
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.77
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	93.76
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.75
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	93.74
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	93.74
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	93.74
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	93.71
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	93.71
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.7
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	93.69
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	93.69
3llu_A	196	RAS-related GTP-binding protein C; structural geno	93.69
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	93.69
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.67
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	93.66
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	93.66
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	93.65
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	93.64
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	93.64
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	93.64
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.63
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	93.63
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	93.62
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	93.61
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	93.6
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	93.59
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	93.59
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	93.58
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	93.58
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	93.57
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	93.55
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.54
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	93.52
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.52
2fh5_B	214	SR-beta, signal recognition particle receptor beta	93.51
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.5
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	93.5
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	93.47
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	93.47
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.46
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	93.45
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	93.45
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	93.43
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	93.43
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	93.42
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	93.42
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	93.42
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.41
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.4
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	93.39
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	93.39
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	93.37
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	93.37
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	93.36
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	93.33
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	93.32
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	93.32
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	93.31
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	93.29
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	93.23
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	93.21
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.21
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	93.18
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	93.16
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.13
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	93.13
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	93.12
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	93.08
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	93.07
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	93.03
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	93.0
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	92.99
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	92.98
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	92.97
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	92.95
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	92.89
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	92.89
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	92.88
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	92.86
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	92.83
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	92.81
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	92.79
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	92.78
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	92.78
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	92.76
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	92.71
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	92.68
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	92.67
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	92.65

>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=99.85  E-value=4.9e-21  Score=176.79  Aligned_cols=119  Identities=18%  Similarity=0.178  Sum_probs=99.9

Q ss_pred             ccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhh--ccccccccceeEEEeeCCCC--CHHHHHHHH
Q 041190          133 YGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFN--DAGVKKYFSFRACAYVSEDF--DAVGVTKVI  208 (261)
Q Consensus       133 ~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~--~~~~~~~f~~~~wv~v~~~~--~~~~i~~~i  208 (261)
                      +||+.++++|.++|...   .+...++|+|+||||+||||||+++|+  +.+++.+|+.++||++++.+  +...++..|
T Consensus       131 ~GR~~~~~~l~~~L~~~---~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~i  207 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM---CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDI  207 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH---TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcc---cCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHH
Confidence            59999999999999764   234689999999999999999999998  67788999999999999985  789999999


Q ss_pred             HHHhcCCC--------CCCCHHHHHHHHHHHhCCC-eEEEEEeCCCCCChhhHHH
Q 041190          209 LQAAAGSA--------DVNDLNLLQLQLENQLKNK-KFLLVLDDMWSENYDVWTN  254 (261)
Q Consensus       209 ~~~l~~~~--------~~~~~~~~~~~l~~~l~~k-r~LiVlDdvw~~~~~~w~~  254 (261)
                      +.+++...        +..+...+...+++.|.++ ||||||||||+.+...|..
T Consensus       208 l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~~~~~  262 (549)
T 2a5y_B          208 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQ  262 (549)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHH
T ss_pred             HHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhhcccc
Confidence            99998321        1234567889999999996 9999999999974334543

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.73  E-value=9.5e-18  Score=122.83  Aligned_cols=81  Identities=19%  Similarity=0.310  Sum_probs=75.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhc--cccChhHHHHHHHHHHHHhhhHhHHHHHHHH
Q 041190           12 TVEMLVEKLALEVIQLFARQEQIEADLKKWEELLVIIKVVLDDAEEK--QITKPLTKKWLGKLQNLAYDAEDMLDEFATE   89 (261)
Q Consensus        12 ~v~~l~~~l~~~~~~~~~~~~~v~~~i~~L~~~l~~i~~~l~~a~~~--~~~~~~~~~wl~~lr~~ayd~ed~ld~~~~~   89 (261)
                      +++++++||.+++.+++..+.+|+++++.|+++|+.|++||.+++..  +..++.++.|+.+||+++||+||+||+|.++
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            45678999999999999999999999999999999999999999987  4578999999999999999999999999998


Q ss_pred             HHH
Q 041190           90 AFR   92 (261)
Q Consensus        90 ~~~   92 (261)
                      ...
T Consensus        82 ~~~   84 (115)
T 3qfl_A           82 VDG   84 (115)
T ss_dssp             HHH
T ss_pred             hcc
Confidence            853

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.70  E-value=3.4e-17  Score=157.30  Aligned_cols=118  Identities=19%  Similarity=0.123  Sum_probs=95.0

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccce-eEEEeeCCCCCHHHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSF-RACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~i~~~i~  209 (261)
                      ..+||+.+++.|.++|...+     ..++|+|+||||+||||||+.+|++.+++.+|+. ++|+++++.++...++..|+
T Consensus       129 ~~VGRe~eLeeL~elL~~~d-----~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll  203 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLELR-----PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ  203 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHCC-----SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhccC-----CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHH
Confidence            34999999999999997532     3689999999999999999999998778889997 78999999999888888888


Q ss_pred             HHhc--C-C-CCC--------CCHHHHHHHHHHHh---CCCeEEEEEeCCCCCChhhHHHh
Q 041190          210 QAAA--G-S-ADV--------NDLNLLQLQLENQL---KNKKFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       210 ~~l~--~-~-~~~--------~~~~~~~~~l~~~l---~~kr~LiVlDdvw~~~~~~w~~l  255 (261)
                      ..++  . . ...        .+.+.+...++..|   .+||+||||||||+.  +.|+.+
T Consensus       204 ~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~--eqLe~f  262 (1221)
T 1vt4_I          204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA--KAWNAF  262 (1221)
T ss_dssp             HHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCH--HHHHHH
T ss_pred             HHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChH--HHHHhh
Confidence            7654  1 1 111        12345566777766   789999999999995  578765

>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=99.65  E-value=3.6e-16  Score=155.81  Aligned_cols=123  Identities=20%  Similarity=0.148  Sum_probs=95.4

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc-ccccc-eeEEEeeCCCCC--HH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV-KKYFS-FRACAYVSEDFD--AV  202 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~-~~~f~-~~~wv~v~~~~~--~~  202 (261)
                      .....++||+.++++|.++|...    +...++|+|+||||+||||||+++|++.+. ..+|. ...|+++++..+  ..
T Consensus       121 ~~~~~~vgR~~~~~~l~~~l~~~----~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~  196 (1249)
T 3sfz_A          121 QRPVIFVTRKKLVHAIQQKLWKL----NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLL  196 (1249)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHTT----TTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHH
T ss_pred             CCCceeccHHHHHHHHHHHHhhc----cCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHH
Confidence            34567999999999999999753    246789999999999999999999998543 44564 567999998543  34


Q ss_pred             HHHHHHHHHhcCC-----CCCCCHHHHHHHHHHHhCCC--eEEEEEeCCCCCChhhHHHh
Q 041190          203 GVTKVILQAAAGS-----ADVNDLNLLQLQLENQLKNK--KFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       203 ~i~~~i~~~l~~~-----~~~~~~~~~~~~l~~~l~~k--r~LiVlDdvw~~~~~~w~~l  255 (261)
                      ..+..++..+...     ....+.+.+...++..+.++  ||||||||||+.  +.|..+
T Consensus       197 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~--~~~~~~  254 (1249)
T 3sfz_A          197 MKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP--WVLKAF  254 (1249)
T ss_dssp             HHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCH--HHHTTT
T ss_pred             HHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCH--HHHHhh
Confidence            4466677777621     23456788899999999887  999999999986  466544

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.60  E-value=2.3e-15  Score=139.82  Aligned_cols=115  Identities=21%  Similarity=0.204  Sum_probs=88.3

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc-ccccc-eeEEEeeCCCCCHHHHH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV-KKYFS-FRACAYVSEDFDAVGVT  205 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~-~~~f~-~~~wv~v~~~~~~~~i~  205 (261)
                      .++.++||+.+++.|.++|...    ....++++|+||||+||||||+.+|++..+ ..+|. .++|+++++. +...++
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~----~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~  196 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKL----KGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLL  196 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTS----TTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHH
T ss_pred             CCCeecccHHHHHHHHHHHhcc----cCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHH
Confidence            4567999999999999999753    235789999999999999999999998655 67894 7899999875 344444


Q ss_pred             HHHH---HHhcC-----CCCCCCHHHHHHHHHHHhCC--CeEEEEEeCCCCC
Q 041190          206 KVIL---QAAAG-----SADVNDLNLLQLQLENQLKN--KKFLLVLDDMWSE  247 (261)
Q Consensus       206 ~~i~---~~l~~-----~~~~~~~~~~~~~l~~~l~~--kr~LiVlDdvw~~  247 (261)
                      ..+.   ..++.     .....+...+...++..+.+  +++||||||||+.
T Consensus       197 ~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~  248 (591)
T 1z6t_A          197 MKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS  248 (591)
T ss_dssp             HHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH
T ss_pred             HHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH
Confidence            4443   34431     12345667788888888865  7899999999985

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.22  E-value=3.7e-11  Score=106.23  Aligned_cols=119  Identities=18%  Similarity=0.125  Sum_probs=84.8

Q ss_pred             CCCccccccchHHHHHHHh-hCCCCCC-CCCceEEeE--eecCCCChHHHHHHHhhccccc---cccc-eeEEEeeCCCC
Q 041190          128 DEEEVYGREKDKEVIVGLL-LGDDLNS-GPGFSVIPI--TGMGGLGKTTLAQLVFNDAGVK---KYFS-FRACAYVSEDF  199 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L-~~~~~~~-~~~~~vi~I--~G~~GiGKTtLa~~v~~~~~~~---~~f~-~~~wv~v~~~~  199 (261)
                      .+..++||+.+++.|.++| ..... + ......+.|  +|++|+|||||++.+++.....   ..|. ..+|+++.+..
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~-~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLS-GAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAP   98 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHT-SSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCC
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhc-CCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCC
Confidence            3467999999999999988 43110 0 012345555  9999999999999999873221   1123 24688877777


Q ss_pred             CHHHHHHHHHHHhcCC-C-CCCCHHHHHHHHHHHhC--CCeEEEEEeCCCCC
Q 041190          200 DAVGVTKVILQAAAGS-A-DVNDLNLLQLQLENQLK--NKKFLLVLDDMWSE  247 (261)
Q Consensus       200 ~~~~i~~~i~~~l~~~-~-~~~~~~~~~~~l~~~l~--~kr~LiVlDdvw~~  247 (261)
                      +...++..++..++.. . ...+...+...+.+.+.  +++++|||||+|..
T Consensus        99 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l  150 (412)
T 1w5s_A           99 NLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSM  150 (412)
T ss_dssp             SHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHH
Confidence            8889999999998832 1 23345666667777664  78999999999884

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.12  E-value=5.7e-10  Score=97.51  Aligned_cols=119  Identities=18%  Similarity=0.122  Sum_probs=87.9

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc---ccc-eeEEEeeCCCCCHHH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK---YFS-FRACAYVSEDFDAVG  203 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~---~f~-~~~wv~v~~~~~~~~  203 (261)
                      .+..++||+.+++.+..+|...-  .....+.+.|+|++|+||||+|+.+++......   ... ..+|+++....+...
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~--~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   94 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPAL--RGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYR   94 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGT--SSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHH--cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHH
Confidence            34779999999999999885531  123456889999999999999999998632110   112 356888888888899


Q ss_pred             HHHHHHHHhcCC--CCCCCHHHHHHHHHHHh--CCCeEEEEEeCCCCCC
Q 041190          204 VTKVILQAAAGS--ADVNDLNLLQLQLENQL--KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       204 i~~~i~~~l~~~--~~~~~~~~~~~~l~~~l--~~kr~LiVlDdvw~~~  248 (261)
                      ++..++..++..  ....+...+...+...+  .+++.+|||||+....
T Consensus        95 ~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~  143 (387)
T 2v1u_A           95 VASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLP  143 (387)
T ss_dssp             HHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHH
T ss_pred             HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhc
Confidence            999999999832  23344666677777777  4568999999998763

>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=99.10  E-value=6e-10  Score=97.62  Aligned_cols=129  Identities=16%  Similarity=0.077  Sum_probs=90.9

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      .+..++||+.+++.|..++........+..+.+.|+|++|+|||||++.+++....... -..+|++++...+...++..
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~   93 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGE   93 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHH
Confidence            34679999999999999886521001122348999999999999999999987322111 13567888887788899999


Q ss_pred             HHHHhcCC--CCCCCHHHHHHHHHHHhC--CCeEEEEEeCCCCCChhhHHHhhc
Q 041190          208 ILQAAAGS--ADVNDLNLLQLQLENQLK--NKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       208 i~~~l~~~--~~~~~~~~~~~~l~~~l~--~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      ++..++..  ....+...+...+...+.  +++.+|+|||+...++.....|..
T Consensus        94 l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~  147 (389)
T 1fnn_A           94 IARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIR  147 (389)
T ss_dssp             HHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHH
T ss_pred             HHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHH
Confidence            99888732  123345566666666653  678999999999886555555543

>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=99.06  E-value=3.6e-10  Score=99.00  Aligned_cols=118  Identities=15%  Similarity=0.022  Sum_probs=86.4

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc----ccc--ceeEEEeeCCCC-CH
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK----KYF--SFRACAYVSEDF-DA  201 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f--~~~~wv~v~~~~-~~  201 (261)
                      +..++||+.+++.+.++|....  .+...+.+.|+|++|+||||||+.+++...-.    ..+  ...+|++++... +.
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~--~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   96 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFV--KNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTP   96 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHH--TTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCH
T ss_pred             CCCCCChHHHHHHHHHHHHHHH--cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCH
Confidence            4779999999999998876521  12345689999999999999999999863111    112  235688877766 88


Q ss_pred             HHHHHHHHHHhc-C--CCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCC
Q 041190          202 VGVTKVILQAAA-G--SADVNDLNLLQLQLENQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       202 ~~i~~~i~~~l~-~--~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~  248 (261)
                      ..++..++..+. .  .....+...+...+...+..++.+|||||++...
T Consensus        97 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~  146 (384)
T 2qby_B           97 QAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLV  146 (384)
T ss_dssp             HHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHH
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhc
Confidence            888999998884 2  1223445667778888888777799999997753

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.99  E-value=4.3e-10  Score=98.18  Aligned_cols=117  Identities=19%  Similarity=0.146  Sum_probs=83.4

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccccc---ceeEEEeeCCCCCHHH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF---SFRACAYVSEDFDAVG  203 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f---~~~~wv~v~~~~~~~~  203 (261)
                      ..+..++||+.+++.|.+++...-  .......+.|+|++|+|||||++.+++..  ...+   ...+|++++...+...
T Consensus        17 ~~p~~~~gr~~e~~~l~~~l~~~~--~~~~~~~vli~G~~G~GKTtl~~~l~~~~--~~~~~~~~~~~~i~~~~~~~~~~   92 (386)
T 2qby_A           17 YIPDELPHREDQIRKIASILAPLY--REEKPNNIFIYGLTGTGKTAVVKFVLSKL--HKKFLGKFKHVYINTRQIDTPYR   92 (386)
T ss_dssp             CCCSCCTTCHHHHHHHHHSSGGGG--GTCCCCCEEEEECTTSSHHHHHHHHHHHH--HHHTCSSCEEEEEEHHHHCSHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHH--cCCCCCeEEEECCCCCCHHHHHHHHHHHH--HHHhcCCceEEEEECCCCCCHHH
Confidence            344779999999999999887421  12345688999999999999999999863  2222   1356787777667777


Q ss_pred             HHHHHHHHhcCC--CCCCCHHHHHHHHHHHhC--CCeEEEEEeCCCCC
Q 041190          204 VTKVILQAAAGS--ADVNDLNLLQLQLENQLK--NKKFLLVLDDMWSE  247 (261)
Q Consensus       204 i~~~i~~~l~~~--~~~~~~~~~~~~l~~~l~--~kr~LiVlDdvw~~  247 (261)
                      ++..++..++..  ....+...+...+.+.+.  +++.+|||||++..
T Consensus        93 ~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l  140 (386)
T 2qby_A           93 VLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAF  140 (386)
T ss_dssp             HHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHH
T ss_pred             HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhh
Confidence            888887777622  123345565666666663  45899999999774

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.93  E-value=1.9e-09  Score=92.83  Aligned_cols=106  Identities=14%  Similarity=0.216  Sum_probs=74.8

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC------CH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF------DA  201 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~------~~  201 (261)
                      .+..++||+.+.+.|.+++...        +++.|+|++|+|||||++.+++..      . .+|+++....      +.
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            4467999999999999988541        689999999999999999998863      1 5677665432      45


Q ss_pred             HHHHHHHHHHhcC-----------------C--CCCCCHHHHHHHHHHHhCC-CeEEEEEeCCCCCC
Q 041190          202 VGVTKVILQAAAG-----------------S--ADVNDLNLLQLQLENQLKN-KKFLLVLDDMWSEN  248 (261)
Q Consensus       202 ~~i~~~i~~~l~~-----------------~--~~~~~~~~~~~~l~~~l~~-kr~LiVlDdvw~~~  248 (261)
                      ..++..+...+..                 .  ....+..++...+.+.... ++++|||||++...
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~  141 (350)
T 2qen_A           75 EELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLR  141 (350)
T ss_dssp             HHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGG
T ss_pred             HHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHh
Confidence            5666666554431                 0  0123556666666665543 38999999998853

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.84  E-value=7.3e-09  Score=88.57  Aligned_cols=116  Identities=14%  Similarity=-0.011  Sum_probs=79.4

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc---cc-c-eeEEEeeCCCCCHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK---YF-S-FRACAYVSEDFDAVGVT  205 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~---~f-~-~~~wv~v~~~~~~~~i~  205 (261)
                      .+.||+++.+.|...|...-  .+...+.+.|+|++|+|||++++.|.+......   .. . ..+++++....+...++
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i--~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~   98 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSL--MSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALY   98 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH--HTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHh--cCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHH
Confidence            38899999999998887632  134567889999999999999999998743211   11 1 34678887878888999


Q ss_pred             HHHHHHhcCC-C-CCCCHHHHHHHHHHH--hCCCeEEEEEeCCCCCC
Q 041190          206 KVILQAAAGS-A-DVNDLNLLQLQLENQ--LKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       206 ~~i~~~l~~~-~-~~~~~~~~~~~l~~~--l~~kr~LiVlDdvw~~~  248 (261)
                      ..|++++... . .......+...+...  -.+++++|+||++....
T Consensus        99 ~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~  145 (318)
T 3te6_A           99 EKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL  145 (318)
T ss_dssp             HHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC
T ss_pred             HHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh
Confidence            9999999622 2 222333333333322  24678999999998864

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.75  E-value=3.1e-08  Score=85.41  Aligned_cols=104  Identities=16%  Similarity=0.217  Sum_probs=69.3

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-----CCHH
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-----FDAV  202 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-----~~~~  202 (261)
                      .+..++||+.+.+.|.+ +..         +++.|+|++|+|||+|++.+.+...  .   ..+|+++...     .+..
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            45679999999999999 631         5899999999999999999998632  1   2467776642     2444


Q ss_pred             HHHHHHHHHhc-------------CC------C-----------CCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          203 GVTKVILQAAA-------------GS------A-----------DVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       203 ~i~~~i~~~l~-------------~~------~-----------~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      .++..+.+.+.             ..      .           .......+...+.+.-. ++++|||||+...
T Consensus        76 ~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~  149 (357)
T 2fna_A           76 DFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQEL  149 (357)
T ss_dssp             HHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGG
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHh
Confidence            44444444331             00      0           12344555555554433 4999999999774

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.67  E-value=1.4e-07  Score=75.38  Aligned_cols=107  Identities=18%  Similarity=0.111  Sum_probs=65.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccc-eeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS-FRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~i~~~i  208 (261)
                      ..++|++..++.+.+++...      ....+.|+|++|+|||++|+.+++.... ..+. ....++.+...+...+... 
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~------~~~~~ll~G~~G~GKT~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-   88 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERK------NIPHLLFSGPPGTGKTATAIALARDLFG-ENWRDNFIEMNASDERGIDVVRHK-   88 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT------CCCCEEEECSTTSSHHHHHHHHHHHHHG-GGGGGGEEEEETTCTTCHHHHHHH-
T ss_pred             HHHcCcHHHHHHHHHHHhCC------CCCeEEEECCCCCCHHHHHHHHHHHHhc-cccccceEEeccccccChHHHHHH-
Confidence            46899999999999999753      2234899999999999999999876311 1222 2233444443333332222 


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      +..+....             ....+++.+|||||+.......++.+..
T Consensus        89 ~~~~~~~~-------------~~~~~~~~vliiDe~~~l~~~~~~~l~~  124 (226)
T 2chg_A           89 IKEFARTA-------------PIGGAPFKIIFLDEADALTADAQAALRR  124 (226)
T ss_dssp             HHHHHTSC-------------CSTTCSCEEEEEETGGGSCHHHHHHHHH
T ss_pred             HHHHhccc-------------CCCccCceEEEEeChhhcCHHHHHHHHH
Confidence            22111000             0113578899999998886555555543

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.60  E-value=1.6e-07  Score=75.93  Aligned_cols=47  Identities=23%  Similarity=0.288  Sum_probs=39.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|++..++.|..++....     ..+.+.|+|++|+||||||+.+++..
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~-----~~~~~ll~G~~G~GKT~l~~~~~~~~   69 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR-----IHHAYLFSGTRGVGKTSIARLLAKGL   69 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC-----CCSEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999999997532     23588999999999999999998763

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.49  E-value=1.9e-07  Score=72.88  Aligned_cols=45  Identities=20%  Similarity=0.298  Sum_probs=38.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|++..++.+.+.+...      ....+.|+|++|+|||+||+.+.+.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~------~~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRR------TKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS------SSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcC------CCCceEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999998653      2356789999999999999999876

>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=98.44  E-value=3.9e-07  Score=77.48  Aligned_cols=107  Identities=17%  Similarity=0.169  Sum_probs=66.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccc-eeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS-FRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~i~~~i  208 (261)
                      ..++|++..++.|..++...      +.+.+.++|++|+||||+|+.+++.... ..+. ..++++.+...+... .+++
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~------~~~~~ll~G~~G~GKt~la~~l~~~l~~-~~~~~~~~~~~~~~~~~~~~-i~~~   92 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDG------NMPHMIISGMPGIGKTTSVHCLAHELLG-RSYADGVLELNASDDRGIDV-VRNQ   92 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC------CCCCEEEECSTTSSHHHHHHHHHHHHHG-GGHHHHEEEECTTSCCSHHH-HHTH
T ss_pred             HHHHCCHHHHHHHHHHHHcC------CCCeEEEECcCCCCHHHHHHHHHHHhcC-CcccCCEEEecCccccChHH-HHHH
Confidence            46899999999999998653      2233889999999999999999876311 1121 233444444333222 2223


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHh-CCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQL-KNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l-~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      +..+....             ..+ .+++.+|||||++......++.|..
T Consensus        93 ~~~~~~~~-------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~  129 (323)
T 1sxj_B           93 IKHFAQKK-------------LHLPPGKHKIVILDEADSMTAGAQQALRR  129 (323)
T ss_dssp             HHHHHHBC-------------CCCCTTCCEEEEEESGGGSCHHHHHTTHH
T ss_pred             HHHHHhcc-------------ccCCCCCceEEEEECcccCCHHHHHHHHH
Confidence            33222000             011 4568999999999876555655543

>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=98.28  E-value=1.5e-06  Score=73.93  Aligned_cols=107  Identities=14%  Similarity=0.072  Sum_probs=63.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccc-eeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS-FRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~i~~~i  208 (261)
                      .+++|++..++.+..++...      ....+.++|++|+||||+|+.+++..... .+. ....++.+...+... +...
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~------~~~~~ll~G~~G~GKT~la~~l~~~l~~~-~~~~~~~~~~~~~~~~~~~-~~~~   96 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTG------SMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINV-IREK   96 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT------CCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHT-THHH
T ss_pred             HHhhCCHHHHHHHHHHHHcC------CCCeEEEECcCCCCHHHHHHHHHHHhcCC-cccCceEEeeccccCchHH-HHHH
Confidence            45899999999999998753      23348999999999999999998862111 111 123344333211111 1111


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      +..+...             .....+++.+||+||+.....+.++.|..
T Consensus        97 ~~~~~~~-------------~~~~~~~~~vliiDe~~~l~~~~~~~L~~  132 (327)
T 1iqp_A           97 VKEFART-------------KPIGGASFKIIFLDEADALTQDAQQALRR  132 (327)
T ss_dssp             HHHHHHS-------------CCGGGCSCEEEEEETGGGSCHHHHHHHHH
T ss_pred             HHHHHhh-------------CCcCCCCCeEEEEeCCCcCCHHHHHHHHH
Confidence            1111100             00112578899999998887666665543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.24  E-value=1.6e-06  Score=68.85  Aligned_cols=96  Identities=19%  Similarity=0.220  Sum_probs=51.0

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCC
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSAD  217 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~  217 (261)
                      ..+.+..++....  .......+.|+|++|+|||+||+.+++...  .......+++++      .+...+...+.    
T Consensus        37 ~~~~~~~~~~~~~--~~~~~~~~~l~G~~GtGKT~la~~i~~~~~--~~~~~~~~~~~~------~~~~~~~~~~~----  102 (202)
T 2w58_A           37 AIRFAERFVAEYE--PGKKMKGLYLHGSFGVGKTYLLAAIANELA--KRNVSSLIVYVP------ELFRELKHSLQ----  102 (202)
T ss_dssp             HHHHHHHHHHHCC--SSCCCCEEEEECSTTSSHHHHHHHHHHHHH--TTTCCEEEEEHH------HHHHHHHHC------
T ss_pred             HHHHHHHHHHHhh--hccCCCeEEEECCCCCCHHHHHHHHHHHHH--HcCCeEEEEEhH------HHHHHHHHHhc----
Confidence            4455566665432  111226789999999999999999998732  222234555543      33333332221    


Q ss_pred             CCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhH
Q 041190          218 VNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVW  252 (261)
Q Consensus       218 ~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w  252 (261)
                      ..........+..     .-+|||||++......|
T Consensus       103 ~~~~~~~~~~~~~-----~~~lilDei~~~~~~~~  132 (202)
T 2w58_A          103 DQTMNEKLDYIKK-----VPVLMLDDLGAEAMSSW  132 (202)
T ss_dssp             -CCCHHHHHHHHH-----SSEEEEEEECCC---CC
T ss_pred             cchHHHHHHHhcC-----CCEEEEcCCCCCcCCHH
Confidence            1122333333322     23999999977543333

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.24  E-value=1e-06  Score=68.45  Aligned_cols=45  Identities=20%  Similarity=0.254  Sum_probs=38.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|++...+.+.+.+...      ....+.|+|++|+|||+||+.+.+.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~------~~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRR------TKNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS------SSCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCC------CCCceEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999998653      2356689999999999999999876

>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=98.11  E-value=1e-05  Score=62.97  Aligned_cols=93  Identities=19%  Similarity=0.115  Sum_probs=50.7

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG  214 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~  214 (261)
                      .....+.+.+++..-.   .+....+.++|++|+|||||++.+++.......+. ..++      +..++...+......
T Consensus        19 ~~~~~~~~~~~~~~~~---~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~-~~~~------~~~~~~~~~~~~~~~   88 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFN---PEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR-GYFF------DTKDLIFRLKHLMDE   88 (180)
T ss_dssp             HHHHHHHHHHHHHSCC---GGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC-CCEE------EHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcc---ccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe-EEEE------EHHHHHHHHHHHhcC
Confidence            3444555555554321   12346889999999999999999988632111221 2233      344445444444431


Q ss_pred             CCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          215 SADVNDLNLLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       215 ~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                      ....    .....+    . +.-+|||||++.
T Consensus        89 ~~~~----~~~~~~----~-~~~llilDE~~~  111 (180)
T 3ec2_A           89 GKDT----KFLKTV----L-NSPVLVLDDLGS  111 (180)
T ss_dssp             TCCS----HHHHHH----H-TCSEEEEETCSS
T ss_pred             chHH----HHHHHh----c-CCCEEEEeCCCC
Confidence            1111    222222    1 456889999984

>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=98.10  E-value=2.6e-06  Score=72.63  Aligned_cols=50  Identities=28%  Similarity=0.377  Sum_probs=38.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|++..+..+..++..... .......+.|+|++|+|||++|+.+++.
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            5689999998888888753110 0123356889999999999999999886

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.07  E-value=6.5e-06  Score=62.02  Aligned_cols=46  Identities=20%  Similarity=0.081  Sum_probs=35.0

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|+......+.+.+..-.    .....|.|+|++|+|||++|+.+++.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a----~~~~~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLS----ETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHT----TCCSCEEEESSTTSSHHHHHHHHHHS
T ss_pred             CceeCCHHHHHHHHHHHHHh----CCCCCEEEECCCCCCHHHHHHHHHHh
Confidence            47899989999888875422    12234789999999999999999876

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.06  E-value=9.8e-06  Score=67.77  Aligned_cols=54  Identities=28%  Similarity=0.172  Sum_probs=39.8

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-.+++|.+..++.|.+.+...-..       +......+.|+|++|+|||+||+.+.+.
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            34457899999999998877431000       0123456899999999999999999886

>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=98.04  E-value=1.5e-05  Score=65.70  Aligned_cols=51  Identities=22%  Similarity=0.138  Sum_probs=35.6

Q ss_pred             CccccccchHHHHHHHhhC---CCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG---DDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~---~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+++..   ...   -+....+.+.++|++|+|||++|+.+.+.
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            4688988887777665432   110   01123456789999999999999999886

>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=98.03  E-value=1.3e-05  Score=67.78  Aligned_cols=105  Identities=15%  Similarity=0.116  Sum_probs=62.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccc-eeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS-FRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~i~~~i  208 (261)
                      .+++|++..++.+.+++...      ....+.++|++|+|||++|+.+.+... ...+. ....++.+...+...     
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~------~~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~~~-----   84 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERK------NIPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDV-----   84 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTT------CCCCEEEESSSSSSHHHHHHHHHHHHH-TTCHHHHCEEEETTSTTCTTT-----
T ss_pred             HHHhCCHHHHHHHHHHHhCC------CCCeEEEECcCCcCHHHHHHHHHHHhc-CCcccCCeEEEeCccccChHH-----
Confidence            45899999999998888543      233389999999999999999987621 11111 123344433211111     


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHH--h-CCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQ--L-KNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~--l-~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                                  .......+...  + .+++.+||+||+.....+.++.|...
T Consensus        85 ------------~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~  125 (319)
T 2chq_A           85 ------------VRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRT  125 (319)
T ss_dssp             ------------SSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGG
T ss_pred             ------------HHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHH
Confidence                        11111111101  1 25688999999988765555555543

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=97.98  E-value=2e-05  Score=68.28  Aligned_cols=47  Identities=23%  Similarity=0.288  Sum_probs=38.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|++..++.|...+....     ..+.+.|+|++|+||||+|+.+.+..
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~-----~~~~~ll~G~~G~GKT~la~~la~~l   62 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR-----IHHAYLFSGTRGVGKTSIARLLAKGL   62 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC-----CCSEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHHhCC-----CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999986532     23578899999999999999998763

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.98  E-value=2.6e-05  Score=67.62  Aligned_cols=49  Identities=18%  Similarity=0.274  Sum_probs=36.4

Q ss_pred             CccccccchHHH---HHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccc
Q 041190          130 EEVYGREKDKEV---IVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       130 ~~~~gr~~~~~~---l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      ..++|++..++.   +.+.+...    ....+.+.++|++|+|||++|+.+.+...
T Consensus        44 ~~ivG~~~~~~~l~~l~~~~~~~----~~~~~~vLl~GppGtGKT~la~~la~~l~   95 (368)
T 3uk6_A           44 QGMVGQLAARRAAGVVLEMIREG----KIAGRAVLIAGQPGTGKTAIAMGMAQALG   95 (368)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTT----CCTTCEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             hhccChHHHHHHHHHHHHHHHcC----CCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            469999888766   44445432    22246889999999999999999998743

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.98  E-value=1.8e-05  Score=70.80  Aligned_cols=97  Identities=15%  Similarity=0.176  Sum_probs=55.8

Q ss_pred             CccccccchH---HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHH
Q 041190          130 EEVYGREKDK---EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVT  205 (261)
Q Consensus       130 ~~~~gr~~~~---~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~  205 (261)
                      ..++|.+..+   ..|...+...      ++..+.++|++|+||||||+.+.+.  ....|     +.++.. ..... +
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~------~~~~vLL~GppGtGKTtlAr~ia~~--~~~~f-----~~l~a~~~~~~~-i   91 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAG------HLHSMILWGPPGTGKTTLAEVIARY--ANADV-----ERISAVTSGVKE-I   91 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHT------CCCEEEEECSTTSSHHHHHHHHHHH--TTCEE-----EEEETTTCCHHH-H
T ss_pred             HHhCCcHHHHhchHHHHHHHHcC------CCcEEEEECCCCCcHHHHHHHHHHH--hCCCe-----EEEEeccCCHHH-H
Confidence            4578877666   6677777543      3467899999999999999999987  32222     222221 22222 2


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHh
Q 041190          206 KVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       206 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l  255 (261)
                      +.++....               .....+++.+|+||++........+.|
T Consensus        92 r~~~~~a~---------------~~~~~~~~~iLfIDEI~~l~~~~q~~L  126 (447)
T 3pvs_A           92 REAIERAR---------------QNRNAGRRTILFVDEVHRFNKSQQDAF  126 (447)
T ss_dssp             HHHHHHHH---------------HHHHTTCCEEEEEETTTCC------CC
T ss_pred             HHHHHHHH---------------HhhhcCCCcEEEEeChhhhCHHHHHHH
Confidence            22222111               111246788999999988754444433

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.97  E-value=3.3e-05  Score=65.84  Aligned_cols=101  Identities=19%  Similarity=0.141  Sum_probs=63.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .+++|.+..++.|.+++....     ..+++.++|++|+|||++|+.+.+...  .   ....++.+.. .. ..++.++
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~-----~~~~~L~~G~~G~GKT~la~~la~~l~--~---~~~~i~~~~~-~~-~~i~~~~   93 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGK-----IPHIILHSPSPGTGKTTVAKALCHDVN--A---DMMFVNGSDC-KI-DFVRGPL   93 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTC-----CCSEEEECSSTTSSHHHHHHHHHHHTT--E---EEEEEETTTC-CH-HHHHTHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-----CCeEEEeeCcCCCCHHHHHHHHHHHhC--C---CEEEEccccc-CH-HHHHHHH
Confidence            468999999999999997532     346788899999999999999988631  1   1334554442 22 2222222


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCC-hhhHHHhh
Q 041190          210 QAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSEN-YDVWTNLC  256 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~-~~~w~~l~  256 (261)
                      .......              .+.+++.+|+|||+.... .+..+.|.
T Consensus        94 ~~~~~~~--------------~~~~~~~vliiDEi~~l~~~~~~~~L~  127 (324)
T 3u61_B           94 TNFASAA--------------SFDGRQKVIVIDEFDRSGLAESQRHLR  127 (324)
T ss_dssp             HHHHHBC--------------CCSSCEEEEEEESCCCGGGHHHHHHHH
T ss_pred             HHHHhhc--------------ccCCCCeEEEEECCcccCcHHHHHHHH
Confidence            2221000              012477899999998875 44444443

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.96  E-value=1.3e-05  Score=68.86  Aligned_cols=51  Identities=25%  Similarity=0.328  Sum_probs=39.6

Q ss_pred             CCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -..++|++..++.+..++..... .......+.|+|++|+|||+||+.+.+.
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~-~~~~~~~vll~G~~GtGKT~la~~ia~~   78 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKK-RNECLDHILFSGPAGLGKTTLANIISYE   78 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHH-TTSCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHh-cCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            34689999999999988865210 1224456899999999999999999876

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.94  E-value=8.1e-06  Score=61.35  Aligned_cols=47  Identities=15%  Similarity=0.099  Sum_probs=33.4

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++|+...+..+.+.+..-.    ....-+.|+|++|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~----~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAA----KRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHH----TCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHh----CCCCcEEEECCCCccHHHHHHHHHHh
Confidence            357899888888888775421    11234779999999999999999876

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.92  E-value=1.8e-05  Score=66.89  Aligned_cols=51  Identities=25%  Similarity=0.127  Sum_probs=36.3

Q ss_pred             ccccccchHHHHHHHhhCC---------CCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          131 EVYGREKDKEVIVGLLLGD---------DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~---------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++|.+..++.|.+++...         ..........+.++|++|+|||++|+.+.+..
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l   91 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLL   91 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4889888888888765421         00012345578999999999999999887653

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.92  E-value=4.6e-05  Score=65.43  Aligned_cols=115  Identities=17%  Similarity=0.089  Sum_probs=63.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccce-eEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSF-RACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~i~~~i  208 (261)
                      ..++|++..++.+..++....      ...+.++|++|+||||+|+.+.+.......+.. ...++.+....... +.+.
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            468999999999999986532      223889999999999999999876321111221 23344444333332 2222


Q ss_pred             HHHhc-CCC-CCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          209 LQAAA-GSA-DVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       209 ~~~l~-~~~-~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      +..+. ... .....     .....-.++.-+|++|++....+.....|.
T Consensus       110 ~~~~~~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll  154 (353)
T 1sxj_D          110 VKNFARLTVSKPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALR  154 (353)
T ss_dssp             HHHHHHSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHH
T ss_pred             HHHHhhhcccccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHH
Confidence            32222 111 00000     001111245568888888777654444443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.86  E-value=8.2e-05  Score=63.63  Aligned_cols=52  Identities=27%  Similarity=0.290  Sum_probs=37.8

Q ss_pred             CCccccccchHHHHHHHhhC----CCC--CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLG----DDL--NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~----~~~--~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|.+..++.|.+.+..    .+.  ......+-+.++|++|+|||+||+.+.+.
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            35688998888888876632    000  01223467889999999999999999986

>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=97.84  E-value=0.00013  Score=58.26  Aligned_cols=87  Identities=17%  Similarity=0.077  Sum_probs=53.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH----------HHHHhc--CCCCCCCHHH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV----------ILQAAA--GSADVNDLNL  223 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~----------i~~~l~--~~~~~~~~~~  223 (261)
                      .-.++.|+|++|+|||||+..+.. .    .-...+|+.....++...+...          ++..+.  ..........
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-~----~~~~v~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-L----SGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFTPSDFKEQRR   93 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-H----HCSEEEEEESSCCCCHHHHHHHHHTTTCCHHHHHHHEEEECCTTTSHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-H----cCCcEEEEECCCCCCHHHHHHHHHhcCCChHHHhhcEEEEecCCHHHHHH
Confidence            446899999999999999999987 1    1124667776654555444331          122222  1112222334


