Citrus Sinensis ID: 041612

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270------
Protein Sequence
MAEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWKD
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHcccccccHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEccccccccccHHHHHHHHHHHHHHHccccccEEEEEccccccHHHHHHHHHcccccccccccEEEEEEcccccHHHHHHHHHHHHccccccccHHcHHcccccccccccEEEEEEccHHHHcccccccccEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHcHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccEccccHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccHHHHHHHHHHHHHccccccccHHHHcccccccccccEEEEEEccHHHHHHHHccccccccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHcccHHHHcc
Coil and Loop (DISEMBL)
MAEIIFIIVVEVVKcmvppayrRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARANNVIEAadnftkdeattnkrcfkgnilsaledpdvnmlgiygmggigKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKlglkfheesesgranslfthghkGCKVLLTARSQdvlsgkmdsrpnfsigvlNEEEAWSLFKKMAgdyiedseFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWKD
Flexible Loop (DISEMBL)
MAEIIFIIVVevvkcmvppAYRRICYLrkskytsnlqnlksevdnlkservrtehqvdeakrkgeeieeNVENWLARANNVIEAAdnftkdeattnkrcfkgnilsaledpdvNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFvevsqnqdirkIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARAlrnkrlfewkd
Low Complexity Region (SEG)
MAeiifiivvevvKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWKD
Disordered region (IsUnstruct)
***IIFIIVVEVVKCMVPPAYRRICYLRKSKYT*************************************VENWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL*************LFTHGHKGCKVLLTARSQDV*********NFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEW**
Disordered Region (DISOPRED)
*AEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTE****************************************TNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK****WK*
Disordered Region (DISEMBL)
MAEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLK******************EIEENVENWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWKD
Disordered Region (DISPRO)
MAEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEA*******************************EATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKR******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEIIFIIVVEVVKCMVPPAYRRICYLRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWKD
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	276	2.2.26 [Sep-21-2011]
Q9T048	985	Disease resistance protei	yes	no	0.557	0.156	0.319	2e-19
O64973	889	Disease resistance protei	no	no	0.572	0.177	0.341	2e-18
Q8L3R3	885	Disease resistance protei	no	no	0.619	0.193	0.314	5e-18
O81825	919	Probable disease resistan	no	no	0.590	0.177	0.303	1e-17
P60839	884	Probable disease resistan	no	no	0.586	0.183	0.309	5e-17
Q8RXS5	888	Probable disease resistan	no	no	0.605	0.188	0.290	3e-16
Q9LVT3	948	Probable disease resistan	no	no	0.601	0.175	0.306	6e-16
Q9LW09	375	Putative disease resistan	no	no	0.684	0.504	0.274	6e-16
O22727	967	Probable disease resistan	no	no	0.586	0.167	0.297	6e-16
O64789	925	Probable disease resistan	no	no	0.586	0.175	0.297	1e-15

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

 Score = 96.3 bits (238), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 60/188 (31%), Positives = 99/188 (52%), Gaps = 34/188 (18%)

Query: 116 LGIYGMGGIGKTMLAEEIARKVK---SDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF 172
           +G++GMGG+GKT L   +  K++   + + F  V+FV VS+  D R++Q++I ++L +  
Sbjct: 167 IGVWGMGGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDIDT 226

Query: 173 H-EESESGRANSLF-----------------------------THGHKGCKVLLTARSQD 202
             EESE   A  ++                             T  +KG KV+LT+R  +
Sbjct: 227 QMEESEEKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTEENKGSKVILTSRFLE 286

Query: 203 VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI 262
           V    M +  +  +  L EE+AW LF K AGD +     + IA+ V++EC GLP++I+T+
Sbjct: 287 VCRS-MKTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITV 345

Query: 263 ARALRNKR 270
             A+R K+
Sbjct: 346 GTAMRGKK 353

Disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

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

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/196 (34%), Positives = 94/196 (47%), Gaps = 38/196 (19%)

Query: 115 MLGIYGMGGIGKTMLAEEIARKV-KSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH 173
           +LG+YGMGG+GKT L  +I  K  K D  FD V++V VS++  +RKIQ +I +K+GL   
Sbjct: 178 ILGLYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGM 237