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          224 LQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       224 ~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      ....++..+..+.-+||||.+-..
T Consensus        94 ~~~~~~~l~~~~~~lliiD~~~~~  117 (220)
T 2cvh_A           94 VIGSLKKTVDSNFALVVVDSITAH  117 (220)
T ss_dssp             HHHHHHHHCCTTEEEEEEECCCCC
T ss_pred             HHHHHHHHhhcCCCEEEEcCcHHH
Confidence            555666666556789999998765

>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=5.8e-05  Score=64.49  Aligned_cols=51  Identities=29%  Similarity=0.242  Sum_probs=38.7

Q ss_pred             CCccccccchHHHHHHHhhCC-------CCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGD-------DLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.+..++.|.+.+...       .. .....+-+.++|++|+|||+||+.+.+.
T Consensus        17 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           17 WEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHH
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            356899999999998877210       10 1223457899999999999999999886

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.83  E-value=6.2e-05  Score=63.26  Aligned_cols=52  Identities=19%  Similarity=0.225  Sum_probs=38.3

Q ss_pred             CCccccccchHHHHHHHhhCCC------CCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDD------LNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~------~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.+..++.|.+.+....      ..-....+.+.++|++|+||||+|+.+.+.
T Consensus        20 ~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~   77 (297)
T 3b9p_A           20 WTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE   77 (297)
T ss_dssp             GGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            3468999999999988764310      000113467899999999999999999886

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.80  E-value=7e-05  Score=63.23  Aligned_cols=119  Identities=13%  Similarity=0.102  Sum_probs=66.1

Q ss_pred             ccccccchHHHHHHHhhCCC---CCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      .++|.+..++.+...+....   .........+.++|++|+|||++|+.+.+...  ..-...+.++++...... ....
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~--~~~~~~~~~~~~~~~~~~-~~~~   94 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF--DTEEAMIRIDMTEYMEKH-AVSR   94 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHH--SCGGGEEEEEGGGCCSTT-HHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHc--CCCcceEEeecccccccc-cHHH
Confidence            47788888888888776531   00122346899999999999999999988631  111123445554422211 1111


Q ss_pred             HHHHhcCCCC--CCC-HHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          208 ILQAAAGSAD--VND-LNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       208 i~~~l~~~~~--~~~-~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                         -++....  ... ...+...+.   .....+++||++....+..+..|...
T Consensus        95 ---l~g~~~~~~~~~~~~~~~~~~~---~~~~~vl~lDEi~~l~~~~~~~Ll~~  142 (311)
T 4fcw_A           95 ---LIGAPPGYVGYEEGGQLTEAVR---RRPYSVILFDAIEKAHPDVFNILLQM  142 (311)
T ss_dssp             ---HHCCCTTSTTTTTCCHHHHHHH---HCSSEEEEEETGGGSCHHHHHHHHHH
T ss_pred             ---hcCCCCccccccccchHHHHHH---hCCCeEEEEeChhhcCHHHHHHHHHH
Confidence               1221111  111 112222222   13346999999988876666665543

>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=97.78  E-value=3.1e-05  Score=70.61  Aligned_cols=110  Identities=19%  Similarity=0.210  Sum_probs=63.4

Q ss_pred             CccccccchHHHHHHHhhCCC-----------CCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC
Q 041190          130 EEVYGREKDKEVIVGLLLGDD-----------LNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED  198 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~-----------~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  198 (261)
                      .+++|++..++.|.++|....           .++.+..+.+.|+|++|+||||+|+.+.+...    + ..+.++++..
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~----~-~~i~in~s~~  113 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQNASDV  113 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC----C-CEEEEeCCCc
Confidence            568999999999999987510           00112356899999999999999999998731    2 1334555554


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHH--HHhCCCeEEEEEeCCCCCC
Q 041190          199 FDAVGVTKVILQAAAGSADVNDLNLLQLQLE--NQLKNKKFLLVLDDMWSEN  248 (261)
Q Consensus       199 ~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~--~~l~~kr~LiVlDdvw~~~  248 (261)
                      .+.. +....+......   ...........  ....+++.+|+|||+....
T Consensus       114 ~~~~-~~~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~  161 (516)
T 1sxj_A          114 RSKT-LLNAGVKNALDN---MSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMS  161 (516)
T ss_dssp             CCHH-HHHHTGGGGTTB---CCSTTTTTC----CCSSTTSEEEEECSGGGCC
T ss_pred             chHH-HHHHHHHHHhcc---ccHHHHHhhhhhhhhccCCCeEEEEECCCccc
Confidence            4432 222222221110   00000000000  0123577899999997764

>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=97.73  E-value=2.1e-05  Score=63.52  Aligned_cols=60  Identities=17%  Similarity=0.083  Sum_probs=37.7

Q ss_pred             Cccccc---cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          130 EEVYGR---EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       130 ~~~~gr---~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      .+++|.   ....+.+..++...      ....+.|+|++|+||||||+.+.+....  ......|++++.
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~------~~~~~ll~G~~G~GKT~la~~l~~~~~~--~~~~~~~~~~~~   90 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD------GVQAIYLWGPVKSGRTHLIHAACARANE--LERRSFYIPLGI   90 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC------SCSEEEEECSTTSSHHHHHHHHHHHHHH--TTCCEEEEEGGG
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC------CCCeEEEECCCCCCHHHHHHHHHHHHHH--cCCeEEEEEHHH
Confidence            345653   24455555555431      3467899999999999999999876322  222345666544

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.73  E-value=0.00013  Score=60.08  Aligned_cols=53  Identities=25%  Similarity=0.252  Sum_probs=35.1

Q ss_pred             CCCccccccchHHHHHHHhh---CCCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLL---GDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~---~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.+++|.+..++.+.+++.   ....   -+....+-+.++|++|+||||||+.+.+.
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            33568898877777665432   2100   00112334789999999999999999886

>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=97.70  E-value=0.00014  Score=61.57  Aligned_cols=52  Identities=25%  Similarity=0.144  Sum_probs=38.1

Q ss_pred             CCccccccchHHHHHHHhhCCC--C-----CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDD--L-----NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~--~-----~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.+..++.|.+++...-  .     -+-...+.+.++|++|+|||+||+.+.+.
T Consensus        14 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           14 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH
Confidence            3468999988888888764310  0     00123467899999999999999999986

>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=97.69  E-value=3.7e-05  Score=65.50  Aligned_cols=71  Identities=20%  Similarity=0.251  Sum_probs=46.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEee--CCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCC
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYV--SEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKN  234 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v--~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  234 (261)
                      -+++.|+|++|+|||+||.++....     -....|+++  ++..+.               ...+.+.....+.+.+..
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~~-----G~~VlyIs~~~eE~v~~---------------~~~~le~~l~~i~~~l~~  182 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEAL-----GGKDKYATVRFGEPLSG---------------YNTDFNVFVDDIARAMLQ  182 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHHH-----HTTSCCEEEEBSCSSTT---------------CBCCHHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhC-----CCCEEEEEecchhhhhh---------------hhcCHHHHHHHHHHHHhh
Confidence            3567899999999999999998751     112345665  332111               013455555666666655


Q ss_pred             CeEEEEEeCCCCCC
Q 041190          235 KKFLLVLDDMWSEN  248 (261)
Q Consensus       235 kr~LiVlDdvw~~~  248 (261)
                      .+ +||+|++-...
T Consensus       183 ~~-LLVIDsI~aL~  195 (331)
T 2vhj_A          183 HR-VIVIDSLKNVI  195 (331)
T ss_dssp             CS-EEEEECCTTTC
T ss_pred             CC-EEEEecccccc
Confidence            55 99999998763

>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=97.67  E-value=0.00018  Score=62.30  Aligned_cols=53  Identities=30%  Similarity=0.264  Sum_probs=38.2

Q ss_pred             CCccccccchHHHHHHHhhCC----C--CCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGD----D--LNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~----~--~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|.+..++.|.+.+...    .  .......+-+.++|++|+|||+||+.+.+..
T Consensus        50 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~  108 (355)
T 2qp9_X           50 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA  108 (355)
T ss_dssp             GGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            346899999999998876311    0  0011223457899999999999999999873

>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=97.66  E-value=0.00013  Score=60.65  Aligned_cols=48  Identities=13%  Similarity=0.126  Sum_probs=34.7

Q ss_pred             CccccccchHHHHHH-------HhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVG-------LLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~-------~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.....+.++.       .+...   .......+.++|++|+|||+||+.+.+.
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~---~~~~~~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNS---DRTPLVSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHC---SSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhcc---CCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            457777766666555       33211   1345678899999999999999999886

>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=97.63  E-value=9.1e-05  Score=64.24  Aligned_cols=51  Identities=24%  Similarity=0.262  Sum_probs=38.0

Q ss_pred             CccccccchHHHHHHHhhC----CCC--CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG----DDL--NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~----~~~--~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|.+.+..    ...  ......+.+.++|++|+|||+||+.+.+.
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            4689999999999887742    000  00123467889999999999999999886

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.60  E-value=0.00018  Score=63.08  Aligned_cols=52  Identities=21%  Similarity=0.289  Sum_probs=38.4

Q ss_pred             CCccccccchHHHHHHHhhCC----CC-C-CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGD----DL-N-SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~----~~-~-~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.+..++.|.+++...    .. . .....+-+.|+|++|+|||+||+.+.+.
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            356899999999998877321    00 0 0122467899999999999999999876

>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=97.60  E-value=6.5e-05  Score=62.13  Aligned_cols=47  Identities=15%  Similarity=0.075  Sum_probs=33.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.......+.+.+.....    ....+.|+|++|+|||++|+.+++.
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            3578998888888877654211    2245779999999999999999876

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.59  E-value=0.00015  Score=62.27  Aligned_cols=45  Identities=20%  Similarity=0.298  Sum_probs=35.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.+..++.|...+...      ++..+.++|++|+||||+|+.+.+.
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g------~~~~~ll~Gp~G~GKTtla~~la~~   69 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEG------KLPHLLFYGPPGTGKTSTIVALARE   69 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT------CCCCEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHhcCcHHHHHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHH
Confidence            34778888888888888653      2223889999999999999999876

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.56  E-value=0.00025  Score=60.94  Aligned_cols=45  Identities=16%  Similarity=0.131  Sum_probs=34.9

Q ss_pred             CccccccchHHHHHHHh-hCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLL-LGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L-~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+...+.+.+++ ...     .... +.++|++|+||||+++.+.+.
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~-----~~~~-~ll~Gp~G~GKTtl~~~la~~   59 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPR-----DLPH-LLLYGPNGTGKKTRCMALLES   59 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTT-----CCCC-EEEECSTTSSHHHHHHTHHHH
T ss_pred             HHhcCCHHHHHHHHHHHhhCC-----CCCe-EEEECCCCCCHHHHHHHHHHH
Confidence            45889988888888877 332     1223 899999999999999988763

>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=97.55  E-value=0.00021  Score=63.87  Aligned_cols=52  Identities=27%  Similarity=0.291  Sum_probs=38.3

Q ss_pred             CCccccccchHHHHHHHhhC----CCC-C-CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLG----DDL-N-SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~----~~~-~-~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|.+..++.|.+.+..    ... . .....+-+.++|++|+|||+||+.+.+.
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            35689999999998887631    000 0 1123467889999999999999999986

>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=97.54  E-value=9.7e-05  Score=65.95  Aligned_cols=76  Identities=20%  Similarity=0.158  Sum_probs=45.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccc--eeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCC
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS--FRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKN  234 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~--~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  234 (261)
                      ...+.|+|++|+||||||+.+++..  ...+.  ..++++.+      .+..++...+...    ..    ..+...+..
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l--~~~~~~~~v~~v~~~------~~~~~~~~~~~~~----~~----~~~~~~~~~  193 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYV--VQNEPDLRVMYITSE------KFLNDLVDSMKEG----KL----NEFREKYRK  193 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHH--HHHCCSSCEEEEEHH------HHHHHHHHHHHTT----CH----HHHHHHHTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH--HHhCCCCeEEEeeHH------HHHHHHHHHHHcc----cH----HHHHHHhcC
Confidence            6689999999999999999999863  22221  12344432      2344444444311    11    123344444


Q ss_pred             CeEEEEEeCCCCCC
Q 041190          235 KKFLLVLDDMWSEN  248 (261)
Q Consensus       235 kr~LiVlDdvw~~~  248 (261)
                      +.-+|+|||+....
T Consensus       194 ~~~vL~IDEi~~l~  207 (440)
T 2z4s_A          194 KVDILLIDDVQFLI  207 (440)
T ss_dssp             TCSEEEEECGGGGS
T ss_pred             CCCEEEEeCccccc
Confidence            66788899987654

>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=97.53  E-value=0.00038  Score=59.27  Aligned_cols=26  Identities=42%  Similarity=0.378  Sum_probs=22.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....+.|+|++|+||||||+.+++..
T Consensus        36 ~~~~lll~G~~GtGKT~la~~i~~~~   61 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLLQAAGNEA   61 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            35678999999999999999999863

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.53  E-value=0.00016  Score=60.95  Aligned_cols=27  Identities=30%  Similarity=0.325  Sum_probs=23.2

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +....+.++|++|+|||+||+.+.+..
T Consensus        34 ~~p~~lLl~GppGtGKT~la~aiA~~l   60 (293)
T 3t15_A           34 KVPLILGIWGGKGQGKSFQCELVFRKM   60 (293)
T ss_dssp             CCCSEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            345678899999999999999999874

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.51  E-value=0.00021  Score=63.57  Aligned_cols=53  Identities=17%  Similarity=0.055  Sum_probs=38.0

Q ss_pred             CCccccccchHHHHHHHhhCC--CC-----CCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGD--DL-----NSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~--~~-----~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.++.|.++.++.|.+.+.-.  ..     -+-+..+=+-+||++|+|||+||+.+.+..
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~  239 (437)
T 4b4t_L          180 FDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATI  239 (437)
T ss_dssp             SGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             hhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            356788888888887765321  00     012345678899999999999999999873

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.51  E-value=6.8e-05  Score=63.60  Aligned_cols=47  Identities=17%  Similarity=0.229  Sum_probs=36.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|....+..+.+.+....    .....+.|+|.+|+|||++|+.+++.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a----~~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVA----PSDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHC----STTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHh----CCCCcEEEECCCCchHHHHHHHHHHh
Confidence            357899888888888876532    12345779999999999999999885

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.51  E-value=0.00011  Score=62.34  Aligned_cols=42  Identities=14%  Similarity=0.139  Sum_probs=29.3

Q ss_pred             chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          137 KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       137 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...+.+.+++....   ......+.++|++|+|||+||+.+++..
T Consensus       135 ~~~~~~~~~i~~~~---~~~~~~lll~G~~GtGKT~La~aia~~~  176 (308)
T 2qgz_A          135 EAFSAILDFVEQYP---SAEQKGLYLYGDMGIGKSYLLAAMAHEL  176 (308)
T ss_dssp             HHHHHHHHHHHHCS---CSSCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc---ccCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            34445556665421   1124678899999999999999998863

>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=97.47  E-value=0.00017  Score=65.23  Aligned_cols=51  Identities=24%  Similarity=0.167  Sum_probs=37.8

Q ss_pred             CccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.+..++.|.+++...-..       +.....-+.|+|++|+|||++|+.+.+.
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            45899999999998877531000       0123456889999999999999999876

>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=97.46  E-value=0.00026  Score=68.38  Aligned_cols=45  Identities=22%  Similarity=0.382  Sum_probs=37.6

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++||+.++..++..|....      ...+.++|++|+|||++|+.+.+.
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            358999999999999997632      234689999999999999999876

>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=97.45  E-value=0.00073  Score=64.45  Aligned_cols=99  Identities=21%  Similarity=0.206  Sum_probs=58.1

Q ss_pred             CccccccchHHHHHHHhh----CCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHH
Q 041190          130 EEVYGREKDKEVIVGLLL----GDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAV  202 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~----~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  202 (261)
                      .++.|.++.+++|.+++.    ..+.   -+-..++-|-++|++|+|||+||+.|.+...  .+|   ..|+.+.     
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg--~~~---~~v~~~~-----  273 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG--AFF---FLINGPE-----  273 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTT--CEE---EEEEHHH-----
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC--CeE---EEEEhHH-----
Confidence            457888888888887643    2110   0223456789999999999999999998732  232   2233211     


Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          203 GVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       203 ~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                               +...........+...+.......+.+|+||++...
T Consensus       274 ---------l~sk~~gese~~lr~lF~~A~~~~PsIIfIDEiDal  309 (806)
T 3cf2_A          274 ---------IMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAI  309 (806)
T ss_dssp             ---------HHSSCTTHHHHHHHHHHHHHTTSCSEEEEEESGGGT
T ss_pred             ---------hhcccchHHHHHHHHHHHHHHHcCCeEEEEehhccc
Confidence                     010111111222222233344567899999999765

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=97.43  E-value=0.00057  Score=52.08  Aligned_cols=22  Identities=50%  Similarity=0.786  Sum_probs=19.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+|+.+ ..
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~   23 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KE   23 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HH
T ss_pred             cEEEEECCCCCCHHHHHHHH-HH
Confidence            47899999999999999999 44

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.42  E-value=0.00022  Score=62.53  Aligned_cols=51  Identities=24%  Similarity=0.113  Sum_probs=36.7

Q ss_pred             CccccccchHHHHHHHhhCC--CC-----CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGD--DL-----NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~--~~-----~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.++.+++|.+.+.-.  ..     -+-+..+=+-++|++|+|||.||+.+.+.
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHh
Confidence            45788888888887754321  00     01233456789999999999999999987

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.38  E-value=0.0003  Score=62.34  Aligned_cols=52  Identities=23%  Similarity=0.112  Sum_probs=37.6

Q ss_pred             CCccccccchHHHHHHHhhCC--CC-----CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLGD--DL-----NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~--~~-----~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|.+..++.|.+.+...  ..     -+-+..+=+-++|++|+|||+||+.+.+.
T Consensus       171 ~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~  229 (428)
T 4b4t_K          171 YADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS  229 (428)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            356888988888887765321  00     01233456889999999999999999987

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.37  E-value=0.00022  Score=53.93  Aligned_cols=25  Identities=32%  Similarity=0.276  Sum_probs=22.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -..+.|+|++|+|||||++.+++..
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~   60 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQA   60 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4589999999999999999998864

>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=97.35  E-value=0.00017  Score=64.58  Aligned_cols=51  Identities=20%  Similarity=0.175  Sum_probs=35.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..++.+..++..-.. +....+-+.++|++|+|||+||+.+.+..
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~-~~~~~~~iLl~GppGtGKT~la~ala~~l   87 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKS-KKMAGRAVLLAGPPGTGKTALALAIAQEL   87 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHT-TCCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHh-CCCCCCeEEEECCCcCCHHHHHHHHHHHh
Confidence            5689998887765554322110 12233567889999999999999999873

>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=97.35  E-value=0.001  Score=63.28  Aligned_cols=45  Identities=27%  Similarity=0.332  Sum_probs=37.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|++.++..+++.|...      ...-+.++|++|+|||++|+.+.+.
T Consensus       186 d~~iGr~~~i~~l~~~l~~~------~~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRR------RKNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS------SSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhcc------CCCCeEEEcCCCCCHHHHHHHHHHH
Confidence            35899999999999999753      2345689999999999999999875

>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=97.33  E-value=0.0016  Score=56.00  Aligned_cols=92  Identities=13%  Similarity=0.024  Sum_probs=57.2

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcccccc----ccceeEEEeeCCCCCHHHHHHHHHHHhcCC-------------CC
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKK----YFSFRACAYVSEDFDAVGVTKVILQAAAGS-------------AD  217 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~-------------~~  217 (261)
                      +.-.++.|+|.+|+|||||+..+........    .-...+|+.....++...+.. ++..++..             .+
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~~~~~~l~~l~~~~~~~  198 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNVDHDAVLDNVLYARAYT  198 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCCCHHHHHhceeEeecCC
Confidence            4557999999999999999999876522211    123567888888777665543 34444311             11


Q ss_pred             CCCHHHHHHHHHHHhC---CCeEEEEEeCCCCC
Q 041190          218 VNDLNLLQLQLENQLK---NKKFLLVLDDMWSE  247 (261)
Q Consensus       218 ~~~~~~~~~~l~~~l~---~kr~LiVlDdvw~~  247 (261)
                      .....++...+...+.   .+--+||+|.+-..
T Consensus       199 ~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l  231 (343)
T 1v5w_A          199 SEHQMELLDYVAAKFHEEAGIFKLLIIDSIMAL  231 (343)
T ss_dssp             TTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGG
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccEEEEechHHH
Confidence            2222234444555553   56779999998654

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.30  E-value=0.00032  Score=62.27  Aligned_cols=51  Identities=25%  Similarity=0.182  Sum_probs=37.4

Q ss_pred             CccccccchHHHHHHHhhC----CCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG----DDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~----~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.++.++.|.+.+..    .+.   -+-+..+=+-+||++|+|||.||+.+.+.
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e  238 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQ  238 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHH
Confidence            5688888888888775322    100   02234567889999999999999999987

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.28  E-value=0.0004  Score=66.19  Aligned_cols=45  Identities=24%  Similarity=0.363  Sum_probs=37.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|++..++.++..|....      ..-+.++|++|+|||++|+.+.+.
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            358999999999999997632      234679999999999999999876

>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=97.26  E-value=0.00065  Score=61.12  Aligned_cols=53  Identities=26%  Similarity=0.136  Sum_probs=35.6

Q ss_pred             CCccccccchHHHHHHHhhCCCC------CCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDL------NSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~------~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|.++.++++.+++..-..      -+....+-+.++|++|+|||+||+.+.+..
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~   73 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA   73 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            34689988877777665432100      011122347899999999999999999863

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.25  E-value=0.00035  Score=62.28  Aligned_cols=51  Identities=24%  Similarity=0.108  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhC----CCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG----DDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~----~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.++.++.|.+.+.-    .+.   -+-...+=|-++|++|+|||+||+.+.+.
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            4688888888888875422    100   01234566889999999999999999987

>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=97.22  E-value=0.0012  Score=57.07  Aligned_cols=100  Identities=17%  Similarity=0.050  Sum_probs=62.3

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-..|...   +-+.-.++.|+|++|+|||||+.++......  .=..++|+.....++..     .+++++..   
T Consensus        46 ~~~LD~~Lg~G---Gi~~G~i~~I~GppGsGKSTLal~la~~~~~--~gg~VlyId~E~s~~~~-----ra~rlgv~~~~  115 (356)
T 3hr8_A           46 SLAIDIATGVG---GYPRGRIVEIFGQESSGKTTLALHAIAEAQK--MGGVAAFIDAEHALDPV-----YAKNLGVDLKS  115 (356)
T ss_dssp             CHHHHHHTSSS---SEETTEEEEEEESTTSSHHHHHHHHHHHHHH--TTCCEEEEESSCCCCHH-----HHHHHTCCGGG
T ss_pred             CHHHHHHhccC---CccCCcEEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEecccccchH-----HHHHcCCchhh
Confidence            34555555411   2234579999999999999999999876321  11235688777666543     34555511   


Q ss_pred             ---CCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCC
Q 041190          216 ---ADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSEN  248 (261)
Q Consensus       216 ---~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~  248 (261)
                         ....+.+++...+...++ .+.-++|+|.+-..-
T Consensus       116 l~i~~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~~l~  152 (356)
T 3hr8_A          116 LLISQPDHGEQALEIVDELVRSGVVDLIVVDSVAALV  152 (356)
T ss_dssp             CEEECCSSHHHHHHHHHHHHHTSCCSEEEEECTTTCC
T ss_pred             hhhhhccCHHHHHHHHHHHhhhcCCCeEEehHhhhhc
Confidence               123455666666665553 556689999986653

>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=97.17  E-value=0.0018  Score=54.88  Aligned_cols=100  Identities=9%  Similarity=-0.068  Sum_probs=56.3

Q ss_pred             cccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccc-cc-cccceeEEEeeCC-CCCHHHHHHHHHH
Q 041190          134 GREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAG-VK-KYFSFRACAYVSE-DFDAVGVTKVILQ  210 (261)
Q Consensus       134 gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~-~~-~~f~~~~wv~v~~-~~~~~~i~~~i~~  210 (261)
                      |.++.++.|...+...      +.+..-++|++|+||||+|+.+.+... .. .+.+. .+++.++ ...... .+++++
T Consensus         1 g~~~~~~~L~~~i~~~------~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~-~~l~~~~~~~~id~-ir~li~   72 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS------EGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDD-IRTIKD   72 (305)
T ss_dssp             ---CHHHHHHHHHHTC------SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHH-HHHHHH
T ss_pred             ChHHHHHHHHHHHHCC------CCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCE-EEEcCCcCCCCHHH-HHHHHH
Confidence            3445566777777542      257888999999999999999976411 11 12232 4455443 333333 344555


Q ss_pred             HhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          211 AAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       211 ~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      .+...+               ..+++-++|+|++...+.+..+.|.
T Consensus        73 ~~~~~p---------------~~~~~kvviIdead~lt~~a~naLL  103 (305)
T 2gno_A           73 FLNYSP---------------ELYTRKYVIVHDCERMTQQAANAFL  103 (305)
T ss_dssp             HHTSCC---------------SSSSSEEEEETTGGGBCHHHHHHTH
T ss_pred             HHhhcc---------------ccCCceEEEeccHHHhCHHHHHHHH
Confidence            554111               1245566777777766655555443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.15  E-value=0.00027  Score=67.39  Aligned_cols=109  Identities=16%  Similarity=0.124  Sum_probs=62.8

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.+...+.....   +.......+.++|++|+|||++|+.+.+..  ...-...+.++++.-.....   
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l--~~~~~~~i~i~~s~~~~~~~---  565 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESI--FGDEESMIRIDMSEYMEKHS---  565 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHH--HSCTTCEEEEEGGGGCSSCC---
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh--cCCCcceEEEechhcccccc---
Confidence            4588999988888887765321   012334478999999999999999998763  11111233445444221100   


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          207 VILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                                  .....+...++.   ....+|+||++....++.+..|...
T Consensus       566 ------------~~~~~l~~~~~~---~~~~vl~lDEi~~~~~~~~~~Ll~~  602 (758)
T 3pxi_A          566 ------------TSGGQLTEKVRR---KPYSVVLLDAIEKAHPDVFNILLQV  602 (758)
T ss_dssp             ------------CC---CHHHHHH---CSSSEEEEECGGGSCHHHHHHHHHH
T ss_pred             ------------cccchhhHHHHh---CCCeEEEEeCccccCHHHHHHHHHH
Confidence                        000111111111   2344899999988876666665443

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.15  E-value=0.00027  Score=63.55  Aligned_cols=45  Identities=24%  Similarity=0.363  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|++.+++.++..|....      ..-+.++|++|+|||++|+.+.+.
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            358999999999999997632      234579999999999999999876

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.12  E-value=0.0019  Score=55.02  Aligned_cols=91  Identities=14%  Similarity=0.081  Sum_probs=57.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccc----cceeEEEeeCCCCCHHHHHHHHHHHhcCC----------CCCCCH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKY----FSFRACAYVSEDFDAVGVTKVILQAAAGS----------ADVNDL  221 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~i~~~i~~~l~~~----------~~~~~~  221 (261)
                      .-.++.|+|.+|+|||||+.++.........    -...+|++....++...+.. ++..++..          ....+.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN-MAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHhCCCHHHHhccEEEEeCCCH
Confidence            4568999999999999999998765222111    13567888888776666543 34444411          012222


Q ss_pred             H---HHHHHHHHHhC--CCeEEEEEeCCCCC
Q 041190          222 N---LLQLQLENQLK--NKKFLLVLDDMWSE  247 (261)
Q Consensus       222 ~---~~~~~l~~~l~--~kr~LiVlDdvw~~  247 (261)
                      +   ++...+...++  .+--+||+|.+-..
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l  215 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVTSH  215 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTTHH
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcHHH
Confidence            2   34445555553  56789999998653

>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=97.12  E-value=0.0012  Score=53.32  Aligned_cols=91  Identities=13%  Similarity=0.030  Sum_probs=53.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcccccc----ccceeEEEeeCCCCCHHHHHHHHHHHhcCCC----------CCCCH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKK----YFSFRACAYVSEDFDAVGVTKVILQAAAGSA----------DVNDL  221 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~----------~~~~~  221 (261)
                      .-.++.|+|++|+|||||++.+........    .-...+|+.....+....+. .++..++...          ...+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCH
Confidence            346999999999999999999887421111    12346777766654544432 3344443110          11222


Q ss_pred             HH---HHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          222 NL---LQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       222 ~~---~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                      .+   +...+.+.+. .+.-+||||++...
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~lliiD~~~~~  131 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVESRYALLIVDSATAL  131 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSSGG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEeCchHH
Confidence            22   2333545553 56789999998764

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.11  E-value=0.0007  Score=59.78  Aligned_cols=51  Identities=25%  Similarity=0.183  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhhC----CCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG----DDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~----~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++-|.++.++.|.+.+.-    .+.   -+-+..+=|-++|++|+|||.||+.+.+.
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHH
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHH
Confidence            4678888888888775432    100   02234567899999999999999999987

>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=97.05  E-value=0.0023  Score=55.64  Aligned_cols=99  Identities=19%  Similarity=0.045  Sum_probs=61.8

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-.+|...   +-+.-.++.|+|.+|+||||||.++.....  ..-...+|+.....++..     ....++..   
T Consensus        59 ~~~LD~~Lg~G---Gl~~G~li~I~G~pGsGKTtlal~la~~~~--~~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~  128 (366)
T 1xp8_A           59 SLSLDLALGVG---GIPRGRITEIYGPESGGKTTLALAIVAQAQ--KAGGTCAFIDAEHALDPV-----YARALGVNTDE  128 (366)
T ss_dssp             CHHHHHHTSSS---SEETTSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHTTCCGGG
T ss_pred             CHHHHHHhCCC---CccCCcEEEEEcCCCCChHHHHHHHHHHHH--HCCCeEEEEECCCChhHH-----HHHHcCCCHHH
Confidence            44555555411   123446889999999999999988876521  122357888888766643     23444411   


Q ss_pred             ---CCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCC
Q 041190          216 ---ADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       216 ---~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~  247 (261)
                         ..+.+.+++...+....+ ++--+||+|.+-..
T Consensus       129 l~i~~~~~~e~~l~~l~~l~~~~~~~lVVIDsl~~l  164 (366)
T 1xp8_A          129 LLVSQPDNGEQALEIMELLVRSGAIDVVVVDSVAAL  164 (366)
T ss_dssp             CEEECCSSHHHHHHHHHHHHTTTCCSEEEEECTTTC
T ss_pred             ceeecCCcHHHHHHHHHHHHhcCCCCEEEEeChHHh
Confidence               123456666666666654 44569999998765

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.05  E-value=0.0007  Score=53.55  Aligned_cols=43  Identities=26%  Similarity=0.306  Sum_probs=32.3

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |+...+.|.+.+....   .....+++|.|++|+||||+++.+...
T Consensus         3 ~~~~~~~l~~~~~~~~---~~~~~~i~i~G~~GsGKstl~~~l~~~   45 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIK---TAGRLVLGIDGLSRSGKTTLANQLSQT   45 (201)
T ss_dssp             HHHHHHHHHHHHHTSC---CSSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhc---cCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3445677777776532   234679999999999999999998764

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.99  E-value=0.002  Score=54.81  Aligned_cols=91  Identities=19%  Similarity=0.192  Sum_probs=57.2

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcccccc---------cc-----ceeEEEeeCCCCCHHHHHHHHHHHhcCC-----
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKK---------YF-----SFRACAYVSEDFDAVGVTKVILQAAAGS-----  215 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~---------~f-----~~~~wv~v~~~~~~~~i~~~i~~~l~~~-----  215 (261)
                      +.-.++.|+|.+|+|||+||.++........         ..     ...+|+.....++...+.. ++..++..     
T Consensus        96 ~~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~  174 (322)
T 2i1q_A           96 ESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVL  174 (322)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHh
Confidence            3457999999999999999998876521111         11     3567888888777666553 34445411     


Q ss_pred             -----CCCCCHH---HHHHHHHHHhC--CCeEEEEEeCCCC
Q 041190          216 -----ADVNDLN---LLQLQLENQLK--NKKFLLVLDDMWS  246 (261)
Q Consensus       216 -----~~~~~~~---~~~~~l~~~l~--~kr~LiVlDdvw~  246 (261)
                           ....+.+   ++...+...+.  .+--+||+|.+-.
T Consensus       175 ~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  215 (322)
T 2i1q_A          175 DNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTS  215 (322)
T ss_dssp             HTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSH
T ss_pred             cCEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence                 1122323   34445555554  4667999999864

>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=96.94  E-value=0.0008  Score=64.98  Aligned_cols=120  Identities=13%  Similarity=0.112  Sum_probs=63.6

Q ss_pred             ccccccchHHHHHHHhhCCC---CCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      .++|.+..++.+...+....   .+.+.....+.++|++|+|||++|+.+.+...  ..-...+.++++....... ...
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~--~~~~~~i~i~~~~~~~~~~-~s~  635 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF--DTEEAMIRIDMTEYMEKHA-VSR  635 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH--SSGGGEEEECTTTCCSSGG-GGG
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc--CCCCcEEEEechhccchhH-HHH
Confidence            57899888888888775421   10123346889999999999999999987621  1111223455444222100 000


Q ss_pred             HHHHhcCCC--CCCC-HHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          208 ILQAAAGSA--DVND-LNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       208 i~~~l~~~~--~~~~-~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      +   ++...  ...+ ...+...++.   ...-+|+||++....++.++.|...|
T Consensus       636 l---~g~~~~~~G~~~~g~l~~~~~~---~~~~vl~lDEi~~l~~~~~~~Ll~~l  684 (854)
T 1qvr_A          636 L---IGAPPGYVGYEEGGQLTEAVRR---RPYSVILFDEIEKAHPDVFNILLQIL  684 (854)
T ss_dssp             C-----------------CHHHHHHH---CSSEEEEESSGGGSCHHHHHHHHHHH
T ss_pred             H---cCCCCCCcCccccchHHHHHHh---CCCeEEEEecccccCHHHHHHHHHHh
Confidence            0   11000  0000 0112222222   23468999999888776666655443

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=96.93  E-value=0.0016  Score=56.59  Aligned_cols=50  Identities=28%  Similarity=0.231  Sum_probs=35.0

Q ss_pred             ccccccchHHHHHHHhh----CCC--------------------CCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLL----GDD--------------------LNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~----~~~--------------------~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.+..++.|...+.    ...                    .........+.++|++|+|||++|+.+.+.
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHH
Confidence            57888888888877662    000                    000112346889999999999999999886

>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=96.92  E-value=0.00083  Score=55.37  Aligned_cols=53  Identities=26%  Similarity=0.234  Sum_probs=36.5

Q ss_pred             CCccccccchHHHHHHHhhCCCCC------CCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDDLN------SGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~~~------~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|.+..++.+.+++..-...      +....+-+.++|++|+|||+||+.+.+..
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~   68 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA   68 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            356899988888888765420000      00112337799999999999999998863

>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=96.92  E-value=0.00027  Score=60.65  Aligned_cols=51  Identities=29%  Similarity=0.444  Sum_probs=35.9

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..++.+...+..... .+..+..+.++|++|+||||||+.+.+..
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~-~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKM-RGEVLDHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH-HTCCCCCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            3577877777776666543100 12234678999999999999999998863

>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=96.92  E-value=0.0049  Score=52.71  Aligned_cols=40  Identities=20%  Similarity=0.271  Sum_probs=29.5

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...+.+...+..+     .-.+.+-++|++|+|||++|+.+.+.
T Consensus         8 ~~~~~~l~~~i~~~-----~~~~a~L~~G~~G~GKt~~a~~la~~   47 (334)
T 1a5t_A            8 RPDFEKLVASYQAG-----RGHHALLIQALPGMGDDALIYALSRY   47 (334)
T ss_dssp             HHHHHHHHHHHHTT-----CCCSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-----CcceeEEEECCCCchHHHHHHHHHHH
Confidence            34456666666543     23457899999999999999988765

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=96.91  E-value=0.0035  Score=54.10  Aligned_cols=100  Identities=16%  Similarity=0.011  Sum_probs=60.9

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-.+|...   +-+.-.++.|+|++|+|||||+.++.....  ..=...+|++....++..     ....++..   
T Consensus        46 ~~~LD~~Lg~G---Gl~~G~iv~I~G~pGsGKTtLal~la~~~~--~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~  115 (349)
T 2zr9_A           46 SISLDVALGIG---GLPRGRVIEIYGPESSGKTTVALHAVANAQ--AAGGIAAFIDAEHALDPE-----YAKKLGVDTDS  115 (349)
T ss_dssp             CHHHHHHTSSS---SEETTSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHTTCCGGG
T ss_pred             CHHHHHHhccC---CccCCeEEEEECCCCCCHHHHHHHHHHHHH--hCCCeEEEEECCCCcCHH-----HHHHcCCCHHH
Confidence            34455555411   123456899999999999999999876522  112346788887766543     23444411   


Q ss_pred             ---CCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCC
Q 041190          216 ---ADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSEN  248 (261)
Q Consensus       216 ---~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~  248 (261)
                         ..+.+.+++...++...+ .+.-+||+|.+-...
T Consensus       116 l~i~~~~~~e~~l~~~~~l~~~~~~~lIVIDsl~~l~  152 (349)
T 2zr9_A          116 LLVSQPDTGEQALEIADMLVRSGALDIIVIDSVAALV  152 (349)
T ss_dssp             CEEECCSSHHHHHHHHHHHHTTTCCSEEEEECGGGCC
T ss_pred             eEEecCCCHHHHHHHHHHHHhcCCCCEEEEcChHhhc
Confidence               123345555555555543 456799999987653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.91  E-value=0.0047  Score=49.25  Aligned_cols=24  Identities=29%  Similarity=0.315  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|+|++|+|||||++.+...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~   46 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAK   46 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999999854

>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=96.91  E-value=0.0014  Score=53.67  Aligned_cols=52  Identities=27%  Similarity=0.297  Sum_probs=33.3

Q ss_pred             CCccccccchHHHHHHHhhCCC-------CCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKDKEVIVGLLLGDD-------LNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~~~-------~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|.+..+..+.++...-.       ..-..... +.|+|++|+|||||++.+.+..
T Consensus        15 ~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g-~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           15 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSE-EEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCCCCHHHHHHHHHHHh
Confidence            3467887766666655432210       00011122 8999999999999999999863

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.90  E-value=0.0017  Score=54.12  Aligned_cols=50  Identities=26%  Similarity=0.282  Sum_probs=32.5

Q ss_pred             CccccccchHHHHHHHhhCC--------CCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGD--------DLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.+..++.|.+.+...        ...-..... +.++|++|+|||||++.+...
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G-vlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG-VLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE-EEEESSTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe-EEEECCCCCcHHHHHHHHHHH
Confidence            45777777777777643210        000011123 899999999999999999886

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.88  E-value=0.001  Score=52.85  Aligned_cols=38  Identities=24%  Similarity=0.355  Sum_probs=28.0

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.|.+.+...    .+...+++|+|++|+|||||++.+..-
T Consensus         8 ~~~~~~~~~~~----~~~g~~v~I~G~sGsGKSTl~~~l~~~   45 (208)
T 3c8u_A            8 CQGVLERLDPR----QPGRQLVALSGAPGSGKSTLSNPLAAA   45 (208)
T ss_dssp             HHHHHHHSCTT----CCSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHhc----CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34455555432    235679999999999999999998765

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.87  E-value=0.0051  Score=55.63  Aligned_cols=54  Identities=26%  Similarity=0.251  Sum_probs=35.5

Q ss_pred             CCCccccccchHHHHHHHhhC---CCC--C-CCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          128 DEEEVYGREKDKEVIVGLLLG---DDL--N-SGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~---~~~--~-~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .-.+++|.+..+.++.++...   ...  + +..-.+-+.|+|++|+||||||+.+....
T Consensus        29 ~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~   88 (499)
T 2dhr_A           29 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   88 (499)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             CHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            345688988777776665432   100  0 01112238999999999999999999863

>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=96.83  E-value=0.0029  Score=54.61  Aligned_cols=92  Identities=22%  Similarity=0.163  Sum_probs=53.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcccccccc----ceeEEEeeCCCCCHHHHHHHHHHHhcC-------------CCC
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYF----SFRACAYVSEDFDAVGVTKVILQAAAG-------------SAD  217 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~~~wv~v~~~~~~~~i~~~i~~~l~~-------------~~~  217 (261)
                      +.-.++.|+|++|+|||||++.+..........    ...+|+...+.+....+ ..+.+..+.             ...
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~  207 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFN  207 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCC
Confidence            345799999999999999999998753111111    13478876655433332 223332220             001


Q ss_pred             CCCHHHHHHHHHHHhC------CCeEEEEEeCCCCC
Q 041190          218 VNDLNLLQLQLENQLK------NKKFLLVLDDMWSE  247 (261)
Q Consensus       218 ~~~~~~~~~~l~~~l~------~kr~LiVlDdvw~~  247 (261)
                      .....++...+...+.      .+.-|||||.+-..
T Consensus       208 ~~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          208 SNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             hHHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence            1112233444555553      46789999999765

>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=96.81  E-value=0.0016  Score=59.66  Aligned_cols=50  Identities=32%  Similarity=0.362  Sum_probs=34.1

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++|.+.-+..+.+.+.-..........++.++|++|+||||||+.+...
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            46777776666655433211001124568999999999999999999886

>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=96.81  E-value=0.0046  Score=52.04  Aligned_cols=25  Identities=28%  Similarity=0.169  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++.++|++|+||||++..+...
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~  128 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAI  128 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999988654

>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=96.80  E-value=0.0064  Score=51.62  Aligned_cols=84  Identities=10%  Similarity=0.045  Sum_probs=53.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCC------CCCCHHHH-HHHHHHH
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSA------DVNDLNLL-QLQLENQ  231 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~------~~~~~~~~-~~~l~~~  231 (261)
                      ++-|+|++|+|||||+-++.........=...+|+...+.++..     .+++++-..      .+.+.+++ ...+...
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l  104 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVNQL  104 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHHHH
Confidence            78999999999999998877652211012346788888777653     256666211      23445555 3333222


Q ss_pred             --h-CCCeEEEEEeCCCCC
Q 041190          232 --L-KNKKFLLVLDDMWSE  247 (261)
Q Consensus       232 --l-~~kr~LiVlDdvw~~  247 (261)
                        + .++.-|||+|.|-..
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 467899999999776

>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=96.79  E-value=0.00088  Score=52.16  Aligned_cols=25  Identities=32%  Similarity=0.497  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.++.|+|++|+|||||++.+...
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3468999999999999999999775

>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=96.79  E-value=0.00071  Score=51.59  Aligned_cols=23  Identities=22%  Similarity=0.213  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+++.+.+.
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            47899999999999999998764

>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=96.79  E-value=0.00079  Score=56.48  Aligned_cols=52  Identities=21%  Similarity=0.257  Sum_probs=37.5

Q ss_pred             CccccccchHHHHHHHhhCC--CC--C----CCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGD--DL--N----SGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~--~~--~----~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..++.+...+...  ..  .    .......+.++|++|+|||++|+.+.+..
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l   74 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            45899999998888877540  00  0    01123567899999999999999998863

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=96.75  E-value=0.002  Score=53.53  Aligned_cols=53  Identities=26%  Similarity=0.291  Sum_probs=34.5

Q ss_pred             CCCccccccchHHHHHHHhhCCC-------CCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDD-------LNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~-------~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .-.+++|.+..+..+.++...-.       ..-..... +.|+|++|+|||||++.+....
T Consensus        38 ~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           38 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             CGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHHHT
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHHHc
Confidence            34568888777666665443210       00001122 8899999999999999999863

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.73  E-value=0.019  Score=50.99  Aligned_cols=42  Identities=19%  Similarity=0.235  Sum_probs=29.0

Q ss_pred             HHHHHHHhhCCCCC---CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLN---SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~---~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.++|......   .....++|.++|.+|+||||++..+...
T Consensus        79 ~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~~  123 (433)
T 2xxa_A           79 RNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKF  123 (433)
T ss_dssp             HHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45666666542210   1235789999999999999998887644

>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=96.73  E-value=0.00082  Score=51.71  Aligned_cols=23  Identities=17%  Similarity=0.278  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|+|++|+||||+++.+.+.
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            57899999999999999999875

>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=96.71  E-value=0.00051  Score=55.49  Aligned_cols=93  Identities=13%  Similarity=-0.060  Sum_probs=49.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHHHHhC
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---ADVNDLNLLQLQLENQLK  233 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---~~~~~~~~~~~~l~~~l~  233 (261)
                      -.++.|+|..|+||||++..+......+ ... ...+....+.  . -...+..+++..   .......++...+.+.+.
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~-g~k-Vli~~~~~d~--r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYA-DVK-YLVFKPKIDT--R-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT-TCC-EEEEEECCCG--G-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTS
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhc-CCE-EEEEEeccCc--h-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhh
Confidence            4689999999999999887776653221 121 2223222211  1 111223333311   112234455566666555


Q ss_pred             CCeE-EEEEeCCCCCChhhHHH
Q 041190          234 NKKF-LLVLDDMWSENYDVWTN  254 (261)
Q Consensus       234 ~kr~-LiVlDdvw~~~~~~w~~  254 (261)
                      +.++ +|++|++.....+..+.
T Consensus        87 ~~~~dvViIDEaQ~l~~~~ve~  108 (223)
T 2b8t_A           87 NDETKVIGIDEVQFFDDRICEV  108 (223)
T ss_dssp             CTTCCEEEECSGGGSCTHHHHH
T ss_pred             CCCCCEEEEecCccCcHHHHHH
Confidence            5545 99999997665443333

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.71  E-value=0.0018  Score=54.31  Aligned_cols=41  Identities=20%  Similarity=0.245  Sum_probs=28.6

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++++.-+..... ......+|.|.|++|+||||+++.+...
T Consensus        16 ~~~~~~~~l~~~~-~~~~~~livl~G~sGsGKSTla~~L~~~   56 (287)
T 1gvn_B           16 LNDNLEELIQGKK-AVESPTAFLLGGQPGSGKTSLRSAIFEE   56 (287)
T ss_dssp             HHHHHHHHHTTCC-CCSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHhcccc-CCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3444444443322 3345678999999999999999999765

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.71  E-value=0.00086  Score=52.04  Aligned_cols=23  Identities=13%  Similarity=0.434  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|++|+|||||++.+...
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            58999999999999999999865

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.70  E-value=0.00097  Score=51.22  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+|.|.|++|+||||+|+.+.+
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            5789999999999999999987

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.70  E-value=0.00091  Score=52.72  Aligned_cols=24  Identities=38%  Similarity=0.426  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|+|++|+||||+++.+...
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~   48 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARK   48 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999999765

>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=96.66  E-value=0.0012  Score=51.99  Aligned_cols=26  Identities=38%  Similarity=0.359  Sum_probs=22.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...+|.|+|++|+|||||++.+....
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999997753

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.64  E-value=0.00087  Score=51.30  Aligned_cols=23  Identities=26%  Similarity=0.361  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|+|++|+|||||++.+...
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            47999999999999999999775

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.63  E-value=0.0012  Score=52.25  Aligned_cols=25  Identities=44%  Similarity=0.343  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++|+|+.|+|||||++.+..-
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            4578999999999999999999764

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=96.62  E-value=0.0058  Score=48.59  Aligned_cols=75  Identities=15%  Similarity=0.202  Sum_probs=43.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHH----------hcCCCCCCCHHHHHHHH
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQA----------AAGSADVNDLNLLQLQL  228 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~----------l~~~~~~~~~~~~~~~l  228 (261)
                      +|.+.|++|+||||+|+.+.+...+       ..+      +..+++++-+..          ....-..-+.+-+...+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g~-------~~i------stGdllR~~i~~~t~lg~~~~~~~~~G~lvpd~iv~~lv   68 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKGF-------VHI------STGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALI   68 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCC-------EEE------EHHHHHHHHHHHTCHHHHHHHHHHHHTCCCCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC-------eEE------cHHHHHHHHHHhcChhhhhHHHHHhcCCcCCHHHHHHHH
Confidence            6789999999999999999876322       112      234444432221          11011122233445667


Q ss_pred             HHHhCCCeEEEEEeCCCCC
Q 041190          229 ENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       229 ~~~l~~kr~LiVlDdvw~~  247 (261)
                      .+.+..... +|||+.-..
T Consensus        69 ~~~l~~~~~-~ilDGfPRt   86 (206)
T 3sr0_A           69 EEVFPKHGN-VIFDGFPRT   86 (206)
T ss_dssp             HHHCCSSSC-EEEESCCCS
T ss_pred             HHhhccCCc-eEecCCchh
Confidence            777765544 578887544

>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=96.62  E-value=0.0057  Score=52.89  Aligned_cols=100  Identities=15%  Similarity=0.007  Sum_probs=59.3

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC---
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS---  215 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~---  215 (261)
                      ...|-.+|...   +-+.-.++.|+|.+|+||||||.++.....  ..-...+|+.....++...     ...++..   
T Consensus        48 ~~~LD~~Lg~G---Gl~~G~ii~I~G~pGsGKTtLal~la~~~~--~~g~~vlyid~E~s~~~~~-----a~~~g~~~~~  117 (356)
T 1u94_A           48 SLSLDIALGAG---GLPMGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDN  117 (356)
T ss_dssp             CHHHHHHTSSS---SEETTSEEEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHHH-----HHHTTCCGGG
T ss_pred             CHHHHHHhccC---CccCCeEEEEECCCCCCHHHHHHHHHHHHH--HCCCeEEEEeCCCCccHHH-----HHHcCCChhh
Confidence            44555555311   123456899999999999999998876522  1112477888877666431     3444411   


Q ss_pred             ---CCCCCHHHHHHHHHHHh-CCCeEEEEEeCCCCCC
Q 041190          216 ---ADVNDLNLLQLQLENQL-KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       216 ---~~~~~~~~~~~~l~~~l-~~kr~LiVlDdvw~~~  248 (261)
                         ..+.+.+++...++... ..+--+||+|.+-...
T Consensus       118 l~i~~~~~~e~~~~~~~~l~~~~~~~lVVIDsl~~l~  154 (356)
T 1u94_A          118 LLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALT  154 (356)
T ss_dssp             CEEECCSSHHHHHHHHHHHHHHTCCSEEEEECGGGCC
T ss_pred             eeeeCCCCHHHHHHHHHHHHhccCCCEEEEcCHHHhc
Confidence               12234455555454443 2455699999986653

>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=96.62  E-value=0.0014  Score=55.04  Aligned_cols=27  Identities=22%  Similarity=0.251  Sum_probs=23.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+..+|+|+|.+|+|||||++.+...
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~   54 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNH   54 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            345789999999999999999988765

>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=96.58  E-value=0.0019  Score=55.88  Aligned_cols=50  Identities=32%  Similarity=0.322  Sum_probs=36.1

Q ss_pred             ccccccchHHHHHHHhhCC-------C--CCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGD-------D--LNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~-------~--~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.+..++.|...+...       .  .........+.++|++|+|||++|+.+.+.
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            3689888888888877210       0  001123456889999999999999999886

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.58  E-value=0.0013  Score=51.75  Aligned_cols=23  Identities=26%  Similarity=0.452  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+...
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            58999999999999999999764

>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=96.58  E-value=0.0015  Score=50.81  Aligned_cols=25  Identities=36%  Similarity=0.393  Sum_probs=22.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.|.|++|+||||+++.+.+.
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999765

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.56  E-value=0.0012  Score=52.04  Aligned_cols=24  Identities=21%  Similarity=0.423  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+|+.+...
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            468999999999999999999765

>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=96.56  E-value=0.0064  Score=57.80  Aligned_cols=118  Identities=16%  Similarity=0.131  Sum_probs=63.5

Q ss_pred             CccccccchHHHHHHHhhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.+..++.+...+.....   +.+.....+.++|++|+|||++|+.+.+..  ..   ..+.++++.......   
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l--~~---~~~~i~~s~~~~~~~---  529 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL--GI---ELLRFDMSEYMERHT---  529 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH--TC---EEEEEEGGGCSSSSC---
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh--cC---CEEEEechhhcchhh---
Confidence            4578888888888776654210   112345578999999999999999998863  11   123344433211100   


Q ss_pred             HHHHHhcCCCCCCCHH-HHHHHHHHHh-CCCeEEEEEeCCCCCChhhHHHhhcc
Q 041190          207 VILQAAAGSADVNDLN-LLQLQLENQL-KNKKFLLVLDDMWSENYDVWTNLCKP  258 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~-~~~~~l~~~l-~~kr~LiVlDdvw~~~~~~w~~l~~~  258 (261)
                       +..-++..  +.... .....+.+.+ +....+|+||++....++.++.|...
T Consensus       530 -~~~l~g~~--~g~~g~~~~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~  580 (758)
T 1r6b_X          530 -VSRLIGAP--PGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQV  580 (758)
T ss_dssp             -CSSSCCCC--SCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHH
T ss_pred             -HhhhcCCC--CCCcCccccchHHHHHHhCCCcEEEEeCccccCHHHHHHHHHH
Confidence             00001100  11111 0001112222 23467999999988877666665443

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.55  E-value=0.0022  Score=52.57  Aligned_cols=42  Identities=21%  Similarity=0.179  Sum_probs=29.7

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+.+...+..... ......+|.++|++|+||||+|+.+...
T Consensus        14 ~~~~~~~~~~~~~~-~~~~~~~i~l~G~~GsGKSTla~~L~~~   55 (253)
T 2p5t_B           14 ALARNLRSLTRGKK-SSKQPIAILLGGQSGAGKTTIHRIKQKE   55 (253)
T ss_dssp             HHHHHHHHHHTTCC-CCSSCEEEEEESCGGGTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCC-cccCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34444444444322 3445679999999999999999999765

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.55  E-value=0.0014  Score=50.77  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+++.+.+.
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            47899999999999999999875

>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=96.54  E-value=0.0018  Score=49.69  Aligned_cols=25  Identities=24%  Similarity=0.433  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|+|++|+||||+++.+...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            3568999999999999999998764

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.54  E-value=0.0013  Score=50.60  Aligned_cols=24  Identities=33%  Similarity=0.588  Sum_probs=20.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|++|+|||||++.++..
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~~   32 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFKP   32 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSCG
T ss_pred             CEEEEEECCCCCCHHHHHHHHccC
Confidence            468999999999999999976543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.53  E-value=0.0014  Score=51.69  Aligned_cols=25  Identities=32%  Similarity=0.450  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|+|++|+|||||++.+...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~   52 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADE   52 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999999765

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.52  E-value=0.0034  Score=54.75  Aligned_cols=96  Identities=15%  Similarity=0.052  Sum_probs=52.1

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc-cccceeEEEeeCCCCCHHHHHHHHHHHhc-----C
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK-KYFSFRACAYVSEDFDAVGVTKVILQAAA-----G  214 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~~~i~~~i~~~l~-----~  214 (261)
                      .+++.+..-     .+-..++|+|.+|+|||||++.+.+..... ..+.| +++-+.+.....   .++.+.+.     .
T Consensus       163 raID~~~pi-----~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~-I~~lIGER~~Ev---~~~~~~~~~~vV~a  233 (422)
T 3ice_A          163 RVLDLASPI-----GRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVL-MVLLIDERPEEV---TEMQRLVKGEVVAS  233 (422)
T ss_dssp             HHHHHHSCC-----BTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEE-EEEEESSCHHHH---HHHHTTCSSEEEEE
T ss_pred             eeeeeeeee-----cCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeE-EEEEecCChHHH---HHHHHHhCeEEEEe
Confidence            345555442     234578999999999999999987652111 12323 356666643221   12223321     1


Q ss_pred             CCCCCCHHH---------HHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          215 SADVNDLNL---------LQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       215 ~~~~~~~~~---------~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      ..+......         ....+++  .++.+||++||+-.-
T Consensus       234 tadep~~~r~~~a~~alt~AEyfrd--~G~dVLil~DslTR~  273 (422)
T 3ice_A          234 TFDEPASRHVQVAEMVIEKAKRLVE--HKKDVIILLDSITRL  273 (422)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHHHHHH--TSCEEEEEEECHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh--cCCCEEEEEeCchHH
Confidence            112111111         1222332  589999999998543

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.52  E-value=0.0024  Score=57.77  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=36.1

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..++.+...+...        .-+.++|++|+|||+||+.+.+..
T Consensus        22 ~~ivGq~~~i~~l~~al~~~--------~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSG--------ESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHT--------CEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhhHHHHHHHHHHHHHHhcC--------CeeEeecCchHHHHHHHHHHHHHH
Confidence            34789888888888777653        368899999999999999998863

>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=96.52  E-value=0.0014  Score=51.01  Aligned_cols=23  Identities=43%  Similarity=0.559  Sum_probs=20.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++|+|++|+|||||++.+....
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999998654

>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=96.51  E-value=0.0068  Score=53.27  Aligned_cols=104  Identities=16%  Similarity=0.066  Sum_probs=57.1

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccccc----ccceeEEEeeCCCCCHHHHHHHHHHHhcC
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKK----YFSFRACAYVSEDFDAVGVTKVILQAAAG  214 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~i~~~i~~~l~~  214 (261)
                      ...|-.+|..    +-+.-.++.|+|++|+|||||+..++-......    .-...+|+.....+....+. .+.+.++-
T Consensus       164 ~~~LD~lLgG----GI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~-~~a~~~gl  238 (400)
T 3lda_A          164 SKNLDTLLGG----GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLV-SIAQRFGL  238 (400)
T ss_dssp             CHHHHHHTTT----SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             ChhHHHHhcC----CcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHH-HHHHHcCC
Confidence            3445555532    223456999999999999999997753211111    12346788776665555433 34454441


Q ss_pred             C----------CCCCCHH---HHHHHHHHHh-CCCeEEEEEeCCCCC
Q 041190          215 S----------ADVNDLN---LLQLQLENQL-KNKKFLLVLDDMWSE  247 (261)
Q Consensus       215 ~----------~~~~~~~---~~~~~l~~~l-~~kr~LiVlDdvw~~  247 (261)
                      .          ....+..   +....+...+ ..+.-+||+|.+-..
T Consensus       239 ~~~~vleni~~~~~~~~~~~~~~l~~~~~~l~~~~~~llVIDs~t~~  285 (400)
T 3lda_A          239 DPDDALNNVAYARAYNADHQLRLLDAAAQMMSESRFSLIVVDSVMAL  285 (400)
T ss_dssp             CHHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHSCEEEEEEETGGGG
T ss_pred             ChHhHhhcEEEeccCChHHHHHHHHHHHHHHHhcCCceEEecchhhh
Confidence            1          0112222   2223333333 346789999997654

>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=96.51  E-value=0.0015  Score=51.87  Aligned_cols=24  Identities=38%  Similarity=0.595  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++.|+|++|+|||||++.+...
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            468999999999999999999765

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.49  E-value=0.0018  Score=50.73  Aligned_cols=26  Identities=38%  Similarity=0.321  Sum_probs=22.8

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|+|.|+.|+||||+++.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            35689999999999999999998764

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.49  E-value=0.0015  Score=50.63  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.|.++|++|+||||+++.+.+.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~   28 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKL   28 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            357889999999999999999765

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.48  E-value=0.0027  Score=54.11  Aligned_cols=27  Identities=22%  Similarity=0.177  Sum_probs=23.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .....+++|.|++|+|||||++.+..-
T Consensus        89 ~~~p~iigI~GpsGSGKSTl~~~L~~l  115 (321)
T 3tqc_A           89 PKVPYIIGIAGSVAVGKSTTSRVLKAL  115 (321)
T ss_dssp             CCCCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            446789999999999999999998654

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.48  E-value=0.0015  Score=55.63  Aligned_cols=42  Identities=19%  Similarity=0.161  Sum_probs=35.1

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|++..++.+...+...        .-+.++|++|+|||+||+.+.+.
T Consensus        28 ~i~g~~~~~~~l~~~l~~~--------~~vll~G~pGtGKT~la~~la~~   69 (331)
T 2r44_A           28 VVVGQKYMINRLLIGICTG--------GHILLEGVPGLAKTLSVNTLAKT   69 (331)
T ss_dssp             TCCSCHHHHHHHHHHHHHT--------CCEEEESCCCHHHHHHHHHHHHH
T ss_pred             ceeCcHHHHHHHHHHHHcC--------CeEEEECCCCCcHHHHHHHHHHH
Confidence            5789988888888877653        35789999999999999999875

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.48  E-value=0.0017  Score=51.15  Aligned_cols=24  Identities=33%  Similarity=0.575  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+++|+|++|+||||+++.+...
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            358999999999999999999765

>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=96.47  E-value=0.0017  Score=50.55  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=20.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .++.|+|++|+|||||++.+..
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

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.46  E-value=0.0098  Score=56.75  Aligned_cols=101  Identities=17%  Similarity=0.077  Sum_probs=58.1

Q ss_pred             CCCccccccchHHHHHHHhhCCCCC-------CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLN-------SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD  200 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  200 (261)
                      .-..+.|.++.++.|.+.+...-..       +....+=+-++|++|+|||.+|+.+.+..  ..+|     +.++.   
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 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC--QANF-----ISIKG---  544 (806)
T ss_dssp             CSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTT--TCEE-----EECCH---
T ss_pred             CHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHh--CCce-----EEecc---
Confidence            3456778888888877765432100       12234456799999999999999999873  2222     22221   


Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          201 AVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       201 ~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                       .+        +....-..+...+...+...-+...++|+||++.+.
T Consensus       545 -~~--------l~s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl  582 (806)
T 3cf2_A          545 -PE--------LLTMWFGESEANVREIFDKARQAAPCVLFFDELDSI  582 (806)
T ss_dssp             -HH--------HHTTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGC
T ss_pred             -ch--------hhccccchHHHHHHHHHHHHHHcCCceeechhhhHH
Confidence             11        111112223333323333333567899999999764

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.45  E-value=0.0022  Score=50.50  Aligned_cols=26  Identities=35%  Similarity=0.386  Sum_probs=22.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|.|.|++|+||||+++.+.+.
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34678999999999999999999865

>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=96.44  E-value=0.0016  Score=50.48  Aligned_cols=23  Identities=39%  Similarity=0.709  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+++.+.+.
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            57999999999999999999775

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.44  E-value=0.017  Score=48.74  Aligned_cols=25  Identities=32%  Similarity=0.284  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|+|++|+||||++..+...
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            4679999999999999999988765

>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=96.44  E-value=0.0021  Score=50.82  Aligned_cols=25  Identities=36%  Similarity=0.407  Sum_probs=22.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|+|+|++|+||||+++.+...
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            4578999999999999999999764

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.42  E-value=0.0017  Score=49.49  Aligned_cols=26  Identities=27%  Similarity=0.285  Sum_probs=21.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|.|.|++|+||||+++.+.+.
T Consensus         5 ~~~~~i~l~G~~GsGKSTva~~La~~   30 (168)
T 1zuh_A            5 HHMQHLVLIGFMGSGKSSLAQELGLA   30 (168)
T ss_dssp             ---CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             cccceEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999775

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=96.40  E-value=0.0016  Score=50.31  Aligned_cols=24  Identities=38%  Similarity=0.541  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|+|++|+||||+++.+.+.
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            457889999999999999999765

>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=96.40  E-value=0.011  Score=52.89  Aligned_cols=88  Identities=18%  Similarity=0.250  Sum_probs=49.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc--------CCCCCCC-HHH----
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA--------GSADVND-LNL----  223 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~--------~~~~~~~-~~~----  223 (261)
                      ..+.|+|.+|+|||||++.+..+.... .-+..+++.+.+..+ ..+++.++...=.        ...+... ...    
T Consensus       152 q~~~i~G~sGvGKTtL~~~l~~~~~~~-~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~  230 (473)
T 1sky_E          152 GKIGLFGGAGVGKTVLIQELIHNIAQE-HGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVAL  230 (473)
T ss_dssp             CEEEEECCSSSCHHHHHHHHHHHHHHH-TCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEECCCCCCccHHHHHHHhhhhhc-cCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHH
Confidence            368899999999999999998763322 123456677766442 3344444432200        0111111 111    


Q ss_pred             HHHHHHHHh---CCCeEEEEEeCCCC
Q 041190          224 LQLQLENQL---KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 ~~~~l~~~l---~~kr~LiVlDdvw~  246 (261)
                      ..-.+-+++   ++++.||++||+-.
T Consensus       231 ~~ltiAEyFrd~~G~~VLl~~D~itR  256 (473)
T 1sky_E          231 TGLTMAEYFRDEQGQDGLLFIDNIFR  256 (473)
T ss_dssp             HHHHHHHHHHHHSCCEEEEEEECTHH
T ss_pred             HHHHHHHHHHHhcCCcEEEEeccHHH
Confidence            011233333   58999999999944

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=96.39  E-value=0.0015  Score=51.51  Aligned_cols=23  Identities=30%  Similarity=0.606  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++++|+|++|+|||||++.+...
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~   27 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQE   27 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            57899999999999999999753

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.39  E-value=0.0021  Score=50.08  Aligned_cols=24  Identities=25%  Similarity=0.351  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+++.+.+.
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            468999999999999999999765

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.38  E-value=0.002  Score=50.00  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+|+.+.+.
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999998765

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.38  E-value=0.0018  Score=50.73  Aligned_cols=22  Identities=32%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|+.|+||||+++.+.+.
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            6899999999999999999875

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=96.36  E-value=0.002  Score=50.79  Aligned_cols=22  Identities=41%  Similarity=0.487  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+|+|+|+.|+||||+++.+..
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            4799999999999999999876

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.36  E-value=0.0019  Score=51.67  Aligned_cols=23  Identities=39%  Similarity=0.548  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|+|+|++|+||||+++.+...
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~   28 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEA   28 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999988654

>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=96.35  E-value=0.0025  Score=49.54  Aligned_cols=25  Identities=36%  Similarity=0.458  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.|+|++|+||||+++.+.+.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999998765

>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=96.35  E-value=0.0019  Score=50.59  Aligned_cols=23  Identities=39%  Similarity=0.621  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|+|++|+|||||++.+...
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            45789999999999999999765

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.34  E-value=0.0018  Score=51.24  Aligned_cols=24  Identities=29%  Similarity=0.542  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|+|++|+|||||++.+...
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            468999999999999999999765

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.34  E-value=0.0021  Score=52.88  Aligned_cols=23  Identities=26%  Similarity=0.212  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.|++|+||||||+.+...
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            47899999999999999998765

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.32  E-value=0.0024  Score=51.26  Aligned_cols=27  Identities=26%  Similarity=0.209  Sum_probs=24.1

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+.++|.|.|++|+||||+|+.+.+.
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            446789999999999999999999876

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.32  E-value=0.0031  Score=48.85  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+++.+.+.
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            468999999999999999999775

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=96.31  E-value=0.0024  Score=52.67  Aligned_cols=24  Identities=29%  Similarity=0.504  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|+|++|+||||+|+.+...
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            468999999999999999999765

>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=0.029  Score=49.79  Aligned_cols=25  Identities=24%  Similarity=0.316  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..+|.++|.+|+||||++..+...
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~  123 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARY  123 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHH
Confidence            4789999999999999998887653

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.30  E-value=0.003  Score=48.97  Aligned_cols=26  Identities=35%  Similarity=0.335  Sum_probs=22.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....+|.+.|++|+||||+++.+...
T Consensus        11 ~~~~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           11 EKGIVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            34578999999999999999999775

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=96.29  E-value=0.0024  Score=50.35  Aligned_cols=22  Identities=41%  Similarity=0.545  Sum_probs=20.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+|+|.|+.|+||||+++.+..
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

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.28  E-value=0.0019  Score=49.59  Aligned_cols=23  Identities=39%  Similarity=0.511  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|.|++|+||||+|+.+...
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            36899999999999999999775

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=96.28  E-value=0.0024  Score=54.55  Aligned_cols=46  Identities=20%  Similarity=0.234  Sum_probs=32.5

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..+..+...+...      ...-+.++|++|+|||++|+.+.+..
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~------~~~~vLl~G~~GtGKT~la~~la~~~   69 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDP------GIGGVLVFGDRGTGKSTAVRALAALL   69 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCG------GGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             hhccChHHHHHHHHHHhhCC------CCceEEEECCCCccHHHHHHHHHHhC
Confidence            45889877655544444321      12238899999999999999998763

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=96.28  E-value=0.0026  Score=52.12  Aligned_cols=26  Identities=15%  Similarity=0.167  Sum_probs=22.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|+|.|++|+||||+|+.+...
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~   45 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQL   45 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999998774

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=96.27  E-value=0.0023  Score=52.10  Aligned_cols=24  Identities=29%  Similarity=0.318  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+++|+|++|+|||||++.+.+.
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~   50 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQN   50 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999844

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.26  E-value=0.0026  Score=49.18  Aligned_cols=24  Identities=25%  Similarity=0.227  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.+.|++|+||||+++.+.+.
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~   27 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQE   27 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357999999999999999999764

>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=96.26  E-value=0.031  Score=50.26  Aligned_cols=25  Identities=32%  Similarity=0.385  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++|+|.+|+|||||++.+..-
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgl  316 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQ  316 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHH
Confidence            4679999999999999999998764

>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=96.25  E-value=0.0024  Score=50.64  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl   43 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRER   43 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999998653

>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=96.25  E-value=0.0019  Score=49.94  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~   25 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKA   25 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            36899999999999999998764

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=96.25  E-value=0.012  Score=52.15  Aligned_cols=25  Identities=28%  Similarity=0.228  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.++|++|+||||++..+...
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999999888754

>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=96.25  E-value=0.0027  Score=53.88  Aligned_cols=26  Identities=27%  Similarity=0.312  Sum_probs=22.8

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....+++|.|++|+|||||++.+..-
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gl  113 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQAL  113 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhh
Confidence            35679999999999999999999764

>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=96.24  E-value=0.003  Score=49.63  Aligned_cols=25  Identities=24%  Similarity=0.222  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.|.|++|+||||+|+.+...
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~   43 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEK   43 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3458999999999999999999765

>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=96.23  E-value=0.0026  Score=49.01  Aligned_cols=25  Identities=28%  Similarity=0.320  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|+|..|+|||||+..+...
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            4679999999999999999998875

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.23  E-value=0.045  Score=46.30  Aligned_cols=39  Identities=13%  Similarity=0.084  Sum_probs=28.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVS  196 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  196 (261)
                      .-.++.|.|.+|+||||||..+..+.-.+.  ...+|++..
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE  105 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE  105 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC
Confidence            446899999999999999998876532222  456666654

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.22  E-value=0.0026  Score=49.64  Aligned_cols=23  Identities=30%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+++.+.+.
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            58999999999999999999775

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.22  E-value=0.003  Score=51.45  Aligned_cols=25  Identities=20%  Similarity=0.254  Sum_probs=22.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++|.|+.|+|||||++.+...
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~   48 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMEL   48 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999998764

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.21  E-value=0.003  Score=49.76  Aligned_cols=24  Identities=29%  Similarity=0.446  Sum_probs=21.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+|.|.|++|+||||+++.+.+..
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHH
Confidence            589999999999999999998763

>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=96.20  E-value=0.044  Score=48.56  Aligned_cols=25  Identities=32%  Similarity=0.196  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.++|++|+||||++..+...
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~  120 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYF  120 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998888654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.18  E-value=0.0018  Score=49.92  Aligned_cols=24  Identities=33%  Similarity=0.375  Sum_probs=17.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+|+.+.+.
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            468999999999999999999765

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=96.17  E-value=0.0033  Score=48.42  Aligned_cols=25  Identities=28%  Similarity=0.321  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-.+|.+.|+.|+||||+++.+...
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~   28 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEY   28 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999764

>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=96.17  E-value=0.0024  Score=48.76  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+|+.+.+.
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            46899999999999999999775

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.15  E-value=0.0029  Score=49.14  Aligned_cols=22  Identities=36%  Similarity=0.617  Sum_probs=20.3

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|.|.|++|+||||+++.+.+.
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            6899999999999999999875

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=96.15  E-value=0.025  Score=50.50  Aligned_cols=65  Identities=23%  Similarity=0.225  Sum_probs=42.8

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHH
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQA  211 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~  211 (261)
                      +.++.|..-.     +-.-++|.|.+|+|||+|++.+.+... +.+-++.+++-+.+... ..++++++...
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-----KGGKIGLFGGAGVGKTVLIMELINNVA-KAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCEE-----TTCEEEEEECTTSSHHHHHHHHHHHTT-TTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEecccccc-----cCCeeeeecCCCCChHHHHHHHHHhhH-hhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            4555555421     234689999999999999999987631 22335567788887543 45566666553

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=96.15  E-value=0.0026  Score=51.00  Aligned_cols=24  Identities=33%  Similarity=0.541  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999998764

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.14  E-value=0.024  Score=48.40  Aligned_cols=26  Identities=35%  Similarity=0.262  Sum_probs=22.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...+++++|++|+||||+++.+..-
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~  152 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANW  152 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999988764

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=96.13  E-value=0.0031  Score=50.36  Aligned_cols=24  Identities=25%  Similarity=0.181  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|.+.|++|+||||+++.+.+.
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            467999999999999999999775

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.13  E-value=0.003  Score=47.97  Aligned_cols=22  Identities=27%  Similarity=0.332  Sum_probs=20.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|++|+||||+++.+.+.
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            5899999999999999999775

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=96.13  E-value=0.0035  Score=49.55  Aligned_cols=24  Identities=21%  Similarity=0.333  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+++.+.+.
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            468999999999999999999875

>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=96.10  E-value=0.0032  Score=49.76  Aligned_cols=25  Identities=16%  Similarity=0.526  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+++.|+|++|+|||||++.+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhh
Confidence            3468999999999999999999865

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.09  E-value=0.0032  Score=50.57  Aligned_cols=25  Identities=24%  Similarity=0.274  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.|.|++|+||||+++.+.+.
T Consensus         6 ~~~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999875

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.08  E-value=0.0036  Score=49.43  Aligned_cols=24  Identities=25%  Similarity=0.325  Sum_probs=21.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+++.+.+.
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            468999999999999999999775

>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=96.05  E-value=0.004  Score=47.37  Aligned_cols=24  Identities=29%  Similarity=0.367  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++++.|+.|+|||||++.+..-
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            468999999999999999999764

>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=96.05  E-value=0.027  Score=47.30  Aligned_cols=24  Identities=38%  Similarity=0.293  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++.++|.+|+||||++..+...
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~  121 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF  121 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999888654

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=96.04  E-value=0.0039  Score=49.78  Aligned_cols=25  Identities=28%  Similarity=0.230  Sum_probs=22.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.++.|+|++|+|||||++.+...
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~   48 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVM   48 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3479999999999999999999763

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.03  E-value=0.048  Score=46.70  Aligned_cols=88  Identities=16%  Similarity=0.011  Sum_probs=51.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc----------------------
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA----------------------  213 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~----------------------  213 (261)
                      .-.++.|.|.+|+||||||..+......  .=..++|++..  .+...+...++....                      
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fSlE--ms~~ql~~Rlls~~~~v~~~~l~~g~Ls~~e~~~l~~  120 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFSLE--MSAEQLALRALSDLTSINMHDLESGRLDDDQWENLAK  120 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEESS--SCHHHHHHHHHHHHHCCCHHHHHHTCCCHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEeCC--CCHHHHHHHHHHHhhCCCHHHHhcCCCCHHHHHHHHH
Confidence            3468999999999999999998766322  11234555543  344454444433211                      


Q ss_pred             ------------CCCCCCCHHHHHHHHHHHhCC--CeEEEEEeCCCCC
Q 041190          214 ------------GSADVNDLNLLQLQLENQLKN--KKFLLVLDDMWSE  247 (261)
Q Consensus       214 ------------~~~~~~~~~~~~~~l~~~l~~--kr~LiVlDdvw~~  247 (261)
                                  ......+..++...++...+.  ..-+||+|-+-..
T Consensus       121 a~~~l~~~~l~I~d~~~~si~~i~~~ir~l~~~~gg~~lIVIDyLqlm  168 (338)
T 4a1f_A          121 CFDHLSQKKLFFYDKSYVRIEQIRLQLRKLKSQHKELGIAFIDYLQLM  168 (338)
T ss_dssp             HHHHHHHSCEEEECCTTCCHHHHHHHHHHHHHHCTTEEEEEEEEEECC
T ss_pred             HHHHHhcCCeEEeCCCCCcHHHHHHHHHHHHHhcCCCCEEEEechHHh
Confidence                        011223566666666655432  5778888876544

>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=96.02  E-value=0.0043  Score=51.80  Aligned_cols=24  Identities=38%  Similarity=0.653  Sum_probs=21.6

Q ss_pred             CCceEEeEeecCCCChHHHHHHHh
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ....+|+|.|++|+||||+|+.+.
T Consensus        73 ~~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           73 SGLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TTCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            346799999999999999999987

>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=96.02  E-value=0.0038  Score=50.17  Aligned_cols=25  Identities=20%  Similarity=0.327  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.+++|+|++|+|||||.+.+...
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc
Confidence            3468999999999999999999875

>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=96.01  E-value=0.002  Score=51.01  Aligned_cols=22  Identities=36%  Similarity=0.585  Sum_probs=20.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|.|.|+.|+||||+++.+...
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            6899999999999999998765

>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=96.01  E-value=0.0041  Score=52.60  Aligned_cols=25  Identities=28%  Similarity=0.299  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++|+|++|+||||+++.+..-
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagl  125 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRY  125 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4579999999999999999998753

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.00  E-value=0.0039  Score=51.09  Aligned_cols=23  Identities=35%  Similarity=0.509  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ..+|+|.|+.|+||||+++.+.+
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            46899999999999999999873

>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=95.99  E-value=0.0048  Score=48.54  Aligned_cols=26  Identities=35%  Similarity=0.473  Sum_probs=23.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+-.+|+|+|+.|+||||+++.+.+.
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHHh
Confidence            45789999999999999999998764

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.98  E-value=0.0037  Score=49.99  Aligned_cols=24  Identities=25%  Similarity=0.250  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|.|.|++|+||||+++.+.+.
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            467899999999999999999775

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.97  E-value=0.0069  Score=52.19  Aligned_cols=44  Identities=20%  Similarity=0.164  Sum_probs=29.4

Q ss_pred             ccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          135 REKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       135 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.-.+.+.+.+...-  .......|.++|++|+||||+++.+...
T Consensus         4 ~~~L~~~il~~l~~~i--~~g~~~~i~l~G~~G~GKTTl~~~la~~   47 (359)
T 2ga8_A            4 THKLADDVLQLLDNRI--EDNYRVCVILVGSPGSGKSTIAEELCQI   47 (359)
T ss_dssp             HHHHHHHHHHHHHHTT--TTCSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHh--ccCCeeEEEEECCCCCcHHHHHHHHHHH
Confidence            3444555555553211  1234567899999999999999988764

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.95  E-value=0.0034  Score=50.08  Aligned_cols=24  Identities=21%  Similarity=0.315  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|.+.|++|+||||+++.+.+.
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~   28 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKE   28 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999999775

>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=95.95  E-value=0.0038  Score=50.71  Aligned_cols=23  Identities=26%  Similarity=0.379  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            35899999999999999999965

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=95.95  E-value=0.0042  Score=50.67  Aligned_cols=22  Identities=23%  Similarity=0.388  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
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            7899999999999999999965

>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=95.93  E-value=0.005  Score=48.87  Aligned_cols=24  Identities=33%  Similarity=0.295  Sum_probs=21.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+++.+...
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            478999999999999999998765

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=95.93  E-value=0.0041  Score=50.12  Aligned_cols=22  Identities=32%  Similarity=0.445  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
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            5899999999999999999965

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.92  E-value=0.0041  Score=49.35  Aligned_cols=22  Identities=32%  Similarity=0.501  Sum_probs=19.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|++|+||||+|+.+...
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            4789999999999999999765

>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=95.91  E-value=0.0055  Score=51.82  Aligned_cols=25  Identities=28%  Similarity=0.258  Sum_probs=22.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++|+|+.|+|||||++.+..-
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~~  103 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQAL  103 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999998764

>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=95.90  E-value=0.0049  Score=48.27  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=21.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|+.|+||||+++.+.+.
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            58999999999999999999875

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.87  E-value=0.004  Score=48.87  Aligned_cols=22  Identities=36%  Similarity=0.395  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++|+|+.|+|||||++.+...
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            6899999999999999998764

>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=95.87  E-value=0.0053  Score=50.01  Aligned_cols=25  Identities=20%  Similarity=0.048  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....|.|.|++|+||||+|+.+.+.
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            4578999999999999999999765

>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=95.86  E-value=0.0057  Score=48.66  Aligned_cols=23  Identities=30%  Similarity=0.397  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ..+|+|.|+.|+||||+++.+..
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            36899999999999999999865

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.85  E-value=0.0026  Score=49.11  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|.+|+|||||++.+..-
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            58999999999999999999765

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.85  E-value=0.0028  Score=51.09  Aligned_cols=21  Identities=29%  Similarity=0.513  Sum_probs=15.9

Q ss_pred             eEEeEeecCCCChHHHHHHHh
Q 041190          158 SVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      .+++|+|+.|+|||||++.+.
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

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.84  E-value=0.0058  Score=48.71  Aligned_cols=38  Identities=24%  Similarity=0.261  Sum_probs=27.9

Q ss_pred             chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          137 KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       137 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.+...+..      .+...|.|+|.+|+|||||+..+...
T Consensus        24 ~~a~~~r~~~~~------~~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           24 RLADKNRKLLNK------HGVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             HHHHHHHHHHHH------TTCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh------CCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            344555555432      24688999999999999999988765

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.84  E-value=0.011  Score=51.14  Aligned_cols=25  Identities=36%  Similarity=0.332  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++|+|++|+||||+++.+..-
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~  180 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHR  180 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhh
Confidence            4679999999999999999988764

>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=95.82  E-value=0.0048  Score=48.99  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|++|+||||+|+.+...
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            4789999999999999999765

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=95.80  E-value=0.0044  Score=49.39  Aligned_cols=23  Identities=30%  Similarity=0.242  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999999753

>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=95.78  E-value=0.005  Score=50.09  Aligned_cols=23  Identities=22%  Similarity=0.546  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
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            58999999999999999999764

>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=95.77  E-value=0.038  Score=49.57  Aligned_cols=88  Identities=18%  Similarity=0.241  Sum_probs=55.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCC-HHHHHHHHHHHhc-C--------------CCCCCCH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFD-AVGVTKVILQAAA-G--------------SADVNDL  221 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~i~~~i~~~l~-~--------------~~~~~~~  221 (261)
                      .-++|.|..|+|||+|++.+.++.. +.+-++.+++-+.+... ..+++.++...=. .              +.+....
T Consensus       166 qr~gIfgg~GvGKT~L~~~l~~~~a-~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d~p~~  244 (498)
T 1fx0_B          166 GKIGLFGGAGVGKTVLIMELINNIA-KAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPG  244 (498)
T ss_dssp             CCEEEEECSSSSHHHHHHHHHHHTT-TTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTTSCHH
T ss_pred             CeEEeecCCCCCchHHHHHHHHHHH-hhCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceEEEEeCCCCCHH
Confidence            4589999999999999999987631 22346778888888654 4566666654311 1              1111111


Q ss_pred             -----HHHHHHHHHHhC---CCeEEEEEeCCCC
Q 041190          222 -----NLLQLQLENQLK---NKKFLLVLDDMWS  246 (261)
Q Consensus       222 -----~~~~~~l~~~l~---~kr~LiVlDdvw~  246 (261)
                           ....-.+-++++   ++.+||++||+-.
T Consensus       245 ~R~~~~~~altiAEyfrd~~G~dVLl~~DsitR  277 (498)
T 1fx0_B          245 ARMRVGLTALTMAEYFRDVNEQDVLLFIDNIFR  277 (498)
T ss_dssp             HHTTHHHHHHHTHHHHTTTSCCEEEEEEECSHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHH
Confidence                 122233445554   6899999999844

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=95.76  E-value=0.005  Score=50.87  Aligned_cols=23  Identities=35%  Similarity=0.408  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999965

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.75  E-value=0.009  Score=47.43  Aligned_cols=37  Identities=16%  Similarity=0.219  Sum_probs=27.4

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+..++..     -++-+.+.++|++|+||||+|..+.+.
T Consensus        45 ~~~l~~~~~~-----iPkkn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           45 LGALKSFLKG-----TPKKNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             HHHHHHHHHT-----CTTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHhc-----CCcccEEEEECCCCCCHHHHHHHHHHH
Confidence            5556666643     233457999999999999998888776

>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=95.73  E-value=0.0052  Score=51.17  Aligned_cols=22  Identities=41%  Similarity=0.463  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
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            5899999999999999999865

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.73  E-value=0.13  Score=46.53  Aligned_cols=42  Identities=24%  Similarity=0.148  Sum_probs=27.7

Q ss_pred             HHHHHHHhhCCCCC---CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLN---SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~---~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.++|......   ...+..+|.|+|.+|+||||++..+...
T Consensus        80 ~~eL~~ll~~~~~~~~~~~~~~~vI~ivG~~GvGKTTl~~kLA~~  124 (504)
T 2j37_W           80 FKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSKLAYY  124 (504)
T ss_dssp             HHHHHHHHCCCCCCCCCCSS--EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhccccchhccccCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45566666542210   1135779999999999999999888743

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.72  E-value=0.0063  Score=51.38  Aligned_cols=25  Identities=36%  Similarity=0.332  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++++|++|+||||+++.+..-
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~  123 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHR  123 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4579999999999999999988754

>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=95.71  E-value=0.0055  Score=49.90  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999653

>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=95.70  E-value=0.0055  Score=50.46  Aligned_cols=22  Identities=36%  Similarity=0.520  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
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            5899999999999999999864

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=95.69  E-value=0.015  Score=46.96  Aligned_cols=27  Identities=30%  Similarity=0.327  Sum_probs=23.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      ...+|.|.|++|+||||+++.+.+...
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~   51 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLV   51 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999988743

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=95.68  E-value=0.01  Score=45.82  Aligned_cols=26  Identities=35%  Similarity=0.336  Sum_probs=22.1

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .....|.++|.+|+|||||.+.+...
T Consensus        46 ~~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           46 SYQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34557899999999999999998765

>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=95.66  E-value=0.0064  Score=47.72  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=20.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +|+|.|+.|+||||+++.+...
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~   25 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAA   25 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            8999999999999999998764

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.66  E-value=0.0071  Score=47.99  Aligned_cols=41  Identities=24%  Similarity=0.212  Sum_probs=30.0

Q ss_pred             cccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          134 GREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       134 gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.++..+.+...+..      .+..++.|+|.+|+|||||+..+...
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            334455555555532      24689999999999999999988765

>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=95.66  E-value=0.0061  Score=49.94  Aligned_cols=22  Identities=32%  Similarity=0.552  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
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            5899999999999999999987

>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=95.65  E-value=0.0065  Score=46.97  Aligned_cols=25  Identities=24%  Similarity=0.377  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|+|..|+|||||++.+...
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHh
Confidence            4678999999999999999998865

>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=95.65  E-value=0.0059  Score=50.48  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcC
Confidence            358999999999999999999653

>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=95.64  E-value=0.0059  Score=50.56  Aligned_cols=22  Identities=36%  Similarity=0.617  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||++.+..
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            5899999999999999999965

>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=95.64  E-value=0.0061  Score=49.26  Aligned_cols=23  Identities=26%  Similarity=0.645  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
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            58999999999999999999764

>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=95.63  E-value=0.0066  Score=49.53  Aligned_cols=23  Identities=35%  Similarity=0.459  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
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            36899999999999999999965

>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=95.62  E-value=0.0054  Score=49.12  Aligned_cols=23  Identities=35%  Similarity=0.537  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999999754

>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=95.62  E-value=0.0062  Score=49.84  Aligned_cols=23  Identities=43%  Similarity=0.580  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999653

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.61  E-value=0.017  Score=49.10  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=22.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....++.|+|++|+||||++..+...
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~~  128 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMANY  128 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999887653

>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=95.61  E-value=0.0065  Score=50.33  Aligned_cols=24  Identities=33%  Similarity=0.362  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999873

>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=95.60  E-value=0.0071  Score=51.36  Aligned_cols=24  Identities=33%  Similarity=0.570  Sum_probs=20.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      +.+||+|+|-||+||||.+-.+.-
T Consensus        47 ~aKVIAIaGKGGVGKTTtavNLA~   70 (314)
T 3fwy_A           47 GAKVFAVYGKGGIGKSTTSSNLSA   70 (314)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CceEEEEECCCccCHHHHHHHHHH
Confidence            578999999999999998876644

>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=95.57  E-value=0.0066  Score=50.00  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.57  E-value=0.0075  Score=49.80  Aligned_cols=24  Identities=29%  Similarity=0.419  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g~   48 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMIDY   48 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHHh
Confidence            469999999999999999988653

>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=95.56  E-value=0.0071  Score=49.05  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.|.|++|+||||+++.+...
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~   32 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARA   32 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999765

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=95.55  E-value=0.0067  Score=50.37  Aligned_cols=24  Identities=38%  Similarity=0.427  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999653

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=95.54  E-value=0.0068  Score=49.99  Aligned_cols=23  Identities=30%  Similarity=0.572  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            58999999999999999999653

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.53  E-value=0.0061  Score=50.00  Aligned_cols=23  Identities=30%  Similarity=0.499  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|+|++|+||||+++.+...
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~   71 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARS   71 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            57999999999999999999764

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.52  E-value=0.0043  Score=52.04  Aligned_cols=25  Identities=24%  Similarity=0.372  Sum_probs=18.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..+|+|.|..|+||||+|+.+.+.
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~   28 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQI   28 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999998764

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=95.51  E-value=0.0079  Score=47.74  Aligned_cols=22  Identities=32%  Similarity=0.357  Sum_probs=19.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|++|+||||+++.+.+.
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            4789999999999999999775

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.50  E-value=0.008  Score=51.53  Aligned_cols=23  Identities=35%  Similarity=0.316  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||||+.+...
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            58999999999999999998875

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.50  E-value=0.045  Score=44.19  Aligned_cols=25  Identities=24%  Similarity=0.300  Sum_probs=20.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-.-++|.|++|+||||+|+.+.+.
T Consensus         7 ~~~~~~~~G~pGsGKsT~a~~L~~~   31 (230)
T 3gmt_A            7 HHMRLILLGAPGAGKGTQANFIKEK   31 (230)
T ss_dssp             --CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccceeeECCCCCCHHHHHHHHHHH
Confidence            3456899999999999999999776

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=95.50  E-value=0.0072  Score=50.02  Aligned_cols=23  Identities=35%  Similarity=0.462  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        34 e~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999998653

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=95.49  E-value=0.0087  Score=48.36  Aligned_cols=27  Identities=30%  Similarity=0.369  Sum_probs=22.4

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .....+|+|.|+.|+||||+++.+...
T Consensus        13 ~~~~~~i~i~G~~gsGKst~~~~l~~~   39 (236)
T 1q3t_A           13 KMKTIQIAIDGPASSGKSTVAKIIAKD   39 (236)
T ss_dssp             -CCCCEEEEECSSCSSHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            345678999999999999999988763

>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=95.49  E-value=0.0086  Score=48.26  Aligned_cols=24  Identities=25%  Similarity=0.153  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|.+.|++|+||||+|+.+.+.
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            457899999999999999999775

>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=95.49  E-value=0.0073  Score=49.49  Aligned_cols=23  Identities=26%  Similarity=0.417  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl   49 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGM   49 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            48999999999999999998753

>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=95.48  E-value=0.017  Score=51.28  Aligned_cols=52  Identities=23%  Similarity=0.259  Sum_probs=36.1

Q ss_pred             CccccccchHHHHHHHhhCC--------CCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLLGD--------DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..++|.+..++.|...+...        ........+-+.++|++|+||||+|+.+....
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l   74 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHc
Confidence            45788888888876665321        00011234568899999999999999998763

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=95.48  E-value=0.0073  Score=50.39  Aligned_cols=23  Identities=30%  Similarity=0.395  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl   70 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAY   70 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            48999999999999999999653

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=95.48  E-value=0.056  Score=45.33  Aligned_cols=25  Identities=28%  Similarity=0.228  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+++++|.+|+||||++..+..-
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~  121 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALY  121 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999988764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=95.48  E-value=0.0076  Score=49.51  Aligned_cols=23  Identities=30%  Similarity=0.602  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
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            48999999999999999999764

>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=95.47  E-value=0.0089  Score=52.77  Aligned_cols=26  Identities=31%  Similarity=0.431  Sum_probs=23.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...+|.|+|++|+||||+|+.+...
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            45679999999999999999998775

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=95.46  E-value=0.029  Score=49.85  Aligned_cols=88  Identities=20%  Similarity=0.190  Sum_probs=51.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccc-cccc-eeEEEeeCCCC-CHHHHHHHHHHH--hc------CCCCCCCHHH----
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVK-KYFS-FRACAYVSEDF-DAVGVTKVILQA--AA------GSADVNDLNL----  223 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~-~~~wv~v~~~~-~~~~i~~~i~~~--l~------~~~~~~~~~~----  223 (261)
                      -++|.|..|+|||+|+..+.+..... ++=+ ..+++-+.+.. ...+++.++...  +.      ...+......    
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            46888999999999999998874431 1112 45667777644 345556655443  11      1112111111    


Q ss_pred             -HHHHHHHHh---CCCeEEEEEeCCCC
Q 041190          224 -LQLQLENQL---KNKKFLLVLDDMWS  246 (261)
Q Consensus       224 -~~~~l~~~l---~~kr~LiVlDdvw~  246 (261)
                       ..-.+-+++   .++.+||++||+-.
T Consensus       233 ~~a~tiAEyfrd~~G~~VLl~~DslTr  259 (465)
T 3vr4_D          233 RMALTAAEYLAYEKGMHVLVIMTDMTN  259 (465)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEECHHH
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence             112244554   37999999999843

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=95.46  E-value=0.0084  Score=49.73  Aligned_cols=22  Identities=41%  Similarity=0.705  Sum_probs=19.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|+|+.|+|||||.+.++.-
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~   25 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKS   25 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5799999999999999999754

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.45  E-value=0.0097  Score=50.90  Aligned_cols=25  Identities=20%  Similarity=0.270  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.|+|+.|+|||||+..+...
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999876

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.45  E-value=0.0081  Score=48.15  Aligned_cols=22  Identities=41%  Similarity=0.425  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|.|++|+||||+++.+...
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            5889999999999999999775

>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=95.44  E-value=0.0087  Score=48.20  Aligned_cols=26  Identities=27%  Similarity=0.107  Sum_probs=22.6

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-.+|+|.|+.|+|||||++.+...
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            34579999999999999999998764

>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=95.40  E-value=0.009  Score=49.97  Aligned_cols=23  Identities=30%  Similarity=0.404  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||+|+.+.+.
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999763

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.40  E-value=0.02  Score=59.58  Aligned_cols=84  Identities=17%  Similarity=0.065  Sum_probs=54.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC------CCCCCHHHHHHHH
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS------ADVNDLNLLQLQL  228 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~------~~~~~~~~~~~~l  228 (261)
                      +.-+++-|+|++|+|||+||.++.....  .+=...+|+.+.+.++...     +..++..      ..+...++....+
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~ea~--~~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~ 1497 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEIC 1497 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHH--TTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHH--HcCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHH
Confidence            3467899999999999999998876522  2212456788887766554     3344411      1223344555555


Q ss_pred             HHHh-CCCeEEEEEeCCC
Q 041190          229 ENQL-KNKKFLLVLDDMW  245 (261)
Q Consensus       229 ~~~l-~~kr~LiVlDdvw  245 (261)
                      +... ..+.-+||+|++.
T Consensus      1498 ~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1498 DALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHHTCCSEEEESCGG
T ss_pred             HHHHhcCCCCEEEEcChh
Confidence            5554 3567899999995

>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=95.38  E-value=0.0094  Score=50.36  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.+++|+|++|+|||||++.+..-
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~gl  149 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIHF  149 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhhh
Confidence            3468999999999999999998653

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.35  E-value=0.1  Score=46.43  Aligned_cols=39  Identities=13%  Similarity=0.056  Sum_probs=27.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVS  196 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  196 (261)
                      .-.++.|.|.+|+||||||..+..+.-.+ . ..++|++..
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~-g-~~vl~fSlE  234 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDN-D-DVVNLHSLE  234 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHT-T-CEEEEECSS
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHc-C-CEEEEEECC
Confidence            34689999999999999999887763222 1 235566543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.33  E-value=0.0096  Score=50.68  Aligned_cols=23  Identities=30%  Similarity=0.338  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|+|++|+||||||+.+...
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            58999999999999999999775

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.32  E-value=0.073  Score=47.39  Aligned_cols=90  Identities=12%  Similarity=0.060  Sum_probs=52.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHH-------------------------
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQ-------------------------  210 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~-------------------------  210 (261)
                      .-.++.|.|.+|+|||||+..+........ =..++|++...  +...+...++.                         
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~E~--s~~~l~~r~~~~~~~~~~~~l~~g~l~~~~~~~~~~  278 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKT-NENVAIFSLEM--SAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTM  278 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHS-SCCEEEEESSS--CHHHHHHHHHHHHHTCCHHHHHTSCCCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhC-CCcEEEEECCC--CHHHHHHHHHHHHcCCCHHHHhcCCCCHHHHHHHHH
Confidence            346899999999999999999877632211 12455665433  23333333321                         


Q ss_pred             ---HhcC------CCCCCCHHHHHHHHHHHhC-CCeEEEEEeCCCCCC
Q 041190          211 ---AAAG------SADVNDLNLLQLQLENQLK-NKKFLLVLDDMWSEN  248 (261)
Q Consensus       211 ---~l~~------~~~~~~~~~~~~~l~~~l~-~kr~LiVlDdvw~~~  248 (261)
                         .+..      .....+..++...++.... .+.-+||+|.+-...
T Consensus       279 a~~~l~~~~l~i~d~~~~s~~~i~~~~~~l~~~~~~~livID~l~~~~  326 (454)
T 2r6a_A          279 AMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQ  326 (454)
T ss_dssp             HHHHHHSSCEEEECCTTCCHHHHHHHHHHHHTTTCCCEEEEECGGGSC
T ss_pred             HHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEccHHHhc
Confidence               1110      1112356667666666553 356789999886543

>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=95.31  E-value=0.011  Score=50.09  Aligned_cols=23  Identities=22%  Similarity=0.410  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||||..+...
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~   26 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKR   26 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             cEEEEECCCcCCHHHHHHHHHHh
Confidence            58899999999999999999765

>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=95.30  E-value=0.011  Score=50.27  Aligned_cols=25  Identities=40%  Similarity=0.591  Sum_probs=22.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.++.|+|+.|+|||||.+.+...
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            4789999999999999999999864

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.29  E-value=0.012  Score=54.57  Aligned_cols=43  Identities=28%  Similarity=0.325  Sum_probs=35.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.+..++.+...+...        ..+.|+|++|+||||||+.+..-
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            35788887787777777542        47899999999999999999875

>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=95.27  E-value=0.013  Score=49.59  Aligned_cols=25  Identities=28%  Similarity=0.084  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.|+|++|+||||||..+.+.
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            3578999999999999999999875

>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=95.26  E-value=0.011  Score=45.90  Aligned_cols=24  Identities=21%  Similarity=0.368  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++|+|.+|+|||||.+.+...
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            457899999999999999998765

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=95.22  E-value=0.01  Score=49.09  Aligned_cols=23  Identities=35%  Similarity=0.369  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999753

>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=95.15  E-value=0.011  Score=51.01  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        31 e~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCchHHHHHHHHhc
Confidence            5899999999999999999965

>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=95.15  E-value=0.015  Score=47.34  Aligned_cols=27  Identities=30%  Similarity=0.309  Sum_probs=22.8

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .....++.+.|.||+||||++..+...
T Consensus        11 ~~~~~i~~~~GkgGvGKTTl~~~La~~   37 (262)
T 1yrb_A           11 GMASMIVVFVGTAGSGKTTLTGEFGRY   37 (262)
T ss_dssp             TCCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CcceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            445788999999999999999998743

>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=95.15  E-value=0.011  Score=48.99  Aligned_cols=24  Identities=29%  Similarity=0.311  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|+|++|+|||||+..+...
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~   53 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQ   53 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999988754

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=95.14  E-value=0.031  Score=44.90  Aligned_cols=26  Identities=35%  Similarity=0.477  Sum_probs=23.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....|.+.|+.|+||||+++.+.+..
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~l   45 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEYL   45 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46789999999999999999998763

>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=95.13  E-value=0.012  Score=51.22  Aligned_cols=25  Identities=28%  Similarity=0.129  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++.|+|++|+|||||++.+...
T Consensus       168 ~~~~i~l~G~~GsGKSTl~~~l~~~  192 (377)
T 1svm_A          168 KKRYWLFKGPIDSGKTTLAAALLEL  192 (377)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            4569999999999999999999864

>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=95.13  E-value=0.1  Score=46.99  Aligned_cols=50  Identities=18%  Similarity=0.087  Sum_probs=32.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i  208 (261)
                      .-.++.|.|.+|+|||||+.++..+...+ +=..++|++...  +..++...+
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~-~g~~vl~~s~E~--s~~~l~~r~  290 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTA-MGKKVGLAMLEE--SVEETAEDL  290 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTT-SCCCEEEEESSS--CHHHHHHHH
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHh-cCCcEEEEeccC--CHHHHHHHH
Confidence            44688999999999999999887663222 112456666544  344444443

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=95.09  E-value=0.012  Score=45.99  Aligned_cols=24  Identities=21%  Similarity=0.368  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++|+|.+|+|||||.+.+...
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            356899999999999999999865

>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=95.09  E-value=0.012  Score=49.36  Aligned_cols=24  Identities=25%  Similarity=0.547  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999999764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=95.08  E-value=0.015  Score=47.06  Aligned_cols=25  Identities=24%  Similarity=0.307  Sum_probs=22.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...|.|.|..|+||||+++.+.+..
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3689999999999999999998763

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.08  E-value=0.15  Score=45.13  Aligned_cols=51  Identities=20%  Similarity=0.083  Sum_probs=32.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .-.++.|.|.+|+||||||..+..+..... =..++|++...  +...+...++
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~-g~~vl~~slE~--~~~~l~~R~~  249 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKE-GVGVGIYSLEM--PAAQLTLRMM  249 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESSS--CHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhC-CCeEEEEECCC--CHHHHHHHHH
Confidence            446899999999999999998876632111 12456665543  3444444443

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=95.07  E-value=0.037  Score=49.66  Aligned_cols=84  Identities=24%  Similarity=0.198  Sum_probs=49.8

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhccccccccce-eEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSF-RACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~-~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~----  222 (261)
                      .-++|.|.+|+|||+|| ..+.+..    +-+. .+++-+++... ..++..++...=. .       ..+.....    
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a  238 (502)
T 2qe7_A          163 QRELIIGDRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYLA  238 (502)
T ss_dssp             CBCEEEECSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHHH
T ss_pred             CEEEEECCCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHHH
Confidence            45789999999999995 5777763    2343 46777777543 4455555544211 1       11111111    


Q ss_pred             -----HHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          223 -----LLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 -----~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                           .+...++.  +++.+||++||+-.-
T Consensus       239 ~~~a~tiAEyfrd--~G~dVLl~~Dsltr~  266 (502)
T 2qe7_A          239 PYAGCAMGEYFMY--KGKHALVVYDDLSKQ  266 (502)
T ss_dssp             HHHHHHHHHHHHT--TTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHH--cCCcEEEEEecHHHH
Confidence                 12233333  589999999998553

>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=95.07  E-value=0.013  Score=49.05  Aligned_cols=24  Identities=29%  Similarity=0.310  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|.|++|+|||||++.+...
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~~   58 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQALQ   58 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            468999999999999999998765

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=95.06  E-value=0.015  Score=43.16  Aligned_cols=23  Identities=22%  Similarity=0.392  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.+.+.
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45889999999999999998765

>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=95.06  E-value=0.027  Score=46.51  Aligned_cols=38  Identities=21%  Similarity=0.186  Sum_probs=28.4

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+..||...    .++-..+.++|++|+|||++|..+.+.
T Consensus        90 ~~~l~~~l~~~----~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           90 ASVFLGWATKK----FGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHHHTTC----STTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhCC----CCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            34466666542    134567999999999999999999874

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=95.02  E-value=0.022  Score=49.07  Aligned_cols=38  Identities=26%  Similarity=0.297  Sum_probs=27.2

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+...+...    ..+..+|+|+|.+|+|||||+..+...
T Consensus        65 ~~~~~~~~~~~----~~~~~~I~i~G~~G~GKSTl~~~L~~~  102 (355)
T 3p32_A           65 AQQLLLRLLPD----SGNAHRVGITGVPGVGKSTAIEALGMH  102 (355)
T ss_dssp             HHHHHHHHGGG----CCCSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhHhh----cCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            34444444432    235789999999999999999888643

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=95.01  E-value=0.042  Score=43.79  Aligned_cols=25  Identities=20%  Similarity=0.235  Sum_probs=22.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -..|.+.|+.|+||||+++.+.+..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l   30 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERL   30 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3688999999999999999998763

>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=95.00  E-value=0.012  Score=45.31  Aligned_cols=22  Identities=41%  Similarity=0.507  Sum_probs=19.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||||.+.+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999998763

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.00  E-value=0.073  Score=46.43  Aligned_cols=100  Identities=13%  Similarity=0.030  Sum_probs=52.7

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc-cccceeEEEeeCCCCCH-HHHHHHHHHHhc-CCC
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK-KYFSFRACAYVSEDFDA-VGVTKVILQAAA-GSA  216 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~-~~i~~~i~~~l~-~~~  216 (261)
                      -.+++.|..-.     +-.-++|+|.+|+|||+|++.+.+..... ..+.| +++-+.+.... .++.+++...+- ...
T Consensus       163 iraID~l~Pig-----rGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~-V~~lIGER~~EV~d~~~~~~G~VV~ata  236 (427)
T 3l0o_A          163 TRLIDLFAPIG-----KGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIR-IILLIDERPEEVTDIRESTNAIVIAAPF  236 (427)
T ss_dssp             HHHHHHHSCCB-----TTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSEE-EEEECSCCHHHHSSSSSSCCSEEEECCT
T ss_pred             chhhhhccccc-----CCceEEEecCCCCChhHHHHHHHHHHhhcCCCeEE-EEEEeccCcchHHHHHHHhCCeEEEECC
Confidence            35667676532     23467999999999999999988763211 12322 45556553221 111111110000 122


Q ss_pred             CCCCHH---------HHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          217 DVNDLN---------LLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       217 ~~~~~~---------~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      +.....         .+...+++  .++.+||++||+-.-
T Consensus       237 dep~~~r~~~a~~altiAEyfrd--~G~dVLil~DslTR~  274 (427)
T 3l0o_A          237 DMPPDKQVKVAELTLEMAKRLVE--FNYDVVILLDSLTRL  274 (427)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEECHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH--cCCCEEEecccchHH
Confidence            211111         12233443  689999999999543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=94.99  E-value=0.02  Score=46.00  Aligned_cols=40  Identities=23%  Similarity=0.171  Sum_probs=26.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE  197 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  197 (261)
                      .-.++.|+|++|+|||||+..+.....  ..=...+|++...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~--~~~~~v~~~~~e~   61 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGL--KMGEPGIYVALEE   61 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHH--HTTCCEEEEESSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEEccC
Confidence            346899999999999999887765421  1112355666444

>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=94.98  E-value=0.0085  Score=50.68  Aligned_cols=23  Identities=30%  Similarity=0.593  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||++.+..
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

>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=94.96  E-value=0.017  Score=43.53  Aligned_cols=23  Identities=22%  Similarity=0.352  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+.++|.+|+|||||.+.+...
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            46899999999999999998764

>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=94.93  E-value=0.023  Score=47.82  Aligned_cols=32  Identities=22%  Similarity=0.396  Sum_probs=26.9

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHh
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      .+++|.+.+..         .+++++|++|+|||||.+.+.
T Consensus       155 gi~~L~~~l~G---------~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          155 GIDELVDYLEG---------FICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             THHHHHHHTTT---------CEEEEECSTTSSHHHHHHHHH
T ss_pred             CHHHHHhhccC---------cEEEEECCCCCCHHHHHHHHH
Confidence            46777777743         488999999999999999998

>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=94.93  E-value=0.044  Score=49.29  Aligned_cols=86  Identities=17%  Similarity=0.130  Sum_probs=50.2

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhccccccccce-eEEEeeCCCCC-HHHHHHHHHHHhc--------CCCCCCCHHHH--
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSF-RACAYVSEDFD-AVGVTKVILQAAA--------GSADVNDLNLL--  224 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~-~~wv~v~~~~~-~~~i~~~i~~~l~--------~~~~~~~~~~~--  224 (261)
                      .-++|.|.+|+|||+|| ..+.+..    .-+. .+++-+.+... ..++..++...=.        ...+.....+.  
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            45789999999999995 5777763    2443 46777777543 4455555544211        11121111111  


Q ss_pred             ---HHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          225 ---QLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       225 ---~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                         .-.+-+++  +++.+||++||+-.-
T Consensus       252 ~~~a~tiAEyfrd~G~dVLli~DslTr~  279 (515)
T 2r9v_A          252 PYAGCAMGEYFAYSGRDALVVYDDLSKH  279 (515)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEeccHHHH
Confidence               11233333  589999999998553

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=94.93  E-value=0.014  Score=50.41  Aligned_cols=22  Identities=32%  Similarity=0.561  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        42 e~~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999864

>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=94.93  E-value=0.016  Score=44.54  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=19.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+..|+|+.|+|||||+..++-
T Consensus        27 g~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            4889999999999999998853

>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=94.91  E-value=0.014  Score=50.53  Aligned_cols=23  Identities=30%  Similarity=0.353  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHhc
Confidence            35899999999999999999865

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=94.88  E-value=0.012  Score=48.38  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=22.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.|.|..|+||||+++.+.+.
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            4679999999999999999998776

>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=94.87  E-value=0.016  Score=43.03  Aligned_cols=22  Identities=27%  Similarity=0.637  Sum_probs=19.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+...
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            4789999999999999999765

>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=94.86  E-value=0.015  Score=50.71  Aligned_cols=22  Identities=27%  Similarity=0.522  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpsGsGKSTLLr~iaG   51 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAG   51 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEEcCCCchHHHHHHHHHc
Confidence            5899999999999999999965

>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=94.84  E-value=0.015  Score=50.27  Aligned_cols=22  Identities=27%  Similarity=0.430  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaG   51 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLLMLAG   51 (359)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEEcCCCchHHHHHHHHHC
Confidence            5899999999999999999965

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=94.81  E-value=0.015  Score=50.27  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAG   51 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            35899999999999999999965

>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=94.79  E-value=0.027  Score=49.94  Aligned_cols=42  Identities=31%  Similarity=0.284  Sum_probs=28.5

Q ss_pred             HHHHHHHhhCCCCC---CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLN---SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~---~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.|.+++......   ......+|.|+|.+|+||||++..+...
T Consensus        78 ~~~l~~ll~~~~~~~~~~~~~~~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C           78 YEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             HHHHHHHHCCSCCCCCCCSSSCCCEEEECCSSSSTTHHHHHHHHH
T ss_pred             HHHHHHHhCCCCcCccccCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45566666543110   1123579999999999999999888664

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=94.78  E-value=0.066  Score=48.69  Aligned_cols=84  Identities=12%  Similarity=0.044  Sum_probs=51.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCH-HHHHHHHHH----Hhc-----------CCCCCCCH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDA-VGVTKVILQ----AAA-----------GSADVNDL  221 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~-~~i~~~i~~----~l~-----------~~~~~~~~  221 (261)
                      .-++|.|..|+|||+|++.+.+..    +-+..+++-+.+..+. .+++.++-+    ..+           ...+....
T Consensus       228 qr~~I~g~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~~el~d~~~g~~~m~rtvvV~~tsd~p~~  303 (588)
T 3mfy_A          228 GTAAIPGPAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVA  303 (588)
T ss_dssp             CEEEECSCCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHTTTCEETTTTEEGGGGEEEEECCTTSCHH
T ss_pred             CeEEeecCCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHHHHhcccccccccccceEEEEECCCCCHH
Confidence            468999999999999999987752    2346778888886653 444444322    011           11111111


Q ss_pred             H---------HHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          222 N---------LLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       222 ~---------~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                      .         .+...+++  .++.+||++|++-.-
T Consensus       304 ~r~~~~~~a~tiAEyfrd--~G~dVLl~~DsltR~  336 (588)
T 3mfy_A          304 AREASIYTGITIAEYFRD--MGYDVALMADSTSRW  336 (588)
T ss_dssp             HHHHHHHHHHHHHHHHHH--TTCEEEEEEECTTTC
T ss_pred             HHHHHHHHHHHHHHHHHH--cCCCEEEeecchHHH
Confidence            1         12333443  589999999999643

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.77  E-value=0.021  Score=43.74  Aligned_cols=24  Identities=21%  Similarity=0.299  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|.++|.+|+|||||.+.+...
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            457899999999999999999864

>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=94.77  E-value=0.016  Score=50.38  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaG   51 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAG   51 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCcHHHHHHHHHHc
Confidence            5899999999999999999965

>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=94.72  E-value=0.017  Score=50.24  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=20.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaG   59 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAG   59 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            35899999999999999999864

>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=94.70  E-value=0.023  Score=42.45  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.++|.+|+|||||.+.+.+.
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            345789999999999999998765

>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=94.67  E-value=0.025  Score=43.58  Aligned_cols=25  Identities=24%  Similarity=0.550  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.++|.+|+|||||.+.+.+.
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999999765

>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=94.63  E-value=0.048  Score=48.63  Aligned_cols=88  Identities=19%  Similarity=0.155  Sum_probs=51.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccc--cceeEEEeeCCCC-CHHHHHHHHHHHhc--------CCCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKY--FSFRACAYVSEDF-DAVGVTKVILQAAA--------GSADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~--f~~~~wv~v~~~~-~~~~i~~~i~~~l~--------~~~~~~~~~----  222 (261)
                      .-++|.|.+|+|||+|+..+.++....+.  =+..+++-+.+.. ...+++.++...=.        ...+.....    
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            34677899999999999999887543221  1245667777654 34556666654311        111111111    


Q ss_pred             -HHHHHHHHHh---CCCeEEEEEeCCC
Q 041190          223 -LLQLQLENQL---KNKKFLLVLDDMW  245 (261)
Q Consensus       223 -~~~~~l~~~l---~~kr~LiVlDdvw  245 (261)
                       ...-.+-+++   +++.+||++||+-
T Consensus       233 ~~~a~tiAEyfrdd~G~dVLl~~Dslt  259 (469)
T 2c61_A          233 PRMALTAAEYLAYEHGMHVLVILTDIT  259 (469)
T ss_dssp             HHHHHHHHHHHHHHHCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeCHH
Confidence             1122234444   3799999999984

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=94.63  E-value=0.051  Score=44.04  Aligned_cols=25  Identities=36%  Similarity=0.501  Sum_probs=22.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..+|.|.|+.|+||||+++.+.+..
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999998764

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.61  E-value=0.022  Score=49.01  Aligned_cols=24  Identities=21%  Similarity=0.206  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ...+++|+|.+|+|||||.+.+..
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            467999999999999999999875

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=94.60  E-value=0.052  Score=45.06  Aligned_cols=42  Identities=12%  Similarity=0.139  Sum_probs=29.7

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++.+.|.............|.|+|.+|+|||||.+.+...
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            455566565432212335668999999999999999999765

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=94.59  E-value=0.022  Score=49.46  Aligned_cols=24  Identities=29%  Similarity=0.419  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|+|++|+||||+++.+..-
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~~  159 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMIDY  159 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999988653

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=94.58  E-value=0.025  Score=42.79  Aligned_cols=25  Identities=32%  Similarity=0.331  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.++|.+|+|||||.+.+.+.
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

>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=94.57  E-value=0.022  Score=49.92  Aligned_cols=23  Identities=35%  Similarity=0.540  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|++|+||||||..+...
T Consensus         3 ~~i~i~GptgsGKttla~~La~~   25 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQK   25 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHH
Confidence            58899999999999999998764

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=94.56  E-value=0.028  Score=43.12  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=22.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ....|.++|.+|+|||||.+.+....
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHcCc
Confidence            34578899999999999999998763

>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=94.55  E-value=0.02  Score=42.58  Aligned_cols=23  Identities=30%  Similarity=0.575  Sum_probs=20.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.+...
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            45789999999999999998765

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=94.55  E-value=0.11  Score=47.38  Aligned_cols=50  Identities=12%  Similarity=0.048  Sum_probs=35.3

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF  199 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  199 (261)
                      ++++.|..-.     +-.-++|.|..|+|||+|++.+.+..    +-+..+++-+.+..
T Consensus       221 rvID~l~Pig-----rGqr~~Ifgg~g~GKT~L~~~ia~~~----~~~v~V~~~iGER~  270 (600)
T 3vr4_A          221 RVIDTFFPVT-----KGGAAAVPGPFGAGKTVVQHQIAKWS----DVDLVVYVGCGERG  270 (600)
T ss_dssp             HHHHHHSCCB-----TTCEEEEECCTTSCHHHHHHHHHHHS----SCSEEEEEEEEECH
T ss_pred             hhhhccCCcc-----CCCEEeeecCCCccHHHHHHHHHhcc----CCCEEEEEEecccH
Confidence            3556665432     33568999999999999999998763    23457777777753

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=94.54  E-value=0.017  Score=49.91  Aligned_cols=23  Identities=39%  Similarity=0.614  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|+.|+|||||++.+..-
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            58999999999999999999764

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=94.54  E-value=0.077  Score=47.05  Aligned_cols=27  Identities=26%  Similarity=0.262  Sum_probs=23.6

Q ss_pred             CCCCceEEeEeecCCCChHHHHHHHhh
Q 041190          153 SGPGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       153 ~~~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .....++..|.|.+|+||||+.+...+
T Consensus       157 ~~~~~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          157 HVSSAKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             CCCCSEEEEEEECTTSCHHHHHHHHCC
T ss_pred             ccccccEEEEEcCCCCCHHHHHHHHhc
Confidence            356788999999999999999988875

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=94.54  E-value=0.06  Score=48.44  Aligned_cols=90  Identities=16%  Similarity=0.163  Sum_probs=50.9

Q ss_pred             eEEeEeecCCCChHHH-HHHHhhcccc----ccccce-eEEEeeCCCCC-HHHHHHHHHHHhc--------CCCCCCCHH
Q 041190          158 SVIPITGMGGLGKTTL-AQLVFNDAGV----KKYFSF-RACAYVSEDFD-AVGVTKVILQAAA--------GSADVNDLN  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtL-a~~v~~~~~~----~~~f~~-~~wv~v~~~~~-~~~i~~~i~~~l~--------~~~~~~~~~  222 (261)
                      .-++|.|.+|+|||+| +..+.+....    .++-+. .+++-+.+... ..++.+++...=.        ...+.....
T Consensus       163 QR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~  242 (510)
T 2ck3_A          163 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPL  242 (510)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHH
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCCCHHH
Confidence            4578999999999999 4566666331    122343 56777877543 4455555544211        111111111


Q ss_pred             HH-----HHHHHHHh--CCCeEEEEEeCCCCC
Q 041190          223 LL-----QLQLENQL--KNKKFLLVLDDMWSE  247 (261)
Q Consensus       223 ~~-----~~~l~~~l--~~kr~LiVlDdvw~~  247 (261)
                      +.     .-.+-+++  +++.+||++||+-.-
T Consensus       243 r~~a~~~a~tiAEyfrd~G~dVLli~Dsltr~  274 (510)
T 2ck3_A          243 QYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQ  274 (510)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCcEEEEEcCHHHH
Confidence            11     11223333  589999999998553

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=94.53  E-value=0.042  Score=49.42  Aligned_cols=84  Identities=18%  Similarity=0.187  Sum_probs=49.2

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhccccccccce-eEEEeeCCCCC-HHHHHHHHHHHhc--------CCCCCCCH-----
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSF-RACAYVSEDFD-AVGVTKVILQAAA--------GSADVNDL-----  221 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~-~~wv~v~~~~~-~~~i~~~i~~~l~--------~~~~~~~~-----  221 (261)
                      .-++|.|.+|+|||+|| ..+.+..    .-+. .+++-+++... ..++..++...=.        ...+....     
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            35789999999999995 5777763    2343 46677777543 3344444433110        11111111     


Q ss_pred             ----HHHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          222 ----NLLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       222 ----~~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                          -.+...++.  +++.+||++||+-.-
T Consensus       240 ~~~a~tiAEyfrd--~G~dVLli~Dsltr~  267 (507)
T 1fx0_A          240 PYTGAALAEYFMY--RERHTLIIYDDLSKQ  267 (507)
T ss_dssp             HHHHHHHHHHHHH--TTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHH--cCCcEEEEEecHHHH
Confidence                123344444  599999999998543

>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=94.52  E-value=0.02  Score=50.00  Aligned_cols=23  Identities=26%  Similarity=0.325  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhC
Confidence            35899999999999999999965

>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=94.49  E-value=0.022  Score=49.18  Aligned_cols=23  Identities=26%  Similarity=0.423  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|+.|+|||||.+.+..-
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~  146 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDY  146 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            59999999999999999988653

>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=94.49  E-value=0.014  Score=50.30  Aligned_cols=23  Identities=30%  Similarity=0.345  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        27 e~~~llGpnGsGKSTLLr~iaGl   49 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAGF   49 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CEEEEECCCCccHHHHHHHHHcC
Confidence            58999999999999999999753

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=94.49  E-value=0.025  Score=48.47  Aligned_cols=24  Identities=29%  Similarity=0.346  Sum_probs=21.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ...+++|+|++|+|||||.+.+..
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            467999999999999999999874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.48  E-value=0.086  Score=54.97  Aligned_cols=86  Identities=15%  Similarity=0.030  Sum_probs=57.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC------CCCCCHHHHHHHHH
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS------ADVNDLNLLQLQLE  229 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~------~~~~~~~~~~~~l~  229 (261)
                      .-.++-|+|++|+||||||.++.....  ..=...+|++....++...     .+.++..      .++.+.+++...++
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~~a--~~G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~  454 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD  454 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHH--TTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH--hcCCeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHH
Confidence            456999999999999999999977632  2223567888877666432     4455521      13445666666665


Q ss_pred             HHh-CCCeEEEEEeCCCCCC
Q 041190          230 NQL-KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       230 ~~l-~~kr~LiVlDdvw~~~  248 (261)
                      ... ..+.-+||+|.+-...
T Consensus       455 ~lv~~~~~~lIVIDSL~al~  474 (2050)
T 3cmu_A          455 ALARSGAVDVIVVDSVAALT  474 (2050)
T ss_dssp             HHHHHTCCSEEEESCGGGCC
T ss_pred             HHHHhcCCcEEEECCHHHhh
Confidence            444 3456799999997654

>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=94.48  E-value=0.028  Score=42.29  Aligned_cols=24  Identities=33%  Similarity=0.479  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            356899999999999999998765

>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=94.47  E-value=0.021  Score=43.85  Aligned_cols=23  Identities=26%  Similarity=0.582  Sum_probs=20.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||++.+...
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            45789999999999999999765

>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=94.47  E-value=0.019  Score=49.66  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...++|+|+.|+|||||++.+..-
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999999998764

>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=94.47  E-value=0.025  Score=44.57  Aligned_cols=26  Identities=35%  Similarity=0.345  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +...|.++|.+|+|||||.+.+.+..
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45678999999999999999988753

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.46  E-value=0.022  Score=42.64  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=19.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+...
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            35789999999999999999764

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=94.46  E-value=0.1  Score=46.29  Aligned_cols=89  Identities=19%  Similarity=0.197  Sum_probs=51.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccc--------cccc-eeEEEeeCCCC-CHHHHHHHHHHH--hc------CCCCCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVK--------KYFS-FRACAYVSEDF-DAVGVTKVILQA--AA------GSADVN  219 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~--------~~f~-~~~wv~v~~~~-~~~~i~~~i~~~--l~------~~~~~~  219 (261)
                      .-++|.|.+|+|||+|+..+.+..+..        ++=+ ..+++-+.+.. ...++..++...  +.      ...+..
T Consensus       148 Qr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t~d~p  227 (464)
T 3gqb_B          148 QKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDP  227 (464)
T ss_dssp             CBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEETTSC
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEECCCCC
Confidence            346888999999999999998875432        1222 45566776644 344555554432  10      111222


Q ss_pred             CHHH-----HHHHHHHHh---CCCeEEEEEeCCCC
Q 041190          220 DLNL-----LQLQLENQL---KNKKFLLVLDDMWS  246 (261)
Q Consensus       220 ~~~~-----~~~~l~~~l---~~kr~LiVlDdvw~  246 (261)
                      ....     ..-.+-+++   .++.+||++||+-.
T Consensus       228 ~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlTr  262 (464)
T 3gqb_B          228 TIERILTPRMALTVAEYLAFEHDYHVLVILTDMTN  262 (464)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence            2221     122244454   37999999999854

>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=94.45  E-value=0.022  Score=42.44  Aligned_cols=22  Identities=27%  Similarity=0.542  Sum_probs=19.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.+.
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            4789999999999999998764

>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=94.44  E-value=0.022  Score=42.65  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.++|.+|+|||||.+.+...
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            346889999999999999998765

>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=94.43  E-value=0.036  Score=46.60  Aligned_cols=34  Identities=24%  Similarity=0.448  Sum_probs=28.1

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++++.+.+..         .+++++|++|+|||||.+.+...
T Consensus       159 gv~~lf~~l~g---------eiv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          159 GIEELKEYLKG---------KISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             THHHHHHHHSS---------SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             CHHHHHHHhcC---------CeEEEECCCCCcHHHHHHHhccc
Confidence            47777777743         48899999999999999999764

>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=94.43  E-value=0.023  Score=42.28  Aligned_cols=23  Identities=26%  Similarity=0.492  Sum_probs=19.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+...
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            35789999999999999888754

>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=94.41  E-value=0.023  Score=42.45  Aligned_cols=22  Identities=14%  Similarity=0.356  Sum_probs=19.3

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.+.
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            4789999999999999988765

>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=94.40  E-value=0.023  Score=42.51  Aligned_cols=23  Identities=22%  Similarity=0.355  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+.+.
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            45789999999999999998765

>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=94.40  E-value=0.016  Score=45.39  Aligned_cols=25  Identities=16%  Similarity=0.183  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....++|+|.+|+|||||.+.+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999988754

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=94.39  E-value=0.065  Score=42.69  Aligned_cols=24  Identities=38%  Similarity=0.526  Sum_probs=21.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..|.+.|+.|+||||+++.+.+..
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999998764

>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=94.39  E-value=0.021  Score=42.65  Aligned_cols=22  Identities=27%  Similarity=0.430  Sum_probs=19.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            4789999999999999988653

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.37  E-value=0.02  Score=45.33  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|.|.|+.|+||||+++.+...
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~   26 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASE   26 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47999999999999999988654

>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=94.37  E-value=0.02  Score=48.88  Aligned_cols=23  Identities=26%  Similarity=0.320  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~  194 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEF  194 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGG
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999999875

>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=94.36  E-value=0.03  Score=42.61  Aligned_cols=23  Identities=22%  Similarity=0.291  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..|.|+|.+|+|||||.+.+...
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            46789999999999999999865

>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=94.35  E-value=0.012  Score=50.68  Aligned_cols=22  Identities=32%  Similarity=0.484  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        32 e~~~llGpnGsGKSTLLr~iaG   53 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAG   53 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999864

>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=94.35  E-value=0.025  Score=42.28  Aligned_cols=23  Identities=30%  Similarity=0.420  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+...
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            45789999999999999998754

>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=94.33  E-value=0.088  Score=54.09  Aligned_cols=80  Identities=15%  Similarity=0.081  Sum_probs=0.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCC------CCCCHHHHHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSA------DVNDLNLLQLQLENQ  231 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~------~~~~~~~~~~~l~~~  231 (261)
                      +++-|+|.+|+||||||.++...  ....=...+|++...+++...     +..++...      .+.+.+++...++..
T Consensus       384 ~lilI~G~pGsGKTtLaLq~a~~--~~~~G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~i~~~~~~e~~l~~l~~l  456 (1706)
T 3cmw_A          384 RIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDAL  456 (1706)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH--HHHhCCCeEEEEccCchHHHH-----HHHcCCCHHHeEEcCCCCHHHHHHHHHHH


Q ss_pred             h-CCCeEEEEEeCC
Q 041190          232 L-KNKKFLLVLDDM  244 (261)
Q Consensus       232 l-~~kr~LiVlDdv  244 (261)
                      . ..+.-+||+|.+
T Consensus       457 v~~~~~~lVVIDSL  470 (1706)
T 3cmw_A          457 ARSGAVDVIVVDSV  470 (1706)
T ss_dssp             HHHTCCSEEEESCS
T ss_pred             HHhcCCCEEEECCH

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.33  E-value=0.045  Score=44.12  Aligned_cols=25  Identities=32%  Similarity=0.379  Sum_probs=19.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -..|.|.|+.|+||||+++.+.+..
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998763

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=94.32  E-value=0.027  Score=44.41  Aligned_cols=23  Identities=30%  Similarity=0.356  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|.|++|+||||||..+...
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            56889999999999999998765

>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=94.32  E-value=0.024  Score=42.78  Aligned_cols=25  Identities=24%  Similarity=0.465  Sum_probs=21.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.++|.+|+|||||.+.+...
T Consensus         6 ~~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            6 SLFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceeEEEEECCCCCCHHHHHHHHHcC
Confidence            3456899999999999999998754

>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=94.30  E-value=0.022  Score=47.99  Aligned_cols=20  Identities=40%  Similarity=0.675  Sum_probs=18.2

Q ss_pred             EeEeecCCCChHHHHHHHhh
Q 041190          160 IPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~  179 (261)
                      |+|+|.+|+|||||.+.++.
T Consensus        21 I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           21 LMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEETTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            49999999999999999765

>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=94.30  E-value=0.031  Score=42.27  Aligned_cols=25  Identities=36%  Similarity=0.492  Sum_probs=21.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.++|.+|+|||||.+.+...
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            4566899999999999999988765

>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=94.29  E-value=0.026  Score=43.26  Aligned_cols=25  Identities=28%  Similarity=0.276  Sum_probs=21.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.++|.+|+|||||.+.+.+.
T Consensus         6 ~~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            6 VKCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEEECCCCCCHHHHHHHHhcC
Confidence            3456789999999999999998765

>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=94.28  E-value=0.036  Score=41.90  Aligned_cols=25  Identities=24%  Similarity=0.436  Sum_probs=21.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.++|.+|+|||||.+.+.+.
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            4567899999999999999998765

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=94.23  E-value=0.026  Score=48.50  Aligned_cols=25  Identities=36%  Similarity=0.401  Sum_probs=22.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|+|+.|+|||||.+.+.+..
T Consensus        71 Gq~~gIiG~nGaGKTTLl~~I~g~~   95 (347)
T 2obl_A           71 GQRIGIFAGSGVGKSTLLGMICNGA   95 (347)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3689999999999999999998873

>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=94.22  E-value=0.026  Score=42.04  Aligned_cols=21  Identities=29%  Similarity=0.338  Sum_probs=18.8

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+...
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            689999999999999998754

>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=94.21  E-value=0.026  Score=43.35  Aligned_cols=24  Identities=29%  Similarity=0.242  Sum_probs=20.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.++|.+|+|||||.+.+.+.
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~~   37 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYSK   37 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhh
Confidence            446789999999999999877653

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=94.21  E-value=0.023  Score=42.99  Aligned_cols=25  Identities=24%  Similarity=0.353  Sum_probs=21.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+...
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            4556899999999999999998765

>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=94.20  E-value=0.027  Score=43.08  Aligned_cols=22  Identities=27%  Similarity=0.366  Sum_probs=19.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+...
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            4789999999999999998765

>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=94.19  E-value=0.033  Score=42.64  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.++|.+|+|||||.+.+...
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            4567899999999999999998765

>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=94.19  E-value=0.027  Score=42.03  Aligned_cols=23  Identities=17%  Similarity=0.284  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+...
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            45789999999999999998764

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=94.18  E-value=0.11  Score=46.51  Aligned_cols=83  Identities=17%  Similarity=0.202  Sum_probs=49.6

Q ss_pred             eEEeEeecCCCChHHHH-HHHhhccccccccce-eEEEeeCCCCC-HHHHHHHHHHHhc-C-------CCCCCCHH----
Q 041190          158 SVIPITGMGGLGKTTLA-QLVFNDAGVKKYFSF-RACAYVSEDFD-AVGVTKVILQAAA-G-------SADVNDLN----  222 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~-~~wv~v~~~~~-~~~i~~~i~~~l~-~-------~~~~~~~~----  222 (261)
                      .-++|.|..|+|||+|+ ..+.+.    .+-+. .+++-+++..+ ..++..++.+.=. .       ..+.....    
T Consensus       163 QR~~Ifg~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~~a  238 (513)
T 3oaa_A          163 QRELIIGDRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLA  238 (513)
T ss_dssp             CBCEEEESSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHHHH
T ss_pred             CEEEeecCCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHHHH
Confidence            45789999999999996 566664    22333 46778887543 4555555443211 1       11111111    


Q ss_pred             -----HHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          223 -----LLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       223 -----~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                           .+...+++  +++.+||++||+-.
T Consensus       239 ~~~a~tiAEyfrd--~G~dVLli~Dsltr  265 (513)
T 3oaa_A          239 PYAGCAMGEYFRD--RGEDALIIYDDLSK  265 (513)
T ss_dssp             HHHHHHHHHHHHH--TTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHh--cCCCEEEEecChHH
Confidence                 22333443  68999999999854

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.17  E-value=0.078  Score=41.61  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .|.|=|.-|+||||.++.+.+..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L   24 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYL   24 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            46778999999999999998763

>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=94.12  E-value=0.028  Score=43.28  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=20.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            446789999999999999877654

>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=94.11  E-value=0.029  Score=42.36  Aligned_cols=26  Identities=23%  Similarity=0.171  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...-|.|+|.+|+|||||.+.+....
T Consensus        14 ~~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           14 YIFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHcCC
Confidence            34568999999999999999987653

>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=94.11  E-value=0.035  Score=41.50  Aligned_cols=22  Identities=32%  Similarity=0.389  Sum_probs=19.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      --|.++|.+|+|||||.+.+..
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            3578999999999999998853

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=94.11  E-value=0.047  Score=41.19  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=20.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+.+.
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            456789999999999999988754

>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=94.10  E-value=0.03  Score=42.73  Aligned_cols=25  Identities=20%  Similarity=0.260  Sum_probs=21.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.++|.+|+|||||.+.+.+.
T Consensus         9 ~~~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A            9 FLFKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECCCCCCHHHHHHHHHcC
Confidence            3456889999999999999998765

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.09  E-value=0.031  Score=43.42  Aligned_cols=23  Identities=30%  Similarity=0.075  Sum_probs=18.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|+.|+||||++..+...
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~   26 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEI   26 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            47889999999999998555443

>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=94.09  E-value=0.03  Score=42.22  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=19.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.|+|.+|+|||||.+.+...
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            45789999999999999998754

>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=94.07  E-value=0.029  Score=42.80  Aligned_cols=23  Identities=22%  Similarity=0.488  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+.+.
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            45789999999999999999765

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=94.06  E-value=0.03  Score=43.26  Aligned_cols=23  Identities=35%  Similarity=0.525  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..|.++|.+|+|||||.+.+.+.
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            46799999999999999998764

>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=94.03  E-value=0.027  Score=49.76  Aligned_cols=21  Identities=48%  Similarity=0.699  Sum_probs=19.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|+|++|+|||||.+.++.-
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            999999999999999999753

>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=94.00  E-value=0.033  Score=46.99  Aligned_cols=27  Identities=22%  Similarity=0.325  Sum_probs=23.7

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+....|+|+|.+|+|||||.+.+...
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            456789999999999999999998765

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=93.99  E-value=0.034  Score=50.48  Aligned_cols=25  Identities=24%  Similarity=0.309  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|.++|++|+||||+|+.+...
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~   58 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRY   58 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999764

>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=93.97  E-value=0.031  Score=42.74  Aligned_cols=25  Identities=20%  Similarity=0.183  Sum_probs=21.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+.+.
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            3456789999999999999999764

>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=93.96  E-value=0.037  Score=43.10  Aligned_cols=23  Identities=30%  Similarity=0.510  Sum_probs=19.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.+.+.
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999998753

>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=93.96  E-value=0.031  Score=43.03  Aligned_cols=25  Identities=24%  Similarity=0.263  Sum_probs=20.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..--|.++|.+|+|||||.+.+.+.
T Consensus        20 ~~~ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           20 LEVNLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHhC
Confidence            3456889999999999999888754

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=93.96  E-value=0.036  Score=48.79  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ...+++|+|++|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            346999999999999999999987

>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=93.94  E-value=0.031  Score=43.05  Aligned_cols=24  Identities=25%  Similarity=0.369  Sum_probs=20.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            456899999999999999998764

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=93.94  E-value=0.027  Score=50.35  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.++.-
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            58999999999999999998764

>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=93.93  E-value=0.035  Score=46.66  Aligned_cols=25  Identities=28%  Similarity=0.399  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...++|+|.+|+|||||.+.+...
T Consensus         7 r~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            7 YCGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHCC
Confidence            4568999999999999999999765

>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=93.93  E-value=0.032  Score=42.39  Aligned_cols=24  Identities=29%  Similarity=0.578  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            456889999999999999998764

>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=93.92  E-value=0.032  Score=42.26  Aligned_cols=24  Identities=25%  Similarity=0.325  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            346789999999999999998765

>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=93.92  E-value=0.033  Score=42.38  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=19.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+.+.
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            45789999999999999888754

>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=93.90  E-value=0.043  Score=41.04  Aligned_cols=24  Identities=33%  Similarity=0.302  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            356889999999999999999754

>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=93.90  E-value=0.034  Score=42.21  Aligned_cols=24  Identities=25%  Similarity=0.349  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+.+.
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            456889999999999999998754

>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=93.89  E-value=0.077  Score=44.42  Aligned_cols=41  Identities=10%  Similarity=0.108  Sum_probs=29.2

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.+.+..-.. ....+..|+|+|.+|+|||||.+.+...
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            4555555543222 1345778999999999999999999764

>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=93.89  E-value=0.034  Score=49.07  Aligned_cols=24  Identities=29%  Similarity=0.401  Sum_probs=21.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|+|+.|+||||+.+.+...
T Consensus       167 ggii~I~GpnGSGKTTlL~allg~  190 (418)
T 1p9r_A          167 HGIILVTGPTGSGKSTTLYAGLQE  190 (418)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999998764

>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=93.88  E-value=0.043  Score=43.72  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.|+|.+|+|||||.+.+...
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            4567899999999999999998765

>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=93.88  E-value=0.05  Score=41.33  Aligned_cols=25  Identities=28%  Similarity=0.489  Sum_probs=21.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..--|.|+|.+|+|||||.+.+.+.
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            3456789999999999999998865

>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=93.83  E-value=0.039  Score=47.23  Aligned_cols=24  Identities=25%  Similarity=0.259  Sum_probs=21.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      +..+++|+|.+|+|||||++.+..
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            568999999999999999998854

>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=93.83  E-value=0.036  Score=42.81  Aligned_cols=24  Identities=21%  Similarity=0.299  Sum_probs=20.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+...
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            346899999999999999998765

>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=93.83  E-value=0.051  Score=42.91  Aligned_cols=25  Identities=16%  Similarity=0.146  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+|+|+|++|+||+|+|..+-+.
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~   34 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSR   34 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHH
Confidence            4579999999999999999888653

>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=93.80  E-value=0.045  Score=48.81  Aligned_cols=23  Identities=30%  Similarity=0.559  Sum_probs=20.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+.|.|.+|+||||++..+....
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            89999999999999999887763

>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=93.79  E-value=0.028  Score=42.58  Aligned_cols=24  Identities=17%  Similarity=0.192  Sum_probs=20.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.++|.+|+|||||.+.+.+.
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            345789999999999999998764

>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=93.77  E-value=0.036  Score=42.02  Aligned_cols=23  Identities=26%  Similarity=0.232  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.++|.+|+|||||.+.+...
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            45789999999999999988765

>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=93.76  E-value=0.036  Score=41.92  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            456899999999999999998764

>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=93.75  E-value=0.036  Score=43.13  Aligned_cols=25  Identities=32%  Similarity=0.401  Sum_probs=21.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+...
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            4567899999999999999998765

>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=93.74  E-value=0.046  Score=45.03  Aligned_cols=24  Identities=21%  Similarity=0.336  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|+++|.+|+|||||.+.+...
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

>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=93.74  E-value=0.036  Score=42.88  Aligned_cols=24  Identities=25%  Similarity=0.383  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            356789999999999999998765

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=93.74  E-value=0.087  Score=41.62  Aligned_cols=24  Identities=33%  Similarity=0.501  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..|.|-|..|+||||+++.+.+..
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L   26 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRL   26 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHH
Confidence            468888999999999999998874

>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=93.71  E-value=0.052  Score=42.09  Aligned_cols=25  Identities=28%  Similarity=0.562  Sum_probs=21.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+...
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            3457899999999999999998754

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=93.71  E-value=0.025  Score=52.24  Aligned_cols=22  Identities=27%  Similarity=0.298  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -+.++|++|+|||+||+.+.+.
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            5789999999999999999875

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.70  E-value=0.027  Score=51.55  Aligned_cols=24  Identities=33%  Similarity=0.409  Sum_probs=21.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.++.|+|+.|+|||||++.+...
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            468999999999999999999875

>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=93.69  E-value=0.037  Score=42.96  Aligned_cols=24  Identities=29%  Similarity=0.314  Sum_probs=20.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+.+.
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            456899999999999999998765

>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=93.69  E-value=0.038  Score=42.58  Aligned_cols=24  Identities=25%  Similarity=0.297  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+.+.
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            345789999999999999998865

>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=93.69  E-value=0.038  Score=42.84  Aligned_cols=25  Identities=24%  Similarity=0.474  Sum_probs=20.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.++|.+|+|||||.+.+.+.
T Consensus        19 ~~~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           19 SKPRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             -CCEEEEEESTTSSHHHHHHHHHSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHhc
Confidence            3456799999999999999977664

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=93.69  E-value=0.037  Score=47.76  Aligned_cols=23  Identities=22%  Similarity=0.433  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|++|+|||||.+.+...
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            48899999999999999999864

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.67  E-value=0.042  Score=42.38  Aligned_cols=26  Identities=23%  Similarity=0.224  Sum_probs=22.1

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....-|.|+|.+|+|||||.+.+.+.
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            35667899999999999999998765

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.66  E-value=0.038  Score=41.95  Aligned_cols=25  Identities=32%  Similarity=0.258  Sum_probs=21.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.++|.+|+|||||.+.+...
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3467889999999999999998753

>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=93.66  E-value=0.037  Score=42.26  Aligned_cols=26  Identities=19%  Similarity=0.220  Sum_probs=22.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +..-|.++|.+|+|||||.+.+.+..
T Consensus        17 ~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           17 RELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            34678999999999999999998654

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=93.65  E-value=0.038  Score=42.47  Aligned_cols=26  Identities=23%  Similarity=0.305  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...-|.|+|.+|+|||||.+.+.+..
T Consensus        15 ~~~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           15 YLFKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcCC
Confidence            34568999999999999999988653

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=93.64  E-value=0.18  Score=54.25  Aligned_cols=61  Identities=18%  Similarity=0.217  Sum_probs=0.0

Q ss_pred             EeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHh---------------cCCCCCCCHHHH
Q 041190          160 IPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAA---------------AGSADVNDLNLL  224 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l---------------~~~~~~~~~~~~  224 (261)
                      +-++|++|+|||++|+.+...    ..--....++.+..-+...+.+.+-..+               +           
T Consensus      1270 vLL~GPpGtGKT~la~~~l~~----~~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~----------- 1334 (2695)
T 4akg_A         1270 IILCGPPGSGKTMIMNNALRN----SSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSD----------- 1334 (2695)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS----CSSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSS-----------
T ss_pred             EEEECCCCCCHHHHHHHHHhc----CCCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCC-----------


Q ss_pred             HHHHHHHhCCCeEEEEEeCC
Q 041190          225 QLQLENQLKNKKFLLVLDDM  244 (261)
Q Consensus       225 ~~~l~~~l~~kr~LiVlDdv  244 (261)
                               +|+.++++||+
T Consensus      1335 ---------gk~~VlFiDEi 1345 (2695)
T 4akg_A         1335 ---------IKNLVLFCDEI 1345 (2695)
T ss_dssp             ---------SSCEEEEEETT
T ss_pred             ---------CceEEEEeccc

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=93.64  E-value=0.04  Score=42.86  Aligned_cols=25  Identities=28%  Similarity=0.433  Sum_probs=21.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.|+|.+|+|||||.+.+.+.
T Consensus        23 ~~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           23 RYRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             CcEEEEEECCCCcCHHHHHHHHHhC
Confidence            3456899999999999999998865

>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=93.64  E-value=0.04  Score=43.17  Aligned_cols=24  Identities=29%  Similarity=0.405  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            456889999999999999988754

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=93.63  E-value=0.045  Score=50.32  Aligned_cols=26  Identities=23%  Similarity=0.139  Sum_probs=22.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++..+|.|.|++|+||||+|+.+.+.
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            34578999999999999999999775

>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=93.63  E-value=0.034  Score=43.28  Aligned_cols=23  Identities=35%  Similarity=0.476  Sum_probs=20.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ...-|.++|.+|+|||||.+.+.
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            45678999999999999999985

>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=93.62  E-value=0.04  Score=43.27  Aligned_cols=24  Identities=29%  Similarity=0.333  Sum_probs=20.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            456889999999999999999765

>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=93.61  E-value=0.039  Score=49.55  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
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            7999999999999999999875

>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=93.60  E-value=0.04  Score=42.32  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            456899999999999999998765

>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=93.59  E-value=0.048  Score=43.86  Aligned_cols=26  Identities=19%  Similarity=0.293  Sum_probs=22.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ...-|.++|.+|+|||||.+.+....
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCCC
Confidence            45678999999999999999998653

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=93.59  E-value=0.036  Score=50.59  Aligned_cols=23  Identities=39%  Similarity=0.738  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.++.-
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            47999999999999999999864

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=93.58  E-value=0.048  Score=42.97  Aligned_cols=24  Identities=21%  Similarity=0.153  Sum_probs=21.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+|.|.|+.|+||||+++.+.+..
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~l   30 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHY   30 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHh
Confidence            589999999999999999997763

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=93.58  E-value=0.04  Score=48.92  Aligned_cols=25  Identities=16%  Similarity=0.183  Sum_probs=22.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -.+++|+|+.|+|||||++.+....
T Consensus       157 Gq~~~IvG~sGsGKSTLl~~Iag~~  181 (438)
T 2dpy_A          157 GQRMGLFAGSGVGKSVLLGMMARYT  181 (438)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccc
Confidence            4689999999999999999998863

>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=93.57  E-value=0.041  Score=42.32  Aligned_cols=24  Identities=21%  Similarity=0.307  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+.+.
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            346789999999999999999764

>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=93.55  E-value=0.041  Score=42.44  Aligned_cols=25  Identities=28%  Similarity=0.276  Sum_probs=21.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..--|.++|.+|+|||||.+.+.+.
T Consensus        22 ~~~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           22 KALKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeeEEEEECcCCCCHHHHHHHHhcC
Confidence            3456789999999999999998765

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.54  E-value=0.045  Score=44.77  Aligned_cols=23  Identities=35%  Similarity=0.557  Sum_probs=19.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|+|.|-||+||||+|-.+...
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            57888899999999999877654

>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=93.52  E-value=0.041  Score=42.81  Aligned_cols=25  Identities=20%  Similarity=0.294  Sum_probs=20.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+...
T Consensus        24 ~~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           24 FLFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             cceEEEEECcCCCCHHHHHHHHHhC
Confidence            3456889999999999999988754

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.52  E-value=0.039  Score=50.37  Aligned_cols=23  Identities=39%  Similarity=0.612  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.++.-
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            58999999999999999999874

>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=93.51  E-value=0.044  Score=42.98  Aligned_cols=25  Identities=20%  Similarity=0.246  Sum_probs=20.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|.++|.+|+|||||.+.+...
T Consensus         6 ~~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            6 SQRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             --CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3456889999999999999998765

>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=93.50  E-value=0.051  Score=50.41  Aligned_cols=25  Identities=28%  Similarity=0.321  Sum_probs=22.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..+|.+.|++|+||||+|+.+.+.
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~   75 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEY   75 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            5678999999999999999998765

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=93.50  E-value=0.062  Score=41.29  Aligned_cols=24  Identities=17%  Similarity=0.236  Sum_probs=20.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+...
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            345789999999999999999875

>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=93.47  E-value=0.042  Score=42.30  Aligned_cols=24  Identities=25%  Similarity=0.272  Sum_probs=20.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+.+.
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            345789999999999999998764

>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=93.47  E-value=0.043  Score=42.09  Aligned_cols=23  Identities=35%  Similarity=0.455  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.+.+.
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            46889999999999999998765

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.46  E-value=0.04  Score=50.27  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        47 Ge~~~LvG~NGaGKSTLlk~l~Gl   70 (538)
T 1yqt_A           47 GMVVGIVGPNGTGKSTAVKILAGQ   70 (538)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999753

>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=93.45  E-value=0.045  Score=42.20  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            356799999999999999998764

>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=93.45  E-value=0.045  Score=42.66  Aligned_cols=24  Identities=25%  Similarity=0.382  Sum_probs=20.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            456899999999999999998764

>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=93.43  E-value=0.044  Score=42.06  Aligned_cols=25  Identities=24%  Similarity=0.231  Sum_probs=21.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.++|.+|+|||||.+.+...
T Consensus        19 ~~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           19 RIFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHcC
Confidence            3456899999999999999998754

>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=93.43  E-value=0.046  Score=48.89  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+|.++|++|+||||+++.+.+.
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~   62 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRY   62 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999999998765

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=93.42  E-value=0.042  Score=50.10  Aligned_cols=25  Identities=24%  Similarity=0.550  Sum_probs=21.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-.+++|+|+.|+|||||.+.+..-
T Consensus        24 ~Gei~gLiGpNGaGKSTLlkiL~Gl   48 (538)
T 3ozx_A           24 NNTILGVLGKNGVGKTTVLKILAGE   48 (538)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            3469999999999999999998763

>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=93.42  E-value=0.043  Score=42.57  Aligned_cols=25  Identities=16%  Similarity=0.260  Sum_probs=21.0

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+...
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhC
Confidence            3467899999999999999998754

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=93.42  E-value=0.044  Score=41.79  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            356789999999999999998764

>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=93.41  E-value=0.054  Score=40.45  Aligned_cols=21  Identities=29%  Similarity=0.520  Sum_probs=19.0

Q ss_pred             eEEeEeecCCCChHHHHHHHh
Q 041190          158 SVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      .+..|+|+.|+||||+...++
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            588999999999999998875

>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=93.40  E-value=0.051  Score=45.08  Aligned_cols=24  Identities=33%  Similarity=0.508  Sum_probs=20.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|+|.|-||+||||+|-.+...
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~   25 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAA   25 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHH
Confidence            367888999999999999877654

>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=93.39  E-value=0.045  Score=42.44  Aligned_cols=23  Identities=30%  Similarity=0.560  Sum_probs=19.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ..-|.|+|.+|+|||||.+.+..
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

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=93.39  E-value=0.043  Score=42.51  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=19.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+.+.
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            456789999999999999988754

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=93.37  E-value=0.066  Score=40.95  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+.+.
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            467899999999999999998854

>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A 3j0j_A* 1um2_C

Probab=93.37  E-value=0.082  Score=48.03  Aligned_cols=37  Identities=19%  Similarity=0.069  Sum_probs=29.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED  198 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  198 (261)
                      .-++|.|..|+|||+|+..+.+..    +-+..+++-+++.
T Consensus       222 qr~~Ifg~~g~GKT~l~~~ia~~~----~~~v~V~~~iGER  258 (578)
T 3gqb_A          222 GTAAIPGPFGSGKSVTQQSLAKWS----NADVVVYVGSGER  258 (578)
T ss_dssp             CEEEECCCTTSCHHHHHHHHHHHS----SCSEEEEEEEEEC
T ss_pred             CEEeeeCCCCccHHHHHHHHHhcc----CCCEEEEEEeccc
Confidence            468999999999999999998763    2345677777775

>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=93.36  E-value=0.32  Score=39.09  Aligned_cols=90  Identities=13%  Similarity=0.120  Sum_probs=48.9

Q ss_pred             EeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC---C---------CCC-----CCHH
Q 041190          160 IPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG---S---------ADV-----NDLN  222 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~---~---------~~~-----~~~~  222 (261)
                      +.++|+.|.|||.+|..+....    .. ..+++. +.    ..+..++.+.+..   .         ...     ...+
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~~----~~-~~liv~-P~----~~L~~q~~~~~~~~~~~~v~~~~g~~~~~~~i~v~T~~  180 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINEL----ST-PTLIVV-PT----LALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYD  180 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS----CS-CEEEEE-SS----HHHHHHHHHHHGGGCGGGEEEESSSCBCCCSEEEEEHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHc----CC-CEEEEe-CC----HHHHHHHHHHHHhCCCCeEEEEeCCCCCcCCEEEEeHH
Confidence            7788999999999998877652    11 123332 22    1223333333221   0         000     0123


Q ss_pred             HHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcccC
Q 041190          223 LLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFK  260 (261)
Q Consensus       223 ~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l~  260 (261)
                      .+.... +.+.++--+||+|++-......|..+...++
T Consensus       181 ~l~~~~-~~~~~~~~llIiDEaH~l~~~~~~~i~~~~~  217 (237)
T 2fz4_A          181 SAYVNA-EKLGNRFMLLIFDEVHHLPAESYVQIAQMSI  217 (237)
T ss_dssp             HHHHTH-HHHTTTCSEEEEECSSCCCTTTHHHHHHTCC
T ss_pred             HHHhhH-HHhcccCCEEEEECCccCCChHHHHHHHhcc
Confidence            333323 2344556799999999876667777665543

>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=93.33  E-value=0.046  Score=43.09  Aligned_cols=24  Identities=29%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.++|.+|+|||||.+.+.+.
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            456889999999999999998754

>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=93.32  E-value=0.041  Score=42.26  Aligned_cols=25  Identities=20%  Similarity=0.169  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..-|.++|.+|+|||||.+.+....
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           21 EVHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             CEEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcCC
Confidence            3467899999999999999997654

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=93.32  E-value=0.041  Score=42.52  Aligned_cols=24  Identities=33%  Similarity=0.432  Sum_probs=19.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+.++
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            345789999999999999998754

>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=93.31  E-value=0.041  Score=48.54  Aligned_cols=21  Identities=38%  Similarity=0.643  Sum_probs=19.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |+|+|.+|+|||||.+.++..
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            499999999999999999764

>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=93.29  E-value=0.049  Score=42.60  Aligned_cols=23  Identities=30%  Similarity=0.421  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.+...
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            46899999999999999998764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=93.23  E-value=0.043  Score=49.71  Aligned_cols=23  Identities=22%  Similarity=0.112  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+.|+|++|+||||+++.+..-
T Consensus       261 ~~i~I~GptGSGKTTlL~aL~~~  283 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLNAIMMF  283 (511)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGG
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            35899999999999999998764

>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=93.21  E-value=0.049  Score=42.50  Aligned_cols=24  Identities=29%  Similarity=0.416  Sum_probs=20.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            456899999999999999998754

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=93.21  E-value=0.065  Score=48.48  Aligned_cols=27  Identities=7%  Similarity=-0.093  Sum_probs=23.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAG  182 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  182 (261)
                      +..+|.+.|++|+||||+|+.+.....
T Consensus       394 ~~~~I~l~GlsGsGKSTIa~~La~~L~  420 (511)
T 1g8f_A          394 QGFSIVLGNSLTVSREQLSIALLSTFL  420 (511)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHHT
T ss_pred             cceEEEecccCCCCHHHHHHHHHHHHH
Confidence            457899999999999999999988743

>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=93.18  E-value=0.053  Score=41.75  Aligned_cols=24  Identities=33%  Similarity=0.378  Sum_probs=20.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+.+.
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            346889999999999999998765

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=93.16  E-value=0.064  Score=41.45  Aligned_cols=24  Identities=25%  Similarity=0.213  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+...
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            356899999999999999998654

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.13  E-value=0.051  Score=43.74  Aligned_cols=22  Identities=18%  Similarity=0.152  Sum_probs=18.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.+.|.||+||||+|-.+...
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~   29 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHA   29 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHH
Confidence            4788899999999998777665

>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=93.13  E-value=0.054  Score=42.23  Aligned_cols=25  Identities=20%  Similarity=0.189  Sum_probs=21.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-|.|+|.+|+|||||.+.+.+.
T Consensus        28 ~~~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           28 FLFKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHhhC
Confidence            3456899999999999999998754

>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=93.12  E-value=0.048  Score=50.48  Aligned_cols=23  Identities=39%  Similarity=0.612  Sum_probs=21.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
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            48999999999999999999864

>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=93.08  E-value=0.055  Score=42.07  Aligned_cols=23  Identities=35%  Similarity=0.434  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.+...
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            45789999999999999998764

>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=93.07  E-value=0.055  Score=42.26  Aligned_cols=24  Identities=25%  Similarity=0.236  Sum_probs=20.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.++|.+|+|||||.+.+.+.
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

>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=93.03  E-value=0.068  Score=43.51  Aligned_cols=25  Identities=20%  Similarity=0.291  Sum_probs=21.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....|.|+|.+|+|||||.+.+...
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            3467899999999999999998754

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=93.00  E-value=0.056  Score=49.78  Aligned_cols=24  Identities=29%  Similarity=0.429  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus       369 G~~~~ivG~sGsGKSTLl~~l~g~  392 (582)
T 3b60_A          369 GKTVALVGRSGSGKSTIASLITRF  392 (582)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhc
Confidence            358999999999999999999653

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=92.99  E-value=0.058  Score=42.22  Aligned_cols=25  Identities=24%  Similarity=0.284  Sum_probs=20.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..--|.|+|.+|+|||||.+.+.+.
T Consensus         8 ~~~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A            8 KFIKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHhcC
Confidence            3456889999999999999988754

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=92.98  E-value=0.052  Score=50.24  Aligned_cols=24  Identities=25%  Similarity=0.477  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus       103 Gei~~LvGpNGaGKSTLLkiL~Gl  126 (608)
T 3j16_B          103 GQVLGLVGTNGIGKSTALKILAGK  126 (608)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcC
Confidence            459999999999999999998753

>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8 d.52.3.1

Probab=92.97  E-value=0.065  Score=45.03  Aligned_cols=25  Identities=24%  Similarity=0.301  Sum_probs=21.9

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...|+|+|.+|+|||||.+.+...
T Consensus         6 ~~g~V~ivG~~nvGKSTLln~l~g~   30 (301)
T 1wf3_A            6 YSGFVAIVGKPNVGKSTLLNNLLGV   30 (301)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567999999999999999998765

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=92.95  E-value=0.052  Score=50.25  Aligned_cols=23  Identities=35%  Similarity=0.575  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||++.+..-
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl  401 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGA  401 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCcHHHHHHHHhcC
Confidence            46899999999999999999764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=92.89  E-value=0.06  Score=43.21  Aligned_cols=24  Identities=33%  Similarity=0.362  Sum_probs=20.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .-.++-|.|.+|+|||+||.++..
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~   52 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIY   52 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHH
Confidence            446899999999999999988653

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=92.89  E-value=0.041  Score=43.41  Aligned_cols=26  Identities=23%  Similarity=0.291  Sum_probs=22.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +...|.|+|.+|+|||||.+.+....
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            45678999999999999999998764

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=92.88  E-value=0.053  Score=50.21  Aligned_cols=27  Identities=15%  Similarity=0.235  Sum_probs=22.9

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-.++.++|+|..|+|||||.+.+..-
T Consensus        42 ~l~lp~iaIvG~nGsGKSTLL~~I~Gl   68 (608)
T 3szr_A           42 DLALPAIAVIGDQSSGKSSVLEALSGV   68 (608)
T ss_dssp             SCCCCCEECCCCTTSCHHHHHHHHHSC
T ss_pred             cccCCeEEEECCCCChHHHHHHHHhCC
Confidence            345677999999999999999999753

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=92.86  E-value=0.076  Score=42.40  Aligned_cols=25  Identities=28%  Similarity=0.450  Sum_probs=22.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -..|.+-|+.|+||||+++.+.+..
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l   29 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKL   29 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3688999999999999999998874

>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=92.83  E-value=0.033  Score=42.39  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=10.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.|+|.+|+|||||.+.+.+.
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            456899999999999999888654

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=92.81  E-value=0.048  Score=41.79  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..-|.++|.+|+|||||.+.+...
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            456899999999999999998654

>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=92.79  E-value=0.058  Score=42.35  Aligned_cols=24  Identities=25%  Similarity=0.308  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .--|.|+|.+|+|||||.+.+...
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

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=92.78  E-value=0.068  Score=43.46  Aligned_cols=23  Identities=26%  Similarity=0.501  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|+|+|..|+||||+++.+-..
T Consensus         2 ~~i~ltG~~~sGK~tv~~~l~~~   24 (241)
T 1dek_A            2 KLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999988653

>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=92.78  E-value=0.056  Score=50.06  Aligned_cols=24  Identities=33%  Similarity=0.432  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus       117 Ge~~~LiG~NGsGKSTLlkiL~Gl  140 (607)
T 3bk7_A          117 GMVVGIVGPNGTGKTTAVKILAGQ  140 (607)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            458999999999999999998753

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=92.76  E-value=0.061  Score=46.54  Aligned_cols=26  Identities=27%  Similarity=0.277  Sum_probs=21.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++++|+|.+|+|||||.+.+....
T Consensus       178 ~~~~V~lvG~~naGKSTLln~L~~~~  203 (364)
T 2qtf_A          178 NIPSIGIVGYTNSGKTSLFNSLTGLT  203 (364)
T ss_dssp             -CCEEEEECBTTSSHHHHHHHHHCC-
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHCCC
Confidence            46679999999999999999998653

>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=92.71  E-value=0.064  Score=42.31  Aligned_cols=23  Identities=26%  Similarity=0.349  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.|+|.+|+|||||.+.+.+.
T Consensus        28 ~ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           28 CKLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            45789999999999999998765

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=92.68  E-value=0.058  Score=44.51  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=19.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.|+|.+|+|||||.+.++..
T Consensus         9 ~~I~vvG~~g~GKSTLin~L~~~   31 (274)
T 3t5d_A            9 FTLMVVGESGLGKSTLINSLFLT   31 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHSSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            35789999999999999987654

>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=92.67  E-value=0.06  Score=49.56  Aligned_cols=24  Identities=29%  Similarity=0.394  Sum_probs=21.0

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus       369 G~~~~ivG~sGsGKSTll~~l~g~  392 (582)
T 3b5x_A          369 GKTVALVGRSGSGKSTIANLFTRF  392 (582)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999998653

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=92.65  E-value=0.029  Score=47.39  Aligned_cols=23  Identities=22%  Similarity=0.449  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|++|+|||||.+.+...
T Consensus       174 ~~~~lvG~sG~GKSTLln~L~g~  196 (307)
T 1t9h_A          174 KTTVFAGQSGVGKSSLLNAISPE  196 (307)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-
T ss_pred             CEEEEECCCCCCHHHHHHHhccc
Confidence            48999999999999999999754

---

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	261
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	8e-23

>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 = 92.2 bits (228), Expect = 8e-23
 Identities = 21/153 (13%), Positives = 41/153 (26%), Gaps = 16/153 (10%)

Query: 119 RPLSTPSLVDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVF 178
           R L   ++  +   Y RE   + ++  L             + + G  G GK+ +A    
Sbjct: 9   RKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDS---FFLFLHGRAGSGKSVIASQAL 65

Query: 179 NDA--GVKKYFSFRACAYVSEDFDAVGVTKVI-----------LQAAAGSADVNDLNLLQ 225
           + +   +   +        S                       L        V  + L +
Sbjct: 66  SKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKR 125

Query: 226 LQLENQLKNKKFLLVLDDMWSENYDVWTNLCKP 258
           +     +     L V DD+  E    W    + 
Sbjct: 126 MICNALIDRPNTLFVFDDVVQEETIRWAQELRL 158

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	261
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.86
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.0
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.74
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.49
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.36
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.36
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.32
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.32
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.17
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.14
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.13
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.1
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.04
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.95
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.93
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.89
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.85
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.83
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.78
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.71
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.61
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.52
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.48
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.48
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.47
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.46
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.46
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.46
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.45
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.37
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.36
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.36
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.33
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.27
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.27
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.26
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.26
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.25
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.23
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.19
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.19
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.13
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.13
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.1
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.08
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.06
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.04
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.04
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.03
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	97.02
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.01
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.98
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.96
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.93
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.91
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.9
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.88
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.86
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.85
d1okkd2	207	GTPase domain of the signal recognition particle r	96.82
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.82
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.8
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.79
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.78
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.76
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.75
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.74
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.72
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.7
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.7
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.66
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.56
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.54
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.52
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.47
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.47
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.42
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.39
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.37
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.37
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.33
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.33
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.3
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.24
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.21
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	96.08
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.04
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	96.03
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.01
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.99
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	95.98
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	95.97
d1g2912	240	Maltose transport protein MalK, N-terminal domain	95.96
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.95
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.95
d2awna2	232	Maltose transport protein MalK, N-terminal domain	95.92
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.91
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.86
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.84
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.82
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	95.79
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.77
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.75
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	95.73
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	95.7
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	95.7
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.7
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	95.69
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.66
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	95.64
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	95.63
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	95.61
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.56
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.48
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.47
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.45
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	95.41
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.41
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	95.4
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.35
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.35
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.33
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.31
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.3
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	95.29
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.26
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.23
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	95.21
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	95.18
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	95.14
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	95.12
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	95.04
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.03
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	95.0
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.0
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.96
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	94.96
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.95
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.95
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.95
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.93
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.9
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	94.89
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.89
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.82
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.81
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.74
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.7
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.69
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.68
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	94.67
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	94.66
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.65
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.65
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.63
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	94.61
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.59
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.56
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.55
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	94.5
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.49
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.48
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.47
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.45
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.44
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.42
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.42
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.4
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.37
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.37
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.36
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.33
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.32
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.3
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.29
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.27
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	94.27
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.24
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	94.17
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	94.12
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.03
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.99
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.96
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.94
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.93
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.92
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	93.92
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.86
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.81
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.79
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	93.74
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.73
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	93.71
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.69
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.69
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	93.65
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	93.63
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	93.62
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.62
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	93.52
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.4
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	93.37
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.27
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.18
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	93.14
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.11
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.98
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	92.94
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	92.87
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.7
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	92.63
d1tuea_	205	Replication protein E1 helicase domain {Human papi	92.51
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.45
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.44
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.26
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	92.25
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	92.07
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	92.03
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.87
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	91.67
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	91.6
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	91.49
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.45
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	91.18
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	90.87
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	90.84
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	90.6
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	90.58
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	90.25
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	90.12
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.03
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	90.0
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	89.6
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	89.58
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	89.41
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	89.15
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	89.15
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	88.56
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	88.51
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	88.01
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	87.77
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	86.39
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	86.15
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	86.14
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	85.95
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	85.15
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	84.92
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	84.11
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	82.7
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	82.24
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	80.82

>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=99.86  E-value=1.2e-21  Score=163.89  Aligned_cols=124  Identities=13%  Similarity=0.061  Sum_probs=95.0

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccc--cccccceeEEEeeCCCCCHHHH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAG--VKKYFSFRACAYVSEDFDAVGV  204 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~--~~~~f~~~~wv~v~~~~~~~~i  204 (261)
                      +.++.++||+.++++|+++|...   .+...++|+|+||||+||||||+++|++..  ...+|++++|+++++.++...+
T Consensus        17 p~~~~~~gR~~~~~~i~~~L~~~---~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l   93 (277)
T d2a5yb3          17 PKQMTCYIREYHVDRVIKKLDEM---CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTF   93 (277)
T ss_dssp             BCCCCSCCCHHHHHHHHHHHHHH---TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHH
T ss_pred             CCCCceeCcHHHHHHHHHHHHhc---cCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHH
Confidence            45667899999999999999753   234578999999999999999999998754  5678999999999999888777


Q ss_pred             HHHHHHHhc---CC-C-----CC--CCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHh
Q 041190          205 TKVILQAAA---GS-A-----DV--NDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       205 ~~~i~~~l~---~~-~-----~~--~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l  255 (261)
                      ...+...+.   .. .     ..  .........+.+.+.++|+|+||||||+..  .|+.+
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~--~~~~~  153 (277)
T d2a5yb3          94 DLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEE--TIRWA  153 (277)
T ss_dssp             HHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHH--HHHHH
T ss_pred             HHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHh--hhhhh
Confidence            666555443   11 0     11  122334556888999999999999999974  56544

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.00  E-value=2.4e-09  Score=86.83  Aligned_cols=122  Identities=16%  Similarity=0.052  Sum_probs=86.5

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccce-eEEEeeCCCCCHHHHH
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSF-RACAYVSEDFDAVGVT  205 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~i~  205 (261)
                      +.+..++||+.+++.|.++|...-.+.+...+.+.|+|++|+|||++|+.+.+..+  +.+.. .+|++.........++
T Consensus        13 y~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~--~~~~~~~~~~~~~~~~~~~~~~   90 (276)
T d1fnna2          13 YVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYK--DKTTARFVYINGFIYRNFTAII   90 (276)
T ss_dssp             CCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHT--TSCCCEEEEEETTTCCSHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHh--cccCCcEEEecchhhhhhhhhh
Confidence            44556899999999999998642100234567899999999999999999998743  33332 3577777777888888


Q ss_pred             HHHHHHhc--CCCCCCCHHHHHHHHHHHh--CCCeEEEEEeCCCCCChh
Q 041190          206 KVILQAAA--GSADVNDLNLLQLQLENQL--KNKKFLLVLDDMWSENYD  250 (261)
Q Consensus       206 ~~i~~~l~--~~~~~~~~~~~~~~l~~~l--~~kr~LiVlDdvw~~~~~  250 (261)
                      ..+....+  ..........+...+.+.+  .....++++|++.+....
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~  139 (276)
T d1fnna2          91 GEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPD  139 (276)
T ss_dssp             HHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHH
T ss_pred             hhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhh
Confidence            88888877  2334445566656555555  346788888988887643

>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=98.74  E-value=3.4e-08  Score=80.26  Aligned_cols=121  Identities=17%  Similarity=0.145  Sum_probs=80.2

Q ss_pred             CCCCCccccccchHHHHHHHhhCC---CCCCCCCceEEeEeecCCCChHHHHHHHhhccccc---ccc-ceeEEEeeCCC
Q 041190          126 LVDEEEVYGREKDKEVIVGLLLGD---DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK---KYF-SFRACAYVSED  198 (261)
Q Consensus       126 ~~~~~~~~gr~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~~f-~~~~wv~v~~~  198 (261)
                      .+.+..+.||+.+.+.|.+++...   .....+...++.++|++|+|||++++.+.+.....   ... ....++++...
T Consensus        12 ~~~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~   91 (287)
T d1w5sa2          12 NYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNA   91 (287)
T ss_dssp             TCCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGC
T ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccc
Confidence            345678999999999998876431   11012223456788999999999999999873211   111 23557788887


Q ss_pred             CCHHHHHHHHHHHhc--CCCCCCCHHHHHHHHHHHh--CCCeEEEEEeCCCC
Q 041190          199 FDAVGVTKVILQAAA--GSADVNDLNLLQLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       199 ~~~~~i~~~i~~~l~--~~~~~~~~~~~~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                      .+....+..+...++  ..........+...+.+..  .+...++++|.+..
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~  143 (287)
T d1w5sa2          92 PNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQS  143 (287)
T ss_dssp             CSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHH
T ss_pred             cchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEE
Confidence            888888888888877  2233445555555555555  35677888887753

>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=98.49  E-value=2.2e-07  Score=74.98  Aligned_cols=43  Identities=23%  Similarity=0.503  Sum_probs=36.3

Q ss_pred             CCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          128 DEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       128 ~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....|+||+++.+.|.+..          .+++.|+|++|+|||+|++++.+.
T Consensus        10 ~~~~f~GR~~el~~l~~~~----------~~~i~i~G~~G~GKTsLl~~~~~~   52 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGLR----------APITLVLGLRRTGKSSIIKIGINE   52 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHTC----------SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhcc----------CCEEEEEcCCCCcHHHHHHHHHHH
Confidence            4578999999999987632          257889999999999999999876

>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=98.36  E-value=4.8e-07  Score=71.39  Aligned_cols=106  Identities=18%  Similarity=0.175  Sum_probs=65.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccc-eeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFS-FRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~i~~~i  208 (261)
                      .+++|.++.++.|..|+....      ...+-++|++|+||||+|+.+.+..... .+. ...-++.+...+...+...+
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~~------~~~~ll~Gp~G~GKTt~a~~la~~l~~~-~~~~~~~~~n~~~~~~~~~i~~~~   87 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDGN------MPHMIISGMPGIGKTTSVHCLAHELLGR-SYADGVLELNASDDRGIDVVRNQI   87 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCC------CCCEEEECSTTSSHHHHHHHHHHHHHGG-GHHHHEEEECTTSCCSHHHHHTHH
T ss_pred             HHhcCCHHHHHHHHHHHHcCC------CCeEEEECCCCCCchhhHHHHHHHHhcc-ccccccccccccccCCceehhhHH
Confidence            568999999999999997642      3346789999999999999887763221 111 13345556555554444333


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHh
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l  255 (261)
                      ..........             ..++.-++|+|++..........+
T Consensus        88 ~~~~~~~~~~-------------~~~~~kviiiDe~d~~~~~~~~~l  121 (224)
T d1sxjb2          88 KHFAQKKLHL-------------PPGKHKIVILDEADSMTAGAQQAL  121 (224)
T ss_dssp             HHHHHBCCCC-------------CTTCCEEEEEESGGGSCHHHHHTT
T ss_pred             HHHHHhhccC-------------CCcceEEEEEecccccchhHHHHH
Confidence            3322211100             124566888999988765444444

>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=98.36  E-value=5.4e-07  Score=71.38  Aligned_cols=117  Identities=18%  Similarity=0.077  Sum_probs=68.2

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccc-cceeEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKY-FSFRACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-f~~~~wv~v~~~~~~~~i~~~i  208 (261)
                      .+++|.+..++.|..++...      ..+.+.++|++|+||||+++.+.+....... ......++.+...+...+...+
T Consensus        12 ~diig~~~~~~~l~~~i~~~------~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKSA------NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKV   85 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTCT------TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHH
T ss_pred             HHccCcHHHHHHHHHHHHcC------CCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHH
Confidence            45889999999999999653      3344789999999999999999876311111 1123345555555544433333


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      -.............    .+......+.-++|||++.......+..+.
T Consensus        86 ~~~~~~~~~~~~~~----~~~~~~~~~~~viiiDe~d~l~~~~~~~l~  129 (237)
T d1sxjd2          86 KNFARLTVSKPSKH----DLENYPCPPYKIIILDEADSMTADAQSALR  129 (237)
T ss_dssp             HHHHHSCCCCCCTT----HHHHSCCCSCEEEEETTGGGSCHHHHHHHH
T ss_pred             HHHhhhhhhhhhHH----HHhhccccCceEEEEecccccCHHHHHHHh
Confidence            22222111111111    122233445557899999887655555443

>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=98.32  E-value=1.6e-07  Score=74.57  Aligned_cols=106  Identities=14%  Similarity=0.075  Sum_probs=63.8

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccce-eEEEeeCCCCCHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSF-RACAYVSEDFDAVGVTKVI  208 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~i~~~i  208 (261)
                      .+++|.+..++.|..++...      +.+.+-++|++|+||||+|+.+.+.... ..+.. ..-++.+...+...+...+
T Consensus        24 ~diig~~~~~~~l~~~i~~~------~~~~lll~Gp~G~GKTtla~~iak~l~~-~~~~~~~~e~n~s~~~~~~~~~~~~   96 (231)
T d1iqpa2          24 DDIVGQEHIVKRLKHYVKTG------SMPHLLFAGPPGVGKTTAALALARELFG-ENWRHNFLELNASDERGINVIREKV   96 (231)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT------CCCEEEEESCTTSSHHHHHHHHHHHHHG-GGHHHHEEEEETTCHHHHHTTHHHH
T ss_pred             HHccCcHHHHHHHHHHHHcC------CCCeEEEECCCCCcHHHHHHHHHHHHHh-cccCCCeeEEecCcccchhHHHHHH
Confidence            56899999999999999754      3455789999999999999999875321 12222 2234444432222222211


Q ss_pred             HHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          209 LQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       209 ~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      .......              .....++.++++||+.......+..+.
T Consensus        97 ~~~~~~~--------------~~~~~~~~iilide~d~~~~~~~~~ll  130 (231)
T d1iqpa2          97 KEFARTK--------------PIGGASFKIIFLDEADALTQDAQQALR  130 (231)
T ss_dssp             HHHHHSC--------------CGGGCSCEEEEEETGGGSCHHHHHHHH
T ss_pred             HHHHhhh--------------hccCCCceEEeehhhhhcchhHHHHHh
Confidence            1111110              011346678888998877666665554

>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=98.32  E-value=2.7e-07  Score=72.87  Aligned_cols=107  Identities=19%  Similarity=0.151  Sum_probs=62.0

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVIL  209 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~  209 (261)
                      .+++|.++.++.|.+|+....      +..+-++|++|+||||+|+.+.+............-.+.+...+.......+.
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            468999999999999997642      33366899999999999999988632222112223344444444333222222


Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhh
Q 041190          210 QAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLC  256 (261)
Q Consensus       210 ~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~  256 (261)
                      ......              ....+++-+||+|++.......-..+.
T Consensus        88 ~~~~~~--------------~~~~~~~kiiiiDe~d~~~~~~~~~Ll  120 (227)
T d1sxjc2          88 DFASTR--------------QIFSKGFKLIILDEADAMTNAAQNALR  120 (227)
T ss_dssp             HHHHBC--------------CSSSCSCEEEEETTGGGSCHHHHHHHH
T ss_pred             hccccc--------------cccCCCeEEEEEeccccchhhHHHHHH
Confidence            211110              011234457778888777544433333

>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=98.17  E-value=7e-06  Score=66.32  Aligned_cols=98  Identities=21%  Similarity=0.244  Sum_probs=60.6

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc---cccccc-ceeEE-EeeCCCCCHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA---GVKKYF-SFRAC-AYVSEDFDAVGVT  205 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~---~~~~~f-~~~~w-v~v~~~~~~~~i~  205 (261)
                      .++||++++++++..|....      -+-+.++|++|+|||+++..+....   ++.... ..++| ++++.-       
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~------k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l-------   85 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRR------KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL-------   85 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSS------SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---------
T ss_pred             cccChHHHHHHHHHHHhcCc------cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH-------
Confidence            47999999999999997643      2345599999999999888776542   222222 34555 333221       


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHh-CCCeEEEEEeCCCCC
Q 041190          206 KVILQAAAGSADVNDLNLLQLQLENQL-KNKKFLLVLDDMWSE  247 (261)
Q Consensus       206 ~~i~~~l~~~~~~~~~~~~~~~l~~~l-~~kr~LiVlDdvw~~  247 (261)
                            +......+..++....+.+.+ ..++.++++||+-..
T Consensus        86 ------iag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l  122 (268)
T d1r6bx2          86 ------LAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTI  122 (268)
T ss_dssp             -------CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTT
T ss_pred             ------hccCccchhHHHHHHHHHHHhhccCCceEEecchHHH
Confidence                  011223445555444444444 456788999997654

>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=98.14  E-value=4.1e-06  Score=64.29  Aligned_cols=44  Identities=20%  Similarity=0.292  Sum_probs=36.3

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++||+.+++++...|....      -.-+.++|.+|+|||+++..+...
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~------k~n~lLvG~pGVGKTalv~~LA~r   66 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRT------KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSS------SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhccC------CCCeEEEecCCcccHHHHHHHHHH
Confidence            47899999999999998753      234679999999999998777654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.13  E-value=2.5e-06  Score=67.67  Aligned_cols=50  Identities=28%  Similarity=0.377  Sum_probs=38.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+.-+++|..++..... ....++-+-++|++|+||||+|+.+.+.
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            4689999999998888754221 1223455678999999999999999886

>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=98.10  E-value=2.4e-06  Score=68.23  Aligned_cols=69  Identities=22%  Similarity=0.156  Sum_probs=48.8

Q ss_pred             CccccccchHHHHHHHhhCC-----------CCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC
Q 041190          130 EEVYGREKDKEVIVGLLLGD-----------DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED  198 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~-----------~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  198 (261)
                      .+++|.+..+++|.++|..-           ...+....+.+.++|++|+||||+|+.+++....     ...+++.+..
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~-----~~~~~~~~~~   88 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY-----DILEQNASDV   88 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC-----EEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHh-----hhhccccccc
Confidence            57899999999999988541           0112334568899999999999999999987321     2345666665


Q ss_pred             CCHHH
Q 041190          199 FDAVG  203 (261)
Q Consensus       199 ~~~~~  203 (261)
                      .+...
T Consensus        89 ~~~~~   93 (253)
T d1sxja2          89 RSKTL   93 (253)
T ss_dssp             CCHHH
T ss_pred             hhhHH
Confidence            55443

>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=98.04  E-value=7.6e-06  Score=65.09  Aligned_cols=46  Identities=15%  Similarity=0.179  Sum_probs=36.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.++.++.|..++....     ...-+-++|++|+||||+|+.+.+.
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            468999888888888775432     2334679999999999999999875

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.95  E-value=2.1e-05  Score=62.35  Aligned_cols=46  Identities=24%  Similarity=0.303  Sum_probs=37.7

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..++.|..++....     -.+.+-++|++|+||||+|+.+.+.
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~-----~~~~~Ll~Gp~G~GKtt~a~~~~~~   57 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGR-----IHHAYLFSGTRGVGKTSIARLLAKG   57 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTC-----CCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHccChHHHHHHHHHHHHcCC-----CCeeEEEECCCCCcHHHHHHHHHHH
Confidence            468999999999999997532     2456789999999999999988664

>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=97.93  E-value=1.8e-05  Score=63.50  Aligned_cols=98  Identities=20%  Similarity=0.147  Sum_probs=55.7

Q ss_pred             CccccccchHHHHHHH---hhCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHH
Q 041190          130 EEVYGREKDKEVIVGL---LLGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVG  203 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~---L~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  203 (261)
                      .++.|.+..+++|.+.   +...+.   -+....+-+-++|++|+|||++|+.+.+....  +   .+.++.+.-.+   
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~--~---~~~i~~~~l~~---   83 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKV--P---FFTISGSDFVE---   83 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTC--C---EEEECSCSSTT---
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCC--C---EEEEEhHHhhh---
Confidence            5788988888777553   332210   01233466789999999999999999986321  1   12233322111   


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCC
Q 041190          204 VTKVILQAAAGSADVNDLNLLQLQLENQLKNKKFLLVLDDMWS  246 (261)
Q Consensus       204 i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~  246 (261)
                                 .........+...+...-...+++|+|||+..
T Consensus        84 -----------~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~  115 (256)
T d1lv7a_          84 -----------MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDA  115 (256)
T ss_dssp             -----------SCCCCCHHHHHHHHHHHHTTCSEEEEETTHHH
T ss_pred             -----------cchhHHHHHHHHHHHHHHHcCCEEEEEEChhh
Confidence                       01112222333333344456788999999953

>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=97.89  E-value=2.6e-05  Score=66.21  Aligned_cols=97  Identities=15%  Similarity=0.251  Sum_probs=53.6

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc---cccc-ccceeEE-EeeCCCCCHHHHHH
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA---GVKK-YFSFRAC-AYVSEDFDAVGVTK  206 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~---~~~~-~f~~~~w-v~v~~~~~~~~i~~  206 (261)
                      ++||+.+++.++..|.+...      .-+.++|.+|+|||+++..+....   .+-. ..+.++| +.++.-..      
T Consensus        24 ~~gr~~ei~~~~~~L~r~~k------~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~a------   91 (387)
T d1qvra2          24 VIGRDEEIRRVIQILLRRTK------NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA------   91 (387)
T ss_dssp             CCSCHHHHHHHHHHHHCSSC------CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------
T ss_pred             CcCcHHHHHHHHHHHhcCCC------CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhc------
Confidence            78999999999999987531      233677999999999775554321   2222 2345665 44333100      


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHh-CC-CeEEEEEeCCCCC
Q 041190          207 VILQAAAGSADVNDLNLLQLQLENQL-KN-KKFLLVLDDMWSE  247 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~~~~l~~~l-~~-kr~LiVlDdvw~~  247 (261)
                             +....+...+....+...+ .. .++++++|++-..
T Consensus        92 -------g~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l  127 (387)
T d1qvra2          92 -------GAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTV  127 (387)
T ss_dssp             -------------CHHHHHHHHHHHHHTTCSSEEEEECCC---
T ss_pred             -------ccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHH
Confidence                   1112234443333333333 33 4799999999765

>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=97.85  E-value=6.2e-06  Score=65.22  Aligned_cols=50  Identities=30%  Similarity=0.461  Sum_probs=38.3

Q ss_pred             CccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.+..+++|..++..... .+...+-+-++|++|+||||+|+.+.+.
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            5689999999999988853210 1223445779999999999999999886

>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=97.83  E-value=5.5e-05  Score=60.22  Aligned_cols=50  Identities=12%  Similarity=0.050  Sum_probs=34.4

Q ss_pred             CCccccccchHHHHHHHhhC------CCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          129 EEEVYGREKDKEVIVGLLLG------DDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       129 ~~~~~gr~~~~~~l~~~L~~------~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.++|...+++.+.+.+..      ..  .....+-|-++|++|+|||++|+.+.+.
T Consensus         8 ~~~~i~~~~~i~~i~~~~~~~~~~~~~~--~~~p~~~vLL~GppGtGKT~la~alA~~   63 (246)
T d1d2na_           8 MNGIIKWGDPVTRVLDDGELLVQQTKNS--DRTPLVSVLLEGPPHSGKTALAAKIAEE   63 (246)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHC--SSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccCCcCcCHHHHHHHHHHHHHHHHHhcc--CCCCCeEEEEECcCCCCHHHHHHHHhhc
Confidence            34578877666655554331      11  1234566789999999999999999986

>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=97.78  E-value=3.2e-05  Score=61.67  Aligned_cols=52  Identities=29%  Similarity=0.316  Sum_probs=35.4

Q ss_pred             CccccccchHHHHHHH---hhCCC---CCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGL---LLGDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~---L~~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+++|.++.++.|.+.   +...+   .-+....+-+-++|++|+|||+||+.+.+..
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~   66 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   66 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc
Confidence            4688988777766553   32210   0012234568899999999999999999863

>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=97.71  E-value=3.5e-05  Score=61.81  Aligned_cols=51  Identities=27%  Similarity=0.231  Sum_probs=36.6

Q ss_pred             CccccccchHHHHHHHh----hCCCC---CCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLL----LGDDL---NSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L----~~~~~---~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.+..+++|.+.+    ...+.   -+-+..+-+-++|++|+|||++|+.+.+.
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            35789998888888864    22100   01223456789999999999999999886

>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=97.61  E-value=5.2e-05  Score=61.08  Aligned_cols=52  Identities=27%  Similarity=0.241  Sum_probs=35.9

Q ss_pred             CccccccchHHHHHHHhh----CCC---CCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          130 EEVYGREKDKEVIVGLLL----GDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~----~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.|.++.++.|.+.+.    ..+   ..+-+..+-|-++|++|+|||+||+.+.+..
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~   65 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC   65 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHT
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHh
Confidence            457888877777776542    100   0022345567899999999999999999873

>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=97.52  E-value=0.00021  Score=55.48  Aligned_cols=49  Identities=35%  Similarity=0.325  Sum_probs=31.9

Q ss_pred             CCccccccch--HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          129 EEEVYGREKD--KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       129 ~~~~~gr~~~--~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ++.++|....  ...+.++....    ++....+.|+|++|+|||.|++.+++..
T Consensus        10 dnF~vg~~N~~a~~~~~~~~~~~----~~~~n~l~l~G~~G~GKTHLl~A~~~~~   60 (213)
T d1l8qa2          10 ENFIVGEGNRLAYEVVKEALENL----GSLYNPIFIYGSVGTGKTHLLQAAGNEA   60 (213)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHTT----TTSCSSEEEECSSSSSHHHHHHHHHHHH
T ss_pred             hhccCCCcHHHHHHHHHHHHhCc----CCCCCcEEEECCCCCcHHHHHHHHHHHh
Confidence            4446675332  23334444332    2234458899999999999999999974

>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=97.48  E-value=3.4e-05  Score=57.44  Aligned_cols=26  Identities=23%  Similarity=0.139  Sum_probs=23.2

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+-.+|.++|++|+||||+|+.+...
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            45689999999999999999999876

>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=97.48  E-value=9.4e-05  Score=61.05  Aligned_cols=119  Identities=17%  Similarity=0.127  Sum_probs=66.8

Q ss_pred             CccccccchHHHHHHHhhCC---CCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHH
Q 041190          130 EEVYGREKDKEVIVGLLLGD---DLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTK  206 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~  206 (261)
                      ..++|.++.++.|...+...   -.+.+....++..+|++|+|||.||+.+..-.     +...+-++++.-.+...   
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l-----~~~~i~~d~s~~~~~~~---   93 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL-----GIELLRFDMSEYMERHT---   93 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH-----TCEEEEEEGGGCSSSSC---
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhc-----cCCeeEeccccccchhh---
Confidence            45889999999888766421   11123446678899999999999999998752     12223333333111000   


Q ss_pred             HHHHHhcCCCCCCCHHHH-HHHHHHHh-CCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          207 VILQAAAGSADVNDLNLL-QLQLENQL-KNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       207 ~i~~~l~~~~~~~~~~~~-~~~l~~~l-~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                        ...+... .+.....- ...+...+ .....+++||++....++.|+.+...|
T Consensus        94 --~~~l~g~-~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa~~~V~~~lLqil  145 (315)
T d1r6bx3          94 --VSRLIGA-PPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVM  145 (315)
T ss_dssp             --CSSSCCC-CSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHH
T ss_pred             --hhhhccc-CCCccccccCChhhHHHHhCccchhhhcccccccchHhhhhHHhh
Confidence              0001101 11111110 01111222 356789999999999988888766543

>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=97.47  E-value=2.7e-05  Score=57.60  Aligned_cols=24  Identities=25%  Similarity=0.441  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|+.|+|.+|+|||||++.+.+.
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~   25 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPA   25 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999999764

>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=97.46  E-value=3e-05  Score=56.44  Aligned_cols=23  Identities=30%  Similarity=0.404  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.|+|++|+||||||+.+...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999988654

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.46  E-value=0.00032  Score=54.22  Aligned_cols=57  Identities=25%  Similarity=0.234  Sum_probs=33.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCH--HHHHHHHHHHhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDA--VGVTKVILQAAA  213 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~--~~i~~~i~~~l~  213 (261)
                      +..+.||.++|+.|+||||.+-++....+ +.  ...+.+-...++..  .+.++...+.++
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~-~~--g~kV~lit~Dt~R~gA~eQL~~~a~~l~   64 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFE-QQ--GKSVMLAAGDTFRAAAVEQLQVWGQRNN   64 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHH-TT--TCCEEEECCCTTCHHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH-HC--CCcEEEEecccccccchhhhhhhhhhcC
Confidence            44578999999999999995555544322 11  22344433344433  444555555555

>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=97.46  E-value=0.00014  Score=60.00  Aligned_cols=120  Identities=13%  Similarity=0.137  Sum_probs=65.9

Q ss_pred             ccccccchHHHHHHHhhCCC---CCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDD---LNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKV  207 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~  207 (261)
                      .++|.+..++.|...+....   .+.+....++..+|++|+|||.+|+.+.+..  -..-...+-++.+.-.+...+- .
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l--~~~~~~~~~~~~~~~~~~~~~~-~  100 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL--FDTEEAMIRIDMTEYMEKHAVS-R  100 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH--HSSGGGEEEECTTTCCSSGGGG-G
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHh--cCCCcceEEEeccccccchhhh-h
Confidence            47888888888877654311   1123345588899999999999999887752  1111122334444322211100 0


Q ss_pred             HHHHhcCCC--CCC-CHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhccc
Q 041190          208 ILQAAAGSA--DVN-DLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPF  259 (261)
Q Consensus       208 i~~~l~~~~--~~~-~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l  259 (261)
                      +   ++...  ... ....+...++   +....+|+||++....++.|+.|...|
T Consensus       101 L---~g~~~gyvG~~~~~~l~~~~~---~~p~~Vvl~DEieK~~~~v~~~ll~~l  149 (315)
T d1qvra3         101 L---IGAPPGYVGYEEGGQLTEAVR---RRPYSVILFDEIEKAHPDVFNILLQIL  149 (315)
T ss_dssp             C-----------------CHHHHHH---HCSSEEEEESSGGGSCHHHHHHHHHHH
T ss_pred             h---cCCCCCCcCcccCChHHHHHH---hCCCcEEEEehHhhcCHHHHHHHHHHh
Confidence            0   01000  000 1112333333   345789999999998888888776554

>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=97.45  E-value=7.2e-05  Score=59.69  Aligned_cols=41  Identities=20%  Similarity=0.245  Sum_probs=29.0

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..++.+..... +...++.|.++|++|+||||||+.+.+.
T Consensus        15 ~~~~~~~~~~~~~-~~~~P~~ilL~GpPGtGKT~la~~la~~   55 (273)
T d1gvnb_          15 LNDNLEELIQGKK-AVESPTAFLLGGQPGSGKTSLRSAIFEE   55 (273)
T ss_dssp             HHHHHHHHHTTCC-CCSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHhccc-CCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3333444433222 3456777889999999999999999886

>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=97.37  E-value=3.4e-05  Score=56.41  Aligned_cols=23  Identities=26%  Similarity=0.361  Sum_probs=20.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.+.|++|+||||+|+.+.+.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            35888899999999999999886

>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=97.36  E-value=3.9e-05  Score=57.33  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=22.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.|.|.|++|+||||||+.+.+.
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999999776

>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=97.36  E-value=4.9e-05  Score=56.13  Aligned_cols=23  Identities=30%  Similarity=0.444  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.|.|++|+||||+|+.+...
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~   25 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999765

>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=97.33  E-value=0.00012  Score=55.28  Aligned_cols=26  Identities=38%  Similarity=0.474  Sum_probs=23.0

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...-+|+|.|.+|+||||||+.+.+.
T Consensus        20 ~~~~iIgI~G~~GSGKSTla~~L~~~   45 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTLANQLSQT   45 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999999765

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.27  E-value=5.3e-05  Score=56.07  Aligned_cols=23  Identities=39%  Similarity=0.535  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|.|++|+||||+|+.+.+.
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            45779999999999999999765

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.27  E-value=8.4e-05  Score=54.96  Aligned_cols=27  Identities=22%  Similarity=0.393  Sum_probs=23.6

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...+++.|.|++|+||||+|+.+...
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            446789999999999999999998765

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.26  E-value=9.2e-05  Score=56.42  Aligned_cols=28  Identities=32%  Similarity=0.313  Sum_probs=24.9

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++.++|.|.|++|+||||+|+.+.+..
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999999998863

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.26  E-value=5.5e-05  Score=56.41  Aligned_cols=24  Identities=33%  Similarity=0.343  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +.|.|+|++|+|||||++.+....
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            468999999999999999998663

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.25  E-value=9.7e-05  Score=56.17  Aligned_cols=26  Identities=27%  Similarity=0.284  Sum_probs=23.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +++.+|.|.|++|+||||+|+.+.+.
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            45789999999999999999999876

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=5.9e-05  Score=57.06  Aligned_cols=27  Identities=30%  Similarity=0.332  Sum_probs=23.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.+-.+|.++|++|+||||+|+.+...
T Consensus        16 ~~~g~vI~L~G~pGSGKTTiAk~La~~   42 (195)
T d1x6va3          16 GFRGCTVWLTGLSGAGKTTVSMALEEY   42 (195)
T ss_dssp             SCCCEEEEEESSCHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            335678999999999999999999765

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=97.19  E-value=0.00011  Score=54.53  Aligned_cols=26  Identities=38%  Similarity=0.538  Sum_probs=22.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++...|.|.|++|+||||+|+.+.+.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            45667999999999999999999875

>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=97.19  E-value=0.00024  Score=54.85  Aligned_cols=40  Identities=20%  Similarity=0.276  Sum_probs=30.1

Q ss_pred             cchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          136 EKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       136 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +...+++...+....     -.+.+-++|++|+||||+|+.+.+.
T Consensus         8 ~~~~~~l~~~~~~~~-----l~h~lLl~Gp~G~GKtt~a~~~a~~   47 (207)
T d1a5ta2           8 RPDFEKLVASYQAGR-----GHHALLIQALPGMGDDALIYALSRY   47 (207)
T ss_dssp             HHHHHHHHHHHHTTC-----CCSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCC-----cCeEEEEECCCCCcHHHHHHHHHHh
Confidence            445677777776432     3456889999999999999987664

>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=97.13  E-value=0.0016  Score=52.15  Aligned_cols=89  Identities=17%  Similarity=0.056  Sum_probs=62.2

Q ss_pred             CCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC------CCCCCHHHHHH
Q 041190          153 SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS------ADVNDLNLLQL  226 (261)
Q Consensus       153 ~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~------~~~~~~~~~~~  226 (261)
                      +-+.-++.-|+|++|+||||+|-+++.......  ...+|+...+.++.+.     +++++-.      ..+...++...
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~  128 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALE  128 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHH
Confidence            345678999999999999999988876643333  3478999988888764     5556621      13345566555


Q ss_pred             HHHHHh-CCCeEEEEEeCCCCCC
Q 041190          227 QLENQL-KNKKFLLVLDDMWSEN  248 (261)
Q Consensus       227 ~l~~~l-~~kr~LiVlDdvw~~~  248 (261)
                      .+.... .++.-|||+|.+-..-
T Consensus       129 ~~~~l~~~~~~~liIiDSi~al~  151 (269)
T d1mo6a1         129 IADMLIRSGALDIVVIDSVAALV  151 (269)
T ss_dssp             HHHHHHHTTCEEEEEEECSTTCC
T ss_pred             HHHHHHhcCCCCEEEEecccccc
Confidence            554444 4568899999997764

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.13  E-value=0.00012  Score=54.20  Aligned_cols=24  Identities=17%  Similarity=0.236  Sum_probs=21.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|.|.|++|+||||+|+.+.+.
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            368999999999999999999876

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=97.10  E-value=4.5e-05  Score=62.85  Aligned_cols=51  Identities=22%  Similarity=0.235  Sum_probs=35.8

Q ss_pred             CccccccchHHHHHHHhh----CCCCC----CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLL----GDDLN----SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~----~~~~~----~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.++.++.|...+.    .....    .+...+-+.++||+|+|||.||+.+.+.
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            357899988888877652    11100    0113456678999999999999999886

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.08  E-value=0.00016  Score=54.20  Aligned_cols=27  Identities=30%  Similarity=0.420  Sum_probs=23.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++..+|.++|++|+||||+|+.+...
T Consensus        11 ~~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          11 SPNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             CSSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            456789999999999999999988654

>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=97.06  E-value=0.00014  Score=53.77  Aligned_cols=23  Identities=30%  Similarity=0.317  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++++|+|..|+|||||+..+...
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            68999999999999999988765

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.04  E-value=0.00014  Score=54.18  Aligned_cols=23  Identities=39%  Similarity=0.709  Sum_probs=21.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.|.|++|+||||+++.+.+.
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            68999999999999999999765

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.04  E-value=0.00016  Score=55.31  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.+|.++|.+|+||||+|+.+.+.
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            468999999999999999999865

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.03  E-value=0.00021  Score=52.80  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -++|.|.|++|+||||+|+.+.+.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999999765

>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=97.02  E-value=0.00015  Score=53.97  Aligned_cols=21  Identities=48%  Similarity=0.658  Sum_probs=19.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|++|+|||||++.+...
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            789999999999999999875

>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=97.01  E-value=0.0025  Score=48.51  Aligned_cols=97  Identities=9%  Similarity=-0.079  Sum_probs=56.1

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc--ccccceeEEEeeCC-CCCHHHHHHHHHHHhcC
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV--KKYFSFRACAYVSE-DFDAVGVTKVILQAAAG  214 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~--~~~f~~~~wv~v~~-~~~~~~i~~~i~~~l~~  214 (261)
                      +++.+..++...      ...-+-++|++|+||||+|..+.+....  ..|-|. .++...+ ....+++ +++.+.+..
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------EGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDI-RTIKDFLNY   73 (198)
T ss_dssp             HHHHHHHHHHTC------SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHH-HHHHHHHTS
T ss_pred             HHHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCE-EEEeCCcCCCCHHHH-HHHHHHHhh
Confidence            345566666543      4678999999999999999988765211  122232 2333222 2234443 345555541


Q ss_pred             CCCCCCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhc
Q 041190          215 SADVNDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCK  257 (261)
Q Consensus       215 ~~~~~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~  257 (261)
                      .+               ..+++=++|+|++...+.+.++.|..
T Consensus        74 ~~---------------~~~~~KviIId~ad~l~~~aqNaLLK  101 (198)
T d2gnoa2          74 SP---------------ELYTRKYVIVHDCERMTQQAANAFLK  101 (198)
T ss_dssp             CC---------------SSSSSEEEEETTGGGBCHHHHHHTHH
T ss_pred             Cc---------------ccCCCEEEEEeCccccchhhhhHHHH
Confidence            11               12445577788887777666666543

>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=96.98  E-value=0.00027  Score=54.46  Aligned_cols=42  Identities=31%  Similarity=0.386  Sum_probs=32.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAA  212 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l  212 (261)
                      +||.|.|++|+||||+|+.+.++....     +        .+..++++.+....
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~gl~-----~--------iStGdLlR~~a~~~   45 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEALQWH-----L--------LDSGAIYRVLALAA   45 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCE-----E--------EEHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCc-----E--------ECHHHHHHHHHHHH
Confidence            599999999999999999998873321     1        26677888766543

>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=96.96  E-value=0.0036  Score=48.17  Aligned_cols=58  Identities=19%  Similarity=-0.003  Sum_probs=33.8

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCC-CCHHHHHHHHHHHhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSED-FDAVGVTKVILQAAA  213 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~i~~~i~~~l~  213 (261)
                      ...+.||.++|+.|+||||.+-++...... .+ ..+..+++.-. ....+.++...+.++
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLAa~~~~-~~-~kV~lit~Dt~R~gA~eQL~~~a~~l~   66 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLAKMFVD-EG-KSVVLAAADTFRAAAIEQLKIWGERVG   66 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHHH-TT-CCEEEEEECTTCHHHHHHHHHHHHHHT
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHH-CC-CceEEEeecccccchhHHHHHHhhhcC
Confidence            346789999999999999955555443221 12 23444544321 233445666666555

>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=96.93  E-value=0.001  Score=53.09  Aligned_cols=86  Identities=16%  Similarity=0.067  Sum_probs=57.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCC------CCCCCHHHHHHHH
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGS------ADVNDLNLLQLQL  228 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~------~~~~~~~~~~~~l  228 (261)
                      +.-+++-|+|++|+|||||+-+++....  ..=...+|+...+.++...     ++.++-.      ......++....+
T Consensus        52 ~~g~itei~G~~gsGKTtl~l~~~~~~q--~~g~~~vyidtE~~~~~~~-----a~~~Gvd~d~v~~~~~~~~E~~~~~i  124 (263)
T d1u94a1          52 PMGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEIC  124 (263)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHH--cCCCEEEEEccccccCHHH-----HHHhCCCHHHEEEecCCCHHHHHHHH
Confidence            4557999999999999999998887643  2223478999888877643     4555621      1234455555555


Q ss_pred             HHHhC-CCeEEEEEeCCCCC
Q 041190          229 ENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       229 ~~~l~-~kr~LiVlDdvw~~  247 (261)
                      ....+ ++.-|||+|.+-..
T Consensus       125 ~~l~~~~~~~liViDSi~al  144 (263)
T d1u94a1         125 DALARSGAVDVIVVDSVAAL  144 (263)
T ss_dssp             HHHHHHTCCSEEEEECGGGC
T ss_pred             HHHHhcCCCCEEEEECcccc
Confidence            55443 44568999999654

>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=96.91  E-value=0.00021  Score=52.90  Aligned_cols=23  Identities=22%  Similarity=0.488  Sum_probs=19.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhcc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ++| +.|++|+||||+++.+.+..
T Consensus         3 ~Iv-liG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           3 KAV-LVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             SEE-EECSTTSSHHHHHHHHHHHH
T ss_pred             cEE-EECCCCCCHHHHHHHHHHHh
Confidence            444 45999999999999998763

>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=96.90  E-value=0.00025  Score=53.72  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=21.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.+|.|.|++|+||||+|+.+++.
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999999886

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.88  E-value=0.0021  Score=51.30  Aligned_cols=86  Identities=20%  Similarity=0.120  Sum_probs=60.6

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCC------CCCCHHHHHHHH
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSA------DVNDLNLLQLQL  228 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~------~~~~~~~~~~~l  228 (261)
                      +.-++.-|+|++|+|||+||-++........  ...+|+.....++..     ++++++-..      .+.+.++....+
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~  127 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIM  127 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             cCceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHH
Confidence            4567999999999999999988877633222  347899988888874     566777221      344566665555


Q ss_pred             HHHhC-CCeEEEEEeCCCCC
Q 041190          229 ENQLK-NKKFLLVLDDMWSE  247 (261)
Q Consensus       229 ~~~l~-~kr~LiVlDdvw~~  247 (261)
                      ...++ ++.-|||+|-+-..
T Consensus       128 ~~l~~~~~~~liIiDSi~al  147 (268)
T d1xp8a1         128 ELLVRSGAIDVVVVDSVAAL  147 (268)
T ss_dssp             HHHHTTTCCSEEEEECTTTC
T ss_pred             HHHHhcCCCcEEEEeccccc
Confidence            55554 45679999999664

>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=96.86  E-value=0.00024  Score=52.43  Aligned_cols=22  Identities=41%  Similarity=0.548  Sum_probs=19.6

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |.+.||+|+||||+++.+....
T Consensus         3 I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6778999999999999998873

>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=96.85  E-value=0.00033  Score=54.08  Aligned_cols=26  Identities=31%  Similarity=0.257  Sum_probs=22.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++..+|.+.|++|+||||||+.+...
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~   47 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQ   47 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999998764

>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=96.82  E-value=0.0047  Score=47.28  Aligned_cols=56  Identities=13%  Similarity=-0.100  Sum_probs=31.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCC-CCCHHHHHHHHHHHhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSE-DFDAVGVTKVILQAAA  213 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~i~~~i~~~l~  213 (261)
                      +.+++.++|+.|+||||.+-++......+ . ..+..+++.. -....+.++...+.++
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~~-g-~kV~lit~Dt~R~gA~eQL~~~a~~l~   61 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQNL-G-KKVMFCAGDTFRAAGGTQLSEWGKRLS   61 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTT-T-CCEEEECCCCSSTTHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHC-C-CcEEEEEeccccccchhhHhhcccccC
Confidence            56899999999999999655555442211 1 2244554422 1233444444444444

>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=96.82  E-value=0.00034  Score=53.84  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=21.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +-+|+|.|.+|+||||+|+.+.+.
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            468999999999999999998775

>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=96.80  E-value=0.00025  Score=52.66  Aligned_cols=23  Identities=26%  Similarity=0.297  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .|.+.|++|+||||+|+.+.+..
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            46688999999999999998763

>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=96.79  E-value=0.0037  Score=47.99  Aligned_cols=27  Identities=30%  Similarity=0.176  Sum_probs=16.7

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+.||.++|++|+||||.+-++...
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~   35 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYF   35 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            346789999999999999955444433

>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=96.78  E-value=0.0004  Score=52.47  Aligned_cols=23  Identities=43%  Similarity=0.433  Sum_probs=20.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ++.+|+|+|..|+||||+|+.+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            56899999999999999999773

>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=96.76  E-value=0.00039  Score=51.91  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.|.|++|+||||+++.+.+.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~   24 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68899999999999999999765

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=96.75  E-value=0.0013  Score=53.91  Aligned_cols=71  Identities=21%  Similarity=0.327  Sum_probs=40.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhCCCeE
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAGSADVNDLNLLQLQLENQLKNKKF  237 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~kr~  237 (261)
                      .++-++|++|+|||.||+.+.....-+..|   +-+..+.-.+               ....+.+.....+.+..+ +.+
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~~~~---~~~~~~~~~~---------------~~~G~~e~~~~~~f~~a~-~~~  184 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGKDKY---ATVRFGEPLS---------------GYNTDFNVFVDDIARAML-QHR  184 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTTSCC---EEEEBSCSST---------------TCBCCHHHHHHHHHHHHH-HCS
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCCCCe---EEEEhhHhhh---------------cccchHHHHHHHHHHHHh-hcc
Confidence            456668999999999999998863222233   1233333221               112233333333333332 356


Q ss_pred             EEEEeCCCCC
Q 041190          238 LLVLDDMWSE  247 (261)
Q Consensus       238 LiVlDdvw~~  247 (261)
                      +|++|++...
T Consensus       185 ilf~DEid~~  194 (321)
T d1w44a_         185 VIVIDSLKNV  194 (321)
T ss_dssp             EEEEECCTTT
T ss_pred             EEEeehhhhh
Confidence            9999999875

>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=96.74  E-value=0.0031  Score=51.34  Aligned_cols=27  Identities=26%  Similarity=0.215  Sum_probs=23.9

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+-+|+|.|.+|+||||+|+.+..-
T Consensus        77 ~k~P~iIGIaG~sgSGKSTla~~L~~l  103 (308)
T d1sq5a_          77 QRIPYIISIAGSVAVGKSTTARVLQAL  103 (308)
T ss_dssp             CCCCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCCCcHHHHHHHHH
Confidence            456789999999999999999998764

>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=96.72  E-value=0.0017  Score=49.93  Aligned_cols=43  Identities=26%  Similarity=0.335  Sum_probs=32.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA  213 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~  213 (261)
                      -+|+|-|++|+||||+|+.+..+....     +        .+..++++.+.....
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~lg~~-----~--------istGdl~R~~a~~~~   46 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKDFGFT-----Y--------LDTGAMYRAATYMAL   46 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCCE-----E--------EEHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCc-----E--------ECHHHHHHHHHHHHH
Confidence            468899999999999999998873321     1        267788887766554

>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=96.70  E-value=0.0043  Score=47.51  Aligned_cols=25  Identities=28%  Similarity=0.228  Sum_probs=19.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.+|+.++|++|+||||.+-++...
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~   33 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALY   33 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4589999999999999965555443

>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=96.70  E-value=0.00039  Score=52.45  Aligned_cols=25  Identities=24%  Similarity=0.211  Sum_probs=21.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +..|.|.|++|+||||+|+.+.+..
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3457899999999999999997763

>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=96.66  E-value=0.0047  Score=49.34  Aligned_cols=101  Identities=20%  Similarity=0.244  Sum_probs=60.5

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCC-CHHHHHHHHHHHhc-C----
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDF-DAVGVTKVILQAAA-G----  214 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~i~~~i~~~l~-~----  214 (261)
                      +.++.|..-.     +-.-++|.|..|+|||+|+..+.++.. +.+=++.+++-+.+.. ...++++++.+.-. .    
T Consensus        57 raID~l~pig-----kGQr~~If~~~g~GKt~l~~~i~~~~~-~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~  130 (276)
T d2jdid3          57 KVVDLLAPYA-----KGGKIGLFGGAGVGKTVLIMELINNVA-KAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDA  130 (276)
T ss_dssp             HHHHHHSCEE-----TTCEEEEEECTTSSHHHHHHHHHHHHT-TTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSS
T ss_pred             eeeeeecccc-----CCCEEEeeCCCCCCHHHHHHHHHHHHH-hhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccc
Confidence            4556665422     223589999999999999999987622 1233456788888754 34566666665311 0    


Q ss_pred             ---------CCCCCCHH-----HHHHHHHHHh---CCCeEEEEEeCCCCC
Q 041190          215 ---------SADVNDLN-----LLQLQLENQL---KNKKFLLVLDDMWSE  247 (261)
Q Consensus       215 ---------~~~~~~~~-----~~~~~l~~~l---~~kr~LiVlDdvw~~  247 (261)
                               ..+.....     ...-.+-+++   +++.+|+++||+-.-
T Consensus       131 ~~~tvvv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~  180 (276)
T d2jdid3         131 TSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRF  180 (276)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHH
T ss_pred             cceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHH
Confidence                     01111111     1222345555   389999999999553

>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=96.56  E-value=0.00069  Score=51.03  Aligned_cols=24  Identities=29%  Similarity=0.437  Sum_probs=20.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++| |.|++|+||||+|+.+.+.
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~   26 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKN   26 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHH
Confidence            45666 6799999999999999765

>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=96.54  E-value=0.0007  Score=51.25  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=22.5

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.++|.|.|++|+||||+|+.+.+.
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999776

>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=96.52  E-value=0.00074  Score=51.05  Aligned_cols=28  Identities=29%  Similarity=0.181  Sum_probs=24.2

Q ss_pred             CCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          153 SGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       153 ~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.+..+|+|-|..|+||||+++.+.+.
T Consensus         5 ~~~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           5 EGTQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             TTCCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            3456779999999999999999998765

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.47  E-value=0.0008  Score=50.68  Aligned_cols=23  Identities=39%  Similarity=0.621  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|+|++|+|||||++.+.+.
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHh
Confidence            34789999999999999999775

>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=96.47  E-value=0.00066  Score=50.55  Aligned_cols=21  Identities=29%  Similarity=0.487  Sum_probs=19.0

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999999999765

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=96.42  E-value=0.0011  Score=50.18  Aligned_cols=25  Identities=24%  Similarity=0.305  Sum_probs=20.7

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|.|.|++|+||||+|+.+...
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHH
Confidence            3445567799999999999999876

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.39  E-value=0.00077  Score=50.33  Aligned_cols=23  Identities=26%  Similarity=0.239  Sum_probs=19.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      -|.|.|++|+||||+|+.+.+..
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36788999999999999998763

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.37  E-value=0.0013  Score=54.14  Aligned_cols=26  Identities=23%  Similarity=0.167  Sum_probs=22.9

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|+|+|++|+|||||...+...
T Consensus        52 ~~~~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          52 GNTLRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            46889999999999999999888654

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=96.37  E-value=0.00081  Score=50.28  Aligned_cols=23  Identities=30%  Similarity=0.414  Sum_probs=20.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .|.|.|++|+||||+|+.+.+..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36789999999999999998863

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.33  E-value=0.0061  Score=48.95  Aligned_cols=82  Identities=18%  Similarity=0.101  Sum_probs=45.5

Q ss_pred             CCCCceEEeEeecCCCChHHHHHHHhhccccccccce-eEEEeeCCCCCHHHHHHHHHHHhc--------CCCCCCCHHH
Q 041190          153 SGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSF-RACAYVSEDFDAVGVTKVILQAAA--------GSADVNDLNL  223 (261)
Q Consensus       153 ~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~i~~~i~~~l~--------~~~~~~~~~~  223 (261)
                      .+..+-+|+|.|..|+|||||+..+......+..+.. ++-+++..=+-...=...+.+...        +.+...|..-
T Consensus        23 ~~~~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~l  102 (286)
T d1odfa_          23 GNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKL  102 (286)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHH
T ss_pred             CCCCCEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHHH
Confidence            3455779999999999999999988765221212222 333444332211111222333321        2345677777


Q ss_pred             HHHHHHHHhCC
Q 041190          224 LQLQLENQLKN  234 (261)
Q Consensus       224 ~~~~l~~~l~~  234 (261)
                      +...+....++
T Consensus       103 l~~~l~~l~~~  113 (286)
T d1odfa_         103 LQEVLNTIFNN  113 (286)
T ss_dssp             HHHHHHHHTC-
T ss_pred             HHHHHHHHHhh
Confidence            77777666654

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.33  E-value=0.00079  Score=50.95  Aligned_cols=22  Identities=32%  Similarity=0.637  Sum_probs=19.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|+|++|+|||||++.+.+.
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            3679999999999999998765

>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=96.30  E-value=0.001  Score=49.83  Aligned_cols=23  Identities=22%  Similarity=0.444  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++|.|+|++|+|||||++.+.+.
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            47889999999999999999765

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.24  E-value=0.0017  Score=53.40  Aligned_cols=26  Identities=27%  Similarity=0.248  Sum_probs=22.8

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..+|+|.|++|+|||||...+...
T Consensus        49 ~~~~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          49 GRAIRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCceEEeeeCCCCCCHHHHHHHHHHH
Confidence            46789999999999999999888754

>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=96.21  E-value=0.0012  Score=49.19  Aligned_cols=21  Identities=33%  Similarity=0.406  Sum_probs=19.0

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            568999999999999999876

>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=96.08  E-value=0.0016  Score=48.78  Aligned_cols=23  Identities=13%  Similarity=0.434  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|+|++|+|||||++.+...
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            57889999999999999998865

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=96.04  E-value=0.0024  Score=51.38  Aligned_cols=97  Identities=13%  Similarity=0.050  Sum_probs=53.2

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEe-eCCCCCHHHHHHHHHHHhc-----C
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAY-VSEDFDAVGVTKVILQAAA-----G  214 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~-v~~~~~~~~i~~~i~~~l~-----~  214 (261)
                      ++++.|..-.     +-.-++|.|..|+|||+|+..+.+.... ++-++++.+. +.+..  ++ ..++.+...     .
T Consensus        32 r~ID~l~Pig-----rGQr~~I~g~~g~GKT~l~~~i~~~~~~-~~~~~v~~~~~iger~--~e-v~~~~~~~~~~vv~~  102 (289)
T d1xpua3          32 RVLDLASPIG-----RGQRGLIVAPPKAGKTMLLQNIAQSIAY-NHPDCVLMVLLIDERP--EE-VTEMQRLVKGEVVAS  102 (289)
T ss_dssp             HHHHHHSCCB-----TTCEEEEEECSSSSHHHHHHHHHHHHHH-HCTTSEEEEEEEEECH--HH-HHHHHHHCSSEEEEE
T ss_pred             eeeeeccccc-----CCCeeeEeCCCCCCHHHHHHHHHHHHhh-cCCCeEEEEEeeceeH--HH-HHhHHhhcceEEEec
Confidence            5788777632     3356899999999999999999876322 2334444433 33321  11 223333222     1


Q ss_pred             CCCCCCHH-----HHHHHHHHHh--CCCeEEEEEeCCCC
Q 041190          215 SADVNDLN-----LLQLQLENQL--KNKKFLLVLDDMWS  246 (261)
Q Consensus       215 ~~~~~~~~-----~~~~~l~~~l--~~kr~LiVlDdvw~  246 (261)
                      ..+.....     ...-.+-+++  .++.+|+++||+-.
T Consensus       103 t~d~~~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dsltr  141 (289)
T d1xpua3         103 TFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITR  141 (289)
T ss_dssp             ETTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEESCHHH
T ss_pred             cCCCchhHHHHHHHHHHHHHHHHHHhccCceeecCcHHH
Confidence            11111111     1122233333  58999999999844

>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=96.03  E-value=0.0085  Score=47.82  Aligned_cols=94  Identities=16%  Similarity=0.186  Sum_probs=51.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCH-HHHHHHHHHHhc-C-------CCCCCC-H----HHH
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDA-VGVTKVILQAAA-G-------SADVND-L----NLL  224 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~-~~i~~~i~~~l~-~-------~~~~~~-~----~~~  224 (261)
                      -++|.|..|+|||+|+......  ...+-...+++.+.+.... .++..++.+.=. .       ..+... .    ...
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            4788999999999999876544  2233446677777775432 233333322100 0       111111 1    122


Q ss_pred             HHHHHHHh--CCCeEEEEEeCCCCCChhhHHHh
Q 041190          225 QLQLENQL--KNKKFLLVLDDMWSENYDVWTNL  255 (261)
Q Consensus       225 ~~~l~~~l--~~kr~LiVlDdvw~~~~~~w~~l  255 (261)
                      .-.+-+++  .+++.|+++||+-.-. ..|..+
T Consensus       147 a~tiAEyfrd~G~~Vlll~Dsltr~A-~A~rEi  178 (276)
T d1fx0a3         147 GAALAEYFMYRERHTLIIYDDLSKQA-QAYRQM  178 (276)
T ss_dssp             HHHHHHHHHHTTCEEEEEEECHHHHH-HHHHHH
T ss_pred             HHHHHHHHHHcCCceeEEeeccHHHH-HHHHHH
Confidence            22333443  4899999999995542 344443

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.01  E-value=0.0016  Score=48.55  Aligned_cols=21  Identities=29%  Similarity=0.311  Sum_probs=18.2

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|.|++|+||||+|+.+.+.
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            446799999999999999775

>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=95.99  E-value=0.0069  Score=46.60  Aligned_cols=60  Identities=17%  Similarity=0.029  Sum_probs=38.0

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccc----cceeEEEeeCCCCCHHH
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKY----FSFRACAYVSEDFDAVG  203 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~  203 (261)
                      ..|-++|..    +-+.-+++-|+|.+|+|||||+.++.........    -...+|+.....++...
T Consensus        21 ~~LD~ll~G----Gi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   84 (251)
T d1szpa2          21 KNLDTLLGG----GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVR   84 (251)
T ss_dssp             HHHHHHHTS----SEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGG
T ss_pred             HHHHhhhCC----CCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHH
Confidence            444455532    2345679999999999999999887654322221    23467777666555433

>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=95.98  E-value=0.0017  Score=50.62  Aligned_cols=23  Identities=26%  Similarity=0.379  Sum_probs=20.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCcchhhHhccC
Confidence            35899999999999999998865

>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=95.97  E-value=0.0015  Score=49.82  Aligned_cols=23  Identities=35%  Similarity=0.537  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcc
Confidence            58999999999999999999763

>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=95.96  E-value=0.0019  Score=50.76  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||++.++.
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            4899999999999999999965

>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=95.95  E-value=0.0019  Score=50.71  Aligned_cols=22  Identities=32%  Similarity=0.448  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.|+.|+|||||++.++-
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            5899999999999999999965

>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=95.95  E-value=0.004  Score=48.27  Aligned_cols=85  Identities=15%  Similarity=0.071  Sum_probs=51.5

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhcC--------C--------CCC
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAAG--------S--------ADV  218 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~~--------~--------~~~  218 (261)
                      +.-.++-|+|.+|+|||+++.++..+  ...+.....|++...+  ...+.+.. ..++.        .        ...
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~   98 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEES--RAQLLRNA-YSWGMDFEEMERQNLLKIVCAYPES   98 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSSC--HHHHHHHH-HTTSCCHHHHHHTTSEEECCCCGGG
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccCC--HHHHHHHH-HHcCCChHHHhhcCceEEEEeecch
Confidence            45679999999999999999999877  4445556777776542  33333222 21110        0        012


Q ss_pred             CCHHHHHHHHHHHh-CCCeEEEEEeCC
Q 041190          219 NDLNLLQLQLENQL-KNKKFLLVLDDM  244 (261)
Q Consensus       219 ~~~~~~~~~l~~~l-~~kr~LiVlDdv  244 (261)
                      .........+...+ ..+.-++|+|.+
T Consensus        99 ~~~~~~~~~i~~~i~~~~~~~vviDs~  125 (242)
T d1tf7a2          99 AGLEDHLQIIKSEINDFKPARIAIDSL  125 (242)
T ss_dssp             SCHHHHHHHHHHHHHTTCCSEEEEECH
T ss_pred             hhHHHHHHHHHHHHHhcCCceeeeecc
Confidence            33445555555544 456678888875

>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=95.92  E-value=0.002  Score=50.29  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=20.4

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|.|+.|+|||||.+.+..
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999854

>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=95.91  E-value=0.0021  Score=51.02  Aligned_cols=23  Identities=35%  Similarity=0.557  Sum_probs=19.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|+|+|-||+||||+|-.+...
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            68999999999999999777554

>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=95.86  E-value=0.0021  Score=50.86  Aligned_cols=23  Identities=30%  Similarity=0.512  Sum_probs=20.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999964

>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=95.84  E-value=0.0022  Score=49.74  Aligned_cols=22  Identities=32%  Similarity=0.371  Sum_probs=20.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ||.|.|+.|+|||||.+.+.+.
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Confidence            7899999999999999998754

>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=95.82  E-value=0.0023  Score=50.11  Aligned_cols=22  Identities=27%  Similarity=0.460  Sum_probs=20.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|+|+.|+|||||.+.+..
T Consensus        33 e~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHHc
Confidence            5899999999999999999854

>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=95.79  E-value=0.0023  Score=50.26  Aligned_cols=23  Identities=43%  Similarity=0.580  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|+|+.|+|||||++.+..-
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            57999999999999999999653

>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=95.77  E-value=0.0033  Score=47.20  Aligned_cols=27  Identities=22%  Similarity=0.480  Sum_probs=23.0

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+++.|+|+|.+|+|||||.+.+.+.
T Consensus        20 ~~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          20 EGGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            345678999999999999999999853

>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=95.75  E-value=0.0024  Score=50.68  Aligned_cols=23  Identities=35%  Similarity=0.408  Sum_probs=20.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||++.+..
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            35899999999999999999965

>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=95.73  E-value=0.0025  Score=50.40  Aligned_cols=23  Identities=39%  Similarity=0.505  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -.+++|+|+.|+|||||++.+..
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            35899999999999999999865

>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=95.70  E-value=0.0028  Score=51.00  Aligned_cols=24  Identities=38%  Similarity=0.592  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            358999999999999999999764

>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=95.70  E-value=0.0028  Score=49.65  Aligned_cols=22  Identities=23%  Similarity=0.388  Sum_probs=19.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.|+.|+|||||.+.+..
T Consensus        25 e~~~liGpnGaGKSTll~~i~G   46 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCChHHHHHHHHHc
Confidence            3788999999999999999965

>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=95.70  E-value=0.0029  Score=48.42  Aligned_cols=23  Identities=22%  Similarity=0.444  Sum_probs=20.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|+|++|+|||||.+.+...
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            57889999999999999999875

>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=95.69  E-value=0.0033  Score=49.43  Aligned_cols=23  Identities=35%  Similarity=0.459  Sum_probs=20.6

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -..++|+|+.|+|||||++.+..
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            46899999999999999999964

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.66  E-value=0.0017  Score=52.33  Aligned_cols=25  Identities=24%  Similarity=0.372  Sum_probs=18.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..+|+|.|.+|+||||+++.+.+-
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i   27 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQI   27 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHH
Confidence            3469999999999999999977553

>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=95.64  E-value=0.0023  Score=52.63  Aligned_cols=46  Identities=20%  Similarity=0.242  Sum_probs=32.0

Q ss_pred             CCCCccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHh
Q 041190          127 VDEEEVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       127 ~~~~~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ++-..++|.+.-+..|.-.....      ..+-+-++|.+|+||||||+.+.
T Consensus         4 ~~f~~I~Gq~~~kral~laa~~~------~~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAVDP------GIGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCG------GGCCEEEECCGGGCTTHHHHHHH
T ss_pred             CChhhccCcHHHHHHHHHHHhcc------CCCeEEEECCCCccHHHHHHHHH
Confidence            34467899987776544333211      12357999999999999999874

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.63  E-value=0.0037  Score=49.26  Aligned_cols=45  Identities=20%  Similarity=0.164  Sum_probs=33.8

Q ss_pred             cccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          132 VYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       132 ~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +||.......+.+.+..-.    ..-..|.|.|..|+|||++|+.++..
T Consensus         2 ~v~~S~~~~~~~~~~~~~a----~~~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKIS----CAECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHT----TCCSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEecCHHHHHHHHHHHHHh----CCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            6777777777777776532    12234789999999999999999864

>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=95.61  E-value=0.0057  Score=52.32  Aligned_cols=51  Identities=22%  Similarity=0.268  Sum_probs=35.5

Q ss_pred             CccccccchHHHHHHHhhC--------CCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG--------DDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~--------~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.++.+..|--.+..        ...+..-..+-|-++||+|+|||.||+.+..-
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            3578888777776665521        11111223557899999999999999999875

>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=95.56  E-value=0.0032  Score=45.19  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=19.0

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |.++|.+|+|||||.+.+..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            5699999999999999987653

>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=95.48  E-value=0.0037  Score=45.20  Aligned_cols=22  Identities=36%  Similarity=0.439  Sum_probs=19.4

Q ss_pred             EeEeecCCCChHHHHHHHhhcc
Q 041190          160 IPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      |.|+|.+|+|||||.+.+.++.
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6799999999999999887663

>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=95.47  E-value=0.024  Score=43.68  Aligned_cols=51  Identities=16%  Similarity=0.046  Sum_probs=34.6

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhccccc----cccceeEEEeeCCCCCHHHH
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDAGVK----KYFSFRACAYVSEDFDAVGV  204 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~i  204 (261)
                      -+.-+++-|+|++|+||||++.++..+....    ......+|+......+...+
T Consensus        33 lp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          33 IETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             ccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            3456799999999999999998886552211    12234667777766665443

>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=95.45  E-value=0.0058  Score=50.89  Aligned_cols=28  Identities=29%  Similarity=0.158  Sum_probs=24.3

Q ss_pred             CCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          154 GPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       154 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .++-+.+.++|++|+|||++|+.+.+..
T Consensus       151 ~~~~~~~~~~g~~~~gk~~~~~~~~~~~  178 (362)
T d1svma_         151 IPKKRYWLFKGPIDSGKTTLAAALLELC  178 (362)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCcCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3466799999999999999999998873

>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=95.41  E-value=0.0039  Score=47.61  Aligned_cols=19  Identities=37%  Similarity=0.571  Sum_probs=17.7

Q ss_pred             EEeEeecCCCChHHHHHHH
Q 041190          159 VIPITGMGGLGKTTLAQLV  177 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v  177 (261)
                      +|+|+|..|+||||+++.+
T Consensus         5 iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHH
Confidence            8999999999999999865

>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=95.41  E-value=0.0032  Score=48.78  Aligned_cols=24  Identities=25%  Similarity=0.300  Sum_probs=21.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+.|+|-|+-|+||||+++.+.+.
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            478999999999999999998775

>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=95.40  E-value=0.0027  Score=49.40  Aligned_cols=22  Identities=32%  Similarity=0.428  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.|+.|+|||||.+.+..
T Consensus        27 e~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            4899999999999999999965

>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=95.35  E-value=0.008  Score=47.91  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=19.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhh
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ..++|.+.|-||+||||+|-.+..
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~   30 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAI   30 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHHH
Confidence            467899999999999997766644

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=95.35  E-value=0.0042  Score=48.71  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.|+.|+|||||.+.+..-
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999999653

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.33  E-value=0.0051  Score=47.68  Aligned_cols=24  Identities=25%  Similarity=0.350  Sum_probs=21.9

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ++.|.|-|+-|+||||+++.+.+.
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH
Confidence            578999999999999999999875

>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=95.31  E-value=0.0047  Score=49.51  Aligned_cols=23  Identities=35%  Similarity=0.534  Sum_probs=19.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+.|+|+|-||+||||+|-.+..
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~   24 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHH
Confidence            36788999999999998877644

>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=95.30  E-value=0.0044  Score=48.51  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=21.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~   51 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTL   51 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999653

>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=95.29  E-value=0.0045  Score=47.08  Aligned_cols=20  Identities=45%  Similarity=0.599  Sum_probs=18.3

Q ss_pred             eEEeEeecCCCChHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLV  177 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v  177 (261)
                      -+|+|+|..|+||||+|+.+
T Consensus         3 ~iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            58999999999999999866

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.26  E-value=0.03  Score=43.03  Aligned_cols=60  Identities=17%  Similarity=0.026  Sum_probs=39.4

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcccc----ccccceeEEEeeCCCCCHH
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGV----KKYFSFRACAYVSEDFDAV  202 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~----~~~f~~~~wv~v~~~~~~~  202 (261)
                      ...|-++|..    +-+.-+++-|+|.+|+|||++|.++......    ...+....|+.....+...
T Consensus        23 i~~LD~~lgG----Gip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          23 SQEFDKLLGG----GIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             CHHHHHHTTS----SBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CHHHHHhhcC----CCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            3445555533    3456789999999999999999988754211    2234456677766665543

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.23  E-value=0.0059  Score=46.66  Aligned_cols=23  Identities=22%  Similarity=0.423  Sum_probs=20.9

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..|+|-|+.|+||||+++.+.+.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~   26 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEA   26 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57889999999999999999876

>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=95.21  E-value=0.0049  Score=48.76  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=20.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+++|.|+.|+|||||++.+..-
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHCC
Confidence            48999999999999999999764

>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=95.18  E-value=0.0065  Score=44.62  Aligned_cols=25  Identities=28%  Similarity=0.399  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ....|+|+|.+|+|||||.+.+.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            4678999999999999999999864

>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=95.14  E-value=0.0066  Score=44.77  Aligned_cols=25  Identities=24%  Similarity=0.301  Sum_probs=22.1

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+.|+++|.+|+|||||.+.+...
T Consensus         4 ~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           4 YSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999999864

>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=95.12  E-value=0.007  Score=46.74  Aligned_cols=25  Identities=40%  Similarity=0.591  Sum_probs=22.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++|..|.|.-|+|||||.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5789999999999999999999875

>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=95.04  E-value=0.0032  Score=49.35  Aligned_cols=22  Identities=32%  Similarity=0.484  Sum_probs=20.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.|+.|+|||||.+.+..
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            5899999999999999999964

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=95.03  E-value=0.0088  Score=49.78  Aligned_cols=51  Identities=29%  Similarity=0.301  Sum_probs=34.5

Q ss_pred             CccccccchHHHHHHHhhC-------------CC-----------CCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          130 EEVYGREKDKEVIVGLLLG-------------DD-----------LNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       130 ~~~~gr~~~~~~l~~~L~~-------------~~-----------~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++|.++.++.+...+..             ..           .+.+.....+-.+|++|+|||.||+.+...
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhh
Confidence            4588998888877655420             00           001224556788899999999999988654

>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=95.00  E-value=0.0038  Score=49.44  Aligned_cols=23  Identities=35%  Similarity=0.496  Sum_probs=20.2

Q ss_pred             ceEEeEeecCCCChHHHHHHHhh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -..++|+|+.|+|||||++.+..
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh
Confidence            35899999999999999998854

>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=95.00  E-value=0.0095  Score=47.17  Aligned_cols=35  Identities=29%  Similarity=0.408  Sum_probs=25.4

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhh
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ...+.+.+..      +..++|.+.|-||+||||++-.+..
T Consensus         8 ~~~~~~~~~~------~~~~iii~sGKGGVGKTT~a~nLA~   42 (279)
T d1ihua2           8 LSALVDDIAR------NEHGLIMLMGKGGVGKTTMAAAIAV   42 (279)
T ss_dssp             HHHHHHHHHT------TSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhhc------CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4455565643      3568999999999999997655533

>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=94.96  E-value=0.012  Score=42.96  Aligned_cols=23  Identities=30%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||...+...
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            44679999999999999988654

>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=94.96  E-value=0.0054  Score=47.74  Aligned_cols=22  Identities=27%  Similarity=0.481  Sum_probs=20.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++|.|+.|+|||||.+.+..
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            4899999999999999998865

>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=94.95  E-value=0.0075  Score=45.26  Aligned_cols=27  Identities=19%  Similarity=0.102  Sum_probs=22.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +.-.++-|.|++|+|||+|+.++..+.
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            345799999999999999998887653

>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=94.95  E-value=0.0069  Score=44.30  Aligned_cols=22  Identities=27%  Similarity=0.419  Sum_probs=19.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.|+|.+|+|||||.+.+...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999998753

>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=94.95  E-value=0.013  Score=44.18  Aligned_cols=22  Identities=36%  Similarity=0.585  Sum_probs=19.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|+|-|.-|+||||+++.+.+.
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~   23 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGA   23 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999988765

>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=94.93  E-value=0.0065  Score=44.10  Aligned_cols=21  Identities=24%  Similarity=0.419  Sum_probs=18.6

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|.+|+|||||.+.+.+.
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            569999999999999998664

>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=94.90  E-value=0.0068  Score=44.53  Aligned_cols=21  Identities=29%  Similarity=0.351  Sum_probs=18.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|++.+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999987765

>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=94.89  E-value=0.014  Score=45.12  Aligned_cols=35  Identities=23%  Similarity=0.422  Sum_probs=28.4

Q ss_pred             chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          137 KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       137 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..++.|.++|..         ++..++|.+|+|||||.+.+..+
T Consensus        84 ~g~~~L~~~l~~---------kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          84 MGIEELKEYLKG---------KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             TTHHHHHHHHSS---------SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             hhHhhHHHHhcC---------CeEEEECCCCCCHHHHHHhhcch
Confidence            457888888843         46788999999999999999765

>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=94.89  E-value=0.0085  Score=43.50  Aligned_cols=21  Identities=24%  Similarity=0.499  Sum_probs=18.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||++.+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999877654

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.82  E-value=0.029  Score=44.78  Aligned_cols=100  Identities=16%  Similarity=0.076  Sum_probs=53.0

Q ss_pred             HHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccc-----cccc-eeEEEeeCCCCC-HHHHHHHHHHHhc
Q 041190          141 VIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVK-----KYFS-FRACAYVSEDFD-AVGVTKVILQAAA  213 (261)
Q Consensus       141 ~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-----~~f~-~~~wv~v~~~~~-~~~i~~~i~~~l~  213 (261)
                      +.++.|..-.     +-.-++|.|.+|+|||+|+..+.......     ..-. ..+++-+.+... ..++...+...-.
T Consensus        57 raID~l~pig-----~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~  131 (285)
T d2jdia3          57 KAVDSLVPIG-----RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADA  131 (285)
T ss_dssp             HHHHHHSCCB-----TTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTC
T ss_pred             eEEecccCcc-----CCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhccccc
Confidence            4555555422     22457889999999999988776543211     1111 235566666443 2344444333211


Q ss_pred             -C-------CCCCCCHH---------HHHHHHHHHhCCCeEEEEEeCCCCC
Q 041190          214 -G-------SADVNDLN---------LLQLQLENQLKNKKFLLVLDDMWSE  247 (261)
Q Consensus       214 -~-------~~~~~~~~---------~~~~~l~~~l~~kr~LiVlDdvw~~  247 (261)
                       .       ..+.....         .+.+.+++  ++|++|+++||+-.-
T Consensus       132 ~~~tvvv~~ts~~~~~~r~~~~~~a~tiAEyfrd--~G~~VLll~Dsltr~  180 (285)
T d2jdia3         132 MKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRD--NGKHALIIYDDLSKQ  180 (285)
T ss_dssp             GGGEEEEEECTTSCHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEETHHHH
T ss_pred             ccceEEEEECCCCCHHHHHHHHHHHHHHHHHHHH--cCCcEEEEEcChHHH
Confidence             1       11111111         12333443  699999999998553

>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=94.81  E-value=0.0076  Score=43.72  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=18.8

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988765

>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=94.74  E-value=0.0081  Score=43.88  Aligned_cols=21  Identities=29%  Similarity=0.626  Sum_probs=18.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568999999999999887654

>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=94.70  E-value=0.0083  Score=43.84  Aligned_cols=22  Identities=32%  Similarity=0.360  Sum_probs=18.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999987654

>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=94.69  E-value=0.0088  Score=43.47  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=18.7

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988765

>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=94.68  E-value=0.0085  Score=43.60  Aligned_cols=22  Identities=27%  Similarity=0.295  Sum_probs=18.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||+|++.+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999887654

>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=94.67  E-value=0.0089  Score=43.71  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=19.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999988764

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=94.66  E-value=0.0093  Score=46.20  Aligned_cols=23  Identities=26%  Similarity=0.501  Sum_probs=20.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+|+|+|..|+||||+|+.+.+.
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            68999999999999999988654

>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=94.65  E-value=0.0088  Score=42.70  Aligned_cols=21  Identities=38%  Similarity=0.596  Sum_probs=18.8

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||...+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999998764

>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=94.65  E-value=0.009  Score=44.95  Aligned_cols=23  Identities=39%  Similarity=0.469  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            36899999999999999999765

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.63  E-value=0.029  Score=42.69  Aligned_cols=24  Identities=29%  Similarity=0.486  Sum_probs=21.5

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -..|+|-|+-|+||||+++.+.+.
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            367999999999999999999876

>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=94.61  E-value=0.0091  Score=43.99  Aligned_cols=22  Identities=27%  Similarity=0.366  Sum_probs=19.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.++|.+|+|||||.+.+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999864

>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=94.59  E-value=0.0085  Score=44.44  Aligned_cols=21  Identities=29%  Similarity=0.376  Sum_probs=18.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|.+|+|||||++.+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999988754

>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=94.56  E-value=0.0095  Score=43.34  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=19.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||+|.+.+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999888765

>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=94.55  E-value=0.0099  Score=43.04  Aligned_cols=21  Identities=29%  Similarity=0.419  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|++.+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999988654

>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=94.50  E-value=0.0067  Score=44.79  Aligned_cols=20  Identities=20%  Similarity=0.371  Sum_probs=18.6

Q ss_pred             EeEeecCCCChHHHHHHHhh
Q 041190          160 IPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~  179 (261)
                      |+|+|.+|+|||||.+.+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999864

>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=94.49  E-value=0.01  Score=43.35  Aligned_cols=21  Identities=29%  Similarity=0.477  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999988654

>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=94.48  E-value=0.009  Score=43.74  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+...
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4679999999999999998664

>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=94.47  E-value=0.01  Score=43.20  Aligned_cols=21  Identities=24%  Similarity=0.449  Sum_probs=18.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999988764

>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=94.45  E-value=0.01  Score=43.62  Aligned_cols=22  Identities=23%  Similarity=0.413  Sum_probs=19.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||++.+.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999987654

>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=94.44  E-value=0.01  Score=43.28  Aligned_cols=21  Identities=19%  Similarity=0.382  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|++.+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999888754

>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=94.42  E-value=0.011  Score=43.36  Aligned_cols=21  Identities=43%  Similarity=0.623  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            679999999999999987654

>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=94.42  E-value=0.011  Score=43.11  Aligned_cols=21  Identities=29%  Similarity=0.463  Sum_probs=18.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|++.+.++
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987654

>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=94.40  E-value=0.011  Score=43.26  Aligned_cols=21  Identities=24%  Similarity=0.431  Sum_probs=18.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||++.+..+
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999987643

>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=94.37  E-value=0.011  Score=43.27  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=18.9

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||+|.+.+.++
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4679999999999999887654

>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=94.37  E-value=0.012  Score=42.84  Aligned_cols=21  Identities=29%  Similarity=0.694  Sum_probs=18.7

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+.+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678899999999999988765

>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=94.36  E-value=0.012  Score=43.07  Aligned_cols=22  Identities=27%  Similarity=0.539  Sum_probs=18.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||+|.+.+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3788999999999999887654

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.33  E-value=0.012  Score=44.44  Aligned_cols=22  Identities=23%  Similarity=0.315  Sum_probs=19.6

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||||.+.+...
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999988764

>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=94.32  E-value=0.012  Score=42.75  Aligned_cols=23  Identities=26%  Similarity=0.404  Sum_probs=19.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.|+|.+|+|||+|.+.+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            34678999999999999987654

>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=94.30  E-value=0.012  Score=42.98  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+...++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568899999999999988765

>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=94.29  E-value=0.012  Score=44.98  Aligned_cols=24  Identities=33%  Similarity=0.472  Sum_probs=20.1

Q ss_pred             ceEEeEe-ecCCCChHHHHHHHhhc
Q 041190          157 FSVIPIT-GMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~-G~~GiGKTtLa~~v~~~  180 (261)
                      .++|+|+ |-||+||||+|..+...
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~~   25 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGVA   25 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCChHHHHHHHHHHH
Confidence            3788888 77999999999887655

>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=94.27  E-value=0.012  Score=44.02  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=19.1

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||||.+.+.++
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            3779999999999999988764

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.27  E-value=0.013  Score=44.48  Aligned_cols=23  Identities=39%  Similarity=0.566  Sum_probs=20.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.|.|-|+.|+||||+++.+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~   25 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVET   25 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            46888999999999999998775

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=94.24  E-value=0.018  Score=41.97  Aligned_cols=23  Identities=26%  Similarity=0.316  Sum_probs=19.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||...+..+
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34679999999999999987654

>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=94.17  E-value=0.01  Score=43.94  Aligned_cols=22  Identities=27%  Similarity=0.456  Sum_probs=19.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|+|+|.+++|||||.+.+.+.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998653

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=94.12  E-value=0.028  Score=40.79  Aligned_cols=28  Identities=29%  Similarity=0.347  Sum_probs=23.8

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcccc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGV  183 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  183 (261)
                      .-.+|.+.|.=|+||||++|.+.+...+
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhccc
Confidence            3468999999999999999999887543

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.03  E-value=0.021  Score=43.69  Aligned_cols=38  Identities=24%  Similarity=0.228  Sum_probs=27.6

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...|-++|..    +-+.-.++-|+|.+|+|||+++.++..+
T Consensus        20 ~~~LD~ll~G----Gl~~G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          20 SSELDSVLGG----GLESQSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             CHHHHHHTTS----SEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CHHHHHhcCC----CccCCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            3445555532    2334579999999999999999999755

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.99  E-value=0.015  Score=42.28  Aligned_cols=21  Identities=29%  Similarity=0.594  Sum_probs=18.3

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+.+..+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678999999999999987654

>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=93.96  E-value=0.015  Score=42.08  Aligned_cols=21  Identities=24%  Similarity=0.464  Sum_probs=17.8

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+...
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            567899999999999987654

>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=93.94  E-value=0.015  Score=42.98  Aligned_cols=21  Identities=38%  Similarity=0.558  Sum_probs=18.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||++.+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988754

>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=93.93  E-value=0.015  Score=42.32  Aligned_cols=22  Identities=27%  Similarity=0.368  Sum_probs=19.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||+|++...+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987654

>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=93.92  E-value=0.016  Score=41.54  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999988643

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.92  E-value=0.016  Score=42.52  Aligned_cols=21  Identities=38%  Similarity=0.464  Sum_probs=18.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.|+|.+|+|||+|...+.++
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999887655

>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=93.86  E-value=0.016  Score=42.16  Aligned_cols=21  Identities=14%  Similarity=0.400  Sum_probs=17.9

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+.+.++
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999987654

>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=0.017  Score=42.81  Aligned_cols=22  Identities=36%  Similarity=0.419  Sum_probs=19.0

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+|||+|.+...++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3788999999999999887654

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=93.79  E-value=0.044  Score=45.23  Aligned_cols=53  Identities=19%  Similarity=0.092  Sum_probs=31.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhccc-cccccceeEEEeeCCCCCHHHHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLVFNDAG-VKKYFSFRACAYVSEDFDAVGVTKVILQ  210 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~~~-~~~~f~~~~wv~v~~~~~~~~i~~~i~~  210 (261)
                      ++..|.|++|+||||++..+..... ....-..++.+..+.......+...+..
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~  217 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  217 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             CeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHH
Confidence            5889999999999998866544311 1111223566666554445555444433

>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=93.74  E-value=0.021  Score=42.11  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=19.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      --|.|+|.+|+|||+|.+.+.++
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            34789999999999999887654

>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=93.73  E-value=0.017  Score=42.34  Aligned_cols=21  Identities=38%  Similarity=0.558  Sum_probs=18.4

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999987654

>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=93.71  E-value=0.018  Score=42.49  Aligned_cols=22  Identities=32%  Similarity=0.540  Sum_probs=19.2

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|+|+|.+|+|||||.+.+.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3789999999999999988754

>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=93.69  E-value=0.018  Score=42.12  Aligned_cols=22  Identities=27%  Similarity=0.534  Sum_probs=18.5

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.++
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3779999999999999877553

>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=93.69  E-value=0.014  Score=43.08  Aligned_cols=24  Identities=33%  Similarity=0.408  Sum_probs=19.6

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++ |.++|.+|+|||||.+.+...
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            454 559999999999999998644

>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=93.65  E-value=0.014  Score=42.66  Aligned_cols=25  Identities=16%  Similarity=0.183  Sum_probs=21.4

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..-|+|+|.+++|||||.+.+...
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999988654

>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=93.63  E-value=0.019  Score=41.85  Aligned_cols=24  Identities=29%  Similarity=0.578  Sum_probs=19.8

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +.-|.++|.+|+|||||.+.+.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            345779999999999999987654

>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=93.62  E-value=0.013  Score=42.88  Aligned_cols=21  Identities=33%  Similarity=0.574  Sum_probs=17.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+...++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999987654

>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=93.62  E-value=0.015  Score=42.43  Aligned_cols=24  Identities=25%  Similarity=0.286  Sum_probs=20.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++ |.++|.+|+|||||.+.+.+.
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            456 558999999999999999765

>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=93.52  E-value=0.02  Score=41.73  Aligned_cols=21  Identities=33%  Similarity=0.699  Sum_probs=18.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+.+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            567899999999999988764

>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=93.40  E-value=0.022  Score=41.96  Aligned_cols=21  Identities=33%  Similarity=0.458  Sum_probs=18.2

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|++.+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999888664

>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=93.37  E-value=0.021  Score=41.72  Aligned_cols=22  Identities=32%  Similarity=0.508  Sum_probs=18.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      --|.++|.+|+|||+|++.+..
T Consensus         4 ~Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           4 YRVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3467899999999999998754

>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=93.27  E-value=0.024  Score=43.30  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=19.5

Q ss_pred             eEEeEe-ecCCCChHHHHHHHhhc
Q 041190          158 SVIPIT-GMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~-G~~GiGKTtLa~~v~~~  180 (261)
                      ++|+|+ +-||+||||+|..+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~   26 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVA   26 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHH
Confidence            689999 56999999999888654

>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=93.18  E-value=0.022  Score=42.29  Aligned_cols=19  Identities=32%  Similarity=0.478  Sum_probs=17.0

Q ss_pred             EEeEeecCCCChHHHHHHH
Q 041190          159 VIPITGMGGLGKTTLAQLV  177 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v  177 (261)
                      -|.++|.+|+|||||.+..
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3678999999999999887

>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=93.14  E-value=0.024  Score=41.80  Aligned_cols=21  Identities=24%  Similarity=0.317  Sum_probs=18.0

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|-+|+|||+|.+....+
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            578999999999999887544

>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=93.11  E-value=0.026  Score=42.91  Aligned_cols=24  Identities=25%  Similarity=0.318  Sum_probs=20.1

Q ss_pred             CCceEEeEeecCCCChHHHHHHHh
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      +.-.++-|+|.+|+|||+||.++.
T Consensus        24 ~~G~~~~I~G~~G~GKT~la~~~~   47 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLFSIQFL   47 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHH
Confidence            455789999999999999997653

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=92.98  E-value=0.052  Score=42.53  Aligned_cols=40  Identities=20%  Similarity=0.339  Sum_probs=27.6

Q ss_pred             hHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhcc
Q 041190          138 DKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       138 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .+.++...+...    +...-.|.++|.+|+|||||.+.++...
T Consensus        17 ~l~e~~~~l~~~----~~~~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          17 KLLELLGNLKQE----DVNSLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             HHHHHHHHHHHT----TCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHHHhhc----CCCCcEEEEECCCCCcHHHHHHHHhCCC
Confidence            334445555442    2234467799999999999999998753

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.94  E-value=0.028  Score=41.72  Aligned_cols=21  Identities=29%  Similarity=0.362  Sum_probs=17.6

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+.+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999998877654

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.87  E-value=0.028  Score=41.31  Aligned_cols=22  Identities=18%  Similarity=0.300  Sum_probs=18.7

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.++|.+|+|||||.+.+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4688999999999999977654

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.70  E-value=0.031  Score=41.31  Aligned_cols=21  Identities=24%  Similarity=0.294  Sum_probs=18.1

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||+|.+....+
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            578999999999999887554

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=92.63  E-value=0.032  Score=45.47  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=19.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -|.|+|.+|+||||+++.++..
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            4788999999999999999875

>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=92.51  E-value=0.059  Score=40.55  Aligned_cols=37  Identities=16%  Similarity=0.219  Sum_probs=29.0

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ...+..+|..     .++-..+.++|++++|||++|..+.+-
T Consensus        40 l~~l~~~l~~-----~PKkn~i~~~GP~~TGKS~f~~sl~~~   76 (205)
T d1tuea_          40 LGALKSFLKG-----TPKKNCLVFCGPANTGKSYFGMSFIHF   76 (205)
T ss_dssp             HHHHHHHHHT-----CTTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHcC-----CCCceEEEEECCCCccHHHHHHHHHHH
Confidence            5666666643     456789999999999999999877654

>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=92.45  E-value=0.041  Score=41.27  Aligned_cols=23  Identities=22%  Similarity=0.278  Sum_probs=19.0

Q ss_pred             eEEeEeecC-CCChHHHHHHHhhc
Q 041190          158 SVIPITGMG-GLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~-GiGKTtLa~~v~~~  180 (261)
                      +-+.|.|-+ |+||||++-.+...
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            468899997 99999988777654

>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=92.44  E-value=0.019  Score=41.98  Aligned_cols=21  Identities=29%  Similarity=0.408  Sum_probs=8.2

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |.++|.+|+|||||.+.+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999866653

>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=92.25  E-value=0.038  Score=43.29  Aligned_cols=23  Identities=30%  Similarity=0.400  Sum_probs=19.4

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .+..|+|.+|+|||||+-.+.-.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            46779999999999999877654

>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=92.07  E-value=0.082  Score=41.90  Aligned_cols=26  Identities=23%  Similarity=0.314  Sum_probs=23.7

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhhc
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.||+|+|+.++|||||+..++..
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            36899999999999999999999875

>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=92.03  E-value=0.013  Score=42.07  Aligned_cols=21  Identities=33%  Similarity=0.570  Sum_probs=18.9

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |+++|.+|+|||||.+.+...
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

>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=91.87  E-value=0.13  Score=40.26  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=19.7

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .++.|.|.+|+|||+++.++..+
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~   58 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQ   58 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHh
Confidence            57889999999999999888654

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.67  E-value=0.045  Score=41.77  Aligned_cols=23  Identities=22%  Similarity=0.257  Sum_probs=19.0

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-|.++|.+|+|||||.+.....
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            45689999999999999887543

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.60  E-value=0.049  Score=43.23  Aligned_cols=25  Identities=24%  Similarity=0.214  Sum_probs=21.8

Q ss_pred             CCceEEeEeecCCCChHHHHHHHhh
Q 041190          155 PGFSVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       155 ~~~~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      .+++-|+|+|-.|.|||||+-.+..
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHH
Confidence            3678899999999999999988853

>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=91.49  E-value=0.054  Score=39.94  Aligned_cols=23  Identities=30%  Similarity=0.356  Sum_probs=19.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-+.|.|.+|+||||+|-.+...
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45788999999999999887654

>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=91.45  E-value=0.059  Score=39.75  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=19.1

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-+.|.|.+|+||||+|-.....
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45788999999999999887653

>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=91.18  E-value=0.13  Score=40.52  Aligned_cols=37  Identities=22%  Similarity=0.191  Sum_probs=27.5

Q ss_pred             HHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          140 EVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       140 ~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      ..+..+|..    ..+.-..+.++|+|+.|||+++..+.+-
T Consensus        91 ~~l~~~L~~----~~~k~n~~~l~G~~~tGKS~f~~~i~~~  127 (267)
T d1u0ja_          91 SVFLGWATK----KFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHHTT----CSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHcC----CCCccEEEEEEcCCCCCHHHHHHHHHHH
Confidence            345555643    2356778999999999999999888653

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=90.87  E-value=0.094  Score=42.71  Aligned_cols=25  Identities=28%  Similarity=0.453  Sum_probs=21.3

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhcc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      +-.|.|=|.-|+||||+++.+.+..
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHh
Confidence            4567777999999999999998864

>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=90.84  E-value=0.072  Score=38.97  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=19.2

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-+.|.|.+|+||||+|-.....
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45789999999999999877654

>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=90.60  E-value=0.075  Score=38.90  Aligned_cols=21  Identities=33%  Similarity=0.374  Sum_probs=19.2

Q ss_pred             EEeEeecCCCChHHHHHHHhh
Q 041190          159 VIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      -|+|+|.+.+|||||.+.+..
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

>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=90.58  E-value=0.13  Score=42.95  Aligned_cols=41  Identities=22%  Similarity=0.307  Sum_probs=29.8

Q ss_pred             cccc-chHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhc
Q 041190          133 YGRE-KDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       133 ~gr~-~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .|.. ...+.+.+++..       .-+.|.|.|+.|+||||....+.+.
T Consensus       140 LG~~~~~~~~l~~l~~~-------~~GliLvtGpTGSGKSTTl~~~l~~  181 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKR-------PHGIILVTGPTGSGKSTTLYAGLQE  181 (401)
T ss_dssp             SCCCHHHHHHHHHHHTS-------SSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHhh-------hhceEEEEcCCCCCccHHHHHHhhh
Confidence            4543 445566665543       3489999999999999988888764

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=90.25  E-value=0.082  Score=40.39  Aligned_cols=22  Identities=27%  Similarity=0.394  Sum_probs=19.6

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ++|+|.|-+++|||||...+..
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            4699999999999999998864

>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=90.12  E-value=0.095  Score=41.28  Aligned_cols=22  Identities=32%  Similarity=0.622  Sum_probs=19.7

Q ss_pred             ceEEeEeecCCCChHHHHHHHh
Q 041190          157 FSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ++.|+|+|-.|.|||||+-.+.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            4789999999999999998874

>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=90.00  E-value=0.071  Score=43.35  Aligned_cols=24  Identities=38%  Similarity=0.452  Sum_probs=20.1

Q ss_pred             ceEEeEeecCCCChHHHHHHHhhc
Q 041190          157 FSVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       157 ~~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..|.|=|.-|+||||+++.+.+.
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHH
Confidence            456888999999999999999654

>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=89.60  E-value=0.6  Score=35.37  Aligned_cols=21  Identities=29%  Similarity=0.290  Sum_probs=18.7

Q ss_pred             EEeEeecCCCChHHHHHHHhh
Q 041190          159 VIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      ++-|.|+...||||+.|.|.-
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            788999999999999998854

>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=89.58  E-value=1.4  Score=32.51  Aligned_cols=113  Identities=17%  Similarity=0.152  Sum_probs=58.5

Q ss_pred             ccccccchHHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHH
Q 041190          131 EVYGREKDKEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQ  210 (261)
Q Consensus       131 ~~~gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~  210 (261)
                      .+.-|+-+.+.+..++..       + +. .|+++.|.|||.+|-.+....      ...+.+-++. ..+...+.+-+.
T Consensus        68 ~~~Lr~yQ~eav~~~~~~-------~-~~-ll~~~tG~GKT~~a~~~~~~~------~~~~Liv~p~-~~L~~q~~~~~~  131 (206)
T d2fz4a1          68 EISLRDYQEKALERWLVD-------K-RG-CIVLPTGSGKTHVAMAAINEL------STPTLIVVPT-LALAEQWKERLG  131 (206)
T ss_dssp             CCCCCHHHHHHHHHHTTT-------S-EE-EEEESSSTTHHHHHHHHHHHS------CSCEEEEESS-HHHHHHHHHHHG
T ss_pred             CCCcCHHHHHHHHHHHhC-------C-Cc-EEEeCCCCCceehHHhHHHHh------cCceeEEEcc-cchHHHHHHHHH
Confidence            344566667766666532       1 22 367899999999888776542      2233333332 223332333333


Q ss_pred             HhcCC--------C-CC-----CCHHHHHHHHHHHhCCCeEEEEEeCCCCCChhhHHHhhcccC
Q 041190          211 AAAGS--------A-DV-----NDLNLLQLQLENQLKNKKFLLVLDDMWSENYDVWTNLCKPFK  260 (261)
Q Consensus       211 ~l~~~--------~-~~-----~~~~~~~~~l~~~l~~kr~LiVlDdvw~~~~~~w~~l~~~l~  260 (261)
                      .++..        . ..     .....+.. ..+.+.++--+||+|++-+.....|..+...++
T Consensus       132 ~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~-~~~~~~~~~~lvIiDEaH~~~a~~~~~i~~~~~  194 (206)
T d2fz4a1         132 IFGEEYVGEFSGRIKELKPLTVSTYDSAYV-NAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSI  194 (206)
T ss_dssp             GGCGGGEEEESSSCBCCCSEEEEEHHHHHH-THHHHTTTCSEEEEECSSCCCTTTHHHHHHTCC
T ss_pred             hhcccchhhcccccccccccccceehhhhh-hhHhhCCcCCEEEEECCeeCCcHHHHHHHhccC
Confidence            33210        0 00     11222222 223333444489999998765457777665554

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=89.41  E-value=0.032  Score=41.01  Aligned_cols=21  Identities=29%  Similarity=0.392  Sum_probs=17.9

Q ss_pred             eEEeEeecCCCChHHHHHHHh
Q 041190          158 SVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      ++..|+|+.|+||||+...++
T Consensus        25 ~~tvi~G~NGsGKStil~Ai~   45 (222)
T d1qhla_          25 LVTTLSGGNGAGKSTTMAAFV   45 (222)
T ss_dssp             HHHHHHSCCSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            356788999999999998885

>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=89.15  E-value=0.042  Score=42.41  Aligned_cols=22  Identities=23%  Similarity=0.468  Sum_probs=18.4

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      +..++|.+|+|||||.+.+..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            4458899999999999999765

>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=89.15  E-value=0.26  Score=33.86  Aligned_cols=52  Identities=15%  Similarity=0.231  Sum_probs=32.3

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhccccccccceeEEEeeCCCCCHHHHHHHHHHHhc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDAGVKKYFSFRACAYVSEDFDAVGVTKVILQAAA  213 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i~~~i~~~l~  213 (261)
                      ..++..|+++.|+|||+++-..+..      ...++.+.+....-..+....+.+.+.
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            4578889999999999988766543      223555555543334444444444443

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=88.56  E-value=0.086  Score=41.62  Aligned_cols=16  Identities=25%  Similarity=0.245  Sum_probs=13.2

Q ss_pred             EEeEeecCCCChHHHH
Q 041190          159 VIPITGMGGLGKTTLA  174 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa  174 (261)
                      .+.|.|.+|+||||.+
T Consensus        16 ~~lI~g~aGTGKTt~l   31 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVI   31 (306)
T ss_dssp             EEEECCCTTSCHHHHH
T ss_pred             CEEEEeeCCccHHHHH
Confidence            3678899999999854

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=88.01  E-value=0.12  Score=42.03  Aligned_cols=23  Identities=35%  Similarity=0.426  Sum_probs=19.8

Q ss_pred             EEeEeecCCCChHHHHHHHhhcc
Q 041190          159 VIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      .|.|=|.-|+||||+++.+.+..
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l   29 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHF   29 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            46777999999999999998763

>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=87.77  E-value=0.11  Score=41.29  Aligned_cols=15  Identities=33%  Similarity=0.414  Sum_probs=12.8

Q ss_pred             EeEeecCCCChHHHH
Q 041190          160 IPITGMGGLGKTTLA  174 (261)
Q Consensus       160 i~I~G~~GiGKTtLa  174 (261)
                      +-|.|.+|+||||.+
T Consensus        27 ~lV~g~aGSGKTt~l   41 (318)
T d1pjra1          27 LLIMAGAGSGKTRVL   41 (318)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEEecCCccHHHHH
Confidence            668899999999854

>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=86.39  E-value=0.24  Score=40.30  Aligned_cols=35  Identities=14%  Similarity=0.151  Sum_probs=27.2

Q ss_pred             HHHHHHHhhCCCCCCCCCceEEeEeecCCCChHHHHHHHh
Q 041190          139 KEVIVGLLLGDDLNSGPGFSVIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       139 ~~~l~~~L~~~~~~~~~~~~vi~I~G~~GiGKTtLa~~v~  178 (261)
                      .+.+.+++..     ..+++-|+|+|-.|.|||||+-.+.
T Consensus         4 ~~~~~~lm~~-----~~~IRNI~iiGhvd~GKTTL~d~Ll   38 (341)
T d1n0ua2           4 VDQMRSLMDK-----VTNVRNMSVIAHVDHGKSTLTDSLV   38 (341)
T ss_dssp             HHHHHHHHHC-----GGGEEEEEEECCGGGTHHHHHHHHH
T ss_pred             HHHHHHHhcC-----cccCcEEEEEeCCCCcHHHHHHHHH
Confidence            4556666543     2468899999999999999998775

>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=86.15  E-value=0.19  Score=41.81  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=19.5

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      --|+|+|.+|+|||||.+.+..
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            3489999999999999999874

>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=86.14  E-value=0.21  Score=39.22  Aligned_cols=22  Identities=27%  Similarity=0.375  Sum_probs=19.3

Q ss_pred             EEeEeecCCCChHHHHHHHhhc
Q 041190          159 VIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      -++|+|.+.+|||||-+.+-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            5899999999999999988654

>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=85.95  E-value=0.23  Score=38.89  Aligned_cols=26  Identities=23%  Similarity=0.244  Sum_probs=22.2

Q ss_pred             CceEEeEeecCCCChHHHHHHHhhcc
Q 041190          156 GFSVIPITGMGGLGKTTLAQLVFNDA  181 (261)
Q Consensus       156 ~~~vi~I~G~~GiGKTtLa~~v~~~~  181 (261)
                      ..-.++|+|++.+|||||++.+....
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~~~  136 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAKKN  136 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEEecCccchhhhhhhhhccc
Confidence            34568999999999999999998753

>d1wxqa1 c.37.1.8 (A:1-319) GTP-binding protein PH0525 {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 PH0525
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=85.15  E-value=0.23  Score=39.67  Aligned_cols=21  Identities=24%  Similarity=0.252  Sum_probs=18.5

Q ss_pred             EeEeecCCCChHHHHHHHhhc
Q 041190          160 IPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       160 i~I~G~~GiGKTtLa~~v~~~  180 (261)
                      |+|+|.+.+|||||-+.+-+.
T Consensus         3 v~lvG~pn~GKStlfn~lt~~   23 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATLV   23 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC-
T ss_pred             EeEECCCCCCHHHHHHHHHCC
Confidence            799999999999999998554

>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=84.92  E-value=0.24  Score=39.26  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=20.3

Q ss_pred             eEEeEeecCCCChHHHHHHHhhc
Q 041190          158 SVIPITGMGGLGKTTLAQLVFND  180 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~~  180 (261)
                      .-++|+|.+.+|||||-+.+-+.
T Consensus        11 ~kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          11 LKTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHCC
Confidence            35899999999999999999864

>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=84.11  E-value=0.28  Score=36.66  Aligned_cols=20  Identities=30%  Similarity=0.267  Sum_probs=17.8

Q ss_pred             EEeEeecCCCChHHHHHHHh
Q 041190          159 VIPITGMGGLGKTTLAQLVF  178 (261)
Q Consensus       159 vi~I~G~~GiGKTtLa~~v~  178 (261)
                      -|+|+|-.+.|||||+..+.
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHH
Confidence            47899999999999998874

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=82.70  E-value=0.28  Score=38.59  Aligned_cols=20  Identities=30%  Similarity=0.544  Sum_probs=17.3

Q ss_pred             eEEeEeecCCCChHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLV  177 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v  177 (261)
                      ++-.|+|+.|+|||++...+
T Consensus        25 ~lnvlvG~NgsGKS~iL~Ai   44 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNIIDAI   44 (308)
T ss_dssp             SEEEEECCTTTCSTHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHH
Confidence            46789999999999998766

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=82.24  E-value=0.35  Score=40.12  Aligned_cols=22  Identities=23%  Similarity=0.348  Sum_probs=17.8

Q ss_pred             eEEeEeecCCCChHHHHHHHhh
Q 041190          158 SVIPITGMGGLGKTTLAQLVFN  179 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v~~  179 (261)
                      +-+.|+|.+|+|||++++.+..
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~   72 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAY   72 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEeCCCCcHHHHHHHHHH
Confidence            3489999999999998865543

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.82  E-value=0.43  Score=39.06  Aligned_cols=20  Identities=25%  Similarity=0.501  Sum_probs=17.3

Q ss_pred             eEEeEeecCCCChHHHHHHH
Q 041190          158 SVIPITGMGGLGKTTLAQLV  177 (261)
Q Consensus       158 ~vi~I~G~~GiGKTtLa~~v  177 (261)
                      ++-.|+|+.|+|||++...+
T Consensus        26 ~l~~i~G~NGsGKS~ileAi   45 (427)
T d1w1wa_          26 NFTSIIGPNGSGKSNMMDAI   45 (427)
T ss_dssp             SEEEEECSTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            35678999999999998877