Query: 174 EESESGRANSLFTHGH--------------------------------KGCKVLLTARSQ 201
           E SE    N +    H                                 GCKV  T RS+
Sbjct: 238 EWSEKN-DNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSR 296

Query: 202 DVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS--EFQSIARDVAKECAGLPVSI 259
           DV  G+M       +  L  EE+W LF+   G     S  +   +AR VA++C GLP+++
Sbjct: 297 DV-CGRMGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLAL 355

Query: 260 VTIARALRNKR-LFEW 274
             I  A+  KR + EW
Sbjct: 356 NVIGEAMACKRTVHEW 371

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 91.7 bits (226), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 101/207 (48%), Gaps = 36/207 (17%)

Query: 104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV-KSDKLFDQVVFVEVSQNQDIRKIQE 162
           + + L +  V ++G+YGMGG+GKT L  +I  K  K    FD V++V VS+N  + KIQ+
Sbjct: 167 VWNCLMEDKVWIVGLYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQK 226

Query: 163 EIGDKLGL---KFHEESESGRANSL----------------------------FTHGHKG 191
            IG+KLGL    + E++++ RA  +                            +  G  G
Sbjct: 227 SIGEKLGLVGKNWDEKNKNQRALDIHNVLRRKKFVLLLDDIWEKVELKVIGVPYPSGENG 286

Query: 192 CKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS--EFQSIARDVA 249
           CKV  T  S++V  G+M       I  L+   AW L KK  G+    S  +   +AR V+
Sbjct: 287 CKVAFTTHSKEV-CGRMGVDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVS 345

Query: 250 KECAGLPVSIVTIARALRNKRLF-EWK 275
           ++C GLP+++  I   +  KR   EW+
Sbjct: 346 EKCCGLPLALNVIGETMSFKRTIQEWR 372

Disease resistance (R) protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O81825|DRL28_ARATH Probable disease resistance protein At4g27220 OS=Arabidopsis thaliana GN=At4g27220 PE=2 SV=1

 Score = 90.5 bits (223), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/198 (30%), Positives = 95/198 (47%), Gaps = 35/198 (17%)

Query: 112 DVNMLGIYGMGGIGKTMLAEEI---ARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKL 168
           +V  +G++GMGG+GKT L   +     K  + + F  V++V VS++ D++++Q +I  +L
Sbjct: 133 NVQKIGVWGMGGVGKTTLVRTLNNDLLKYAATQQFALVIWVTVSKDFDLKRVQMDIAKRL 192

Query: 169 GLKFHEESESGRANS------------------------------LFTHGHKGCKVLLTA 198
           G +F  E  +    +                              L     K  KV+LT+
Sbjct: 193 GKRFTREQMNQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKDSKVVLTS 252

Query: 199 RSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVS 258
           R  +V   +M +  N  +  L E+EAW LF    G+       + IA+DV+ EC GLP++
Sbjct: 253 RRLEVCQ-QMMTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHECCGLPLA 311

Query: 259 IVTIARALRNKRLFE-WK 275
           I+TI R LR K   E WK
Sbjct: 312 IITIGRTLRGKPQVEVWK 329

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 88.6 bits (218), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 61/197 (30%), Positives = 94/197 (47%), Gaps = 35/197 (17%)

Query: 108 LEDPDVNMLGIYGMGGIGKTMLAEEI-ARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGD 166
           L D    ++G+YGMGG+GKT L  +I  R   +D   + V++V VS +  I KIQ+EIG+
Sbjct: 170 LMDDGTKIMGLYGMGGVGKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGE 229

Query: 167 K---LGLKFHEESESGRANSLFTHGHK----------------------------GCKVL 195
           K   +G++++++SE+ +A  +     K                            GCK+ 
Sbjct: 230 KIGFIGVEWNQKSENQKAVDILNFLSKKRFVLLLDDIWKRVELTEIGIPNPTSENGCKIA 289

Query: 196 LTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS--EFQSIARDVAKECA 253
            T R Q V    M       +  L  ++AW LFKK  GD    S  +   IAR VA+ C 
Sbjct: 290 FTTRCQSV-CASMGVHDPMEVRCLGADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACC 348

Query: 254 GLPVSIVTIARALRNKR 270
           GLP+++  I   +  K+
Sbjct: 349 GLPLALNVIGETMACKK 365

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 85.5 bits (210), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 102/203 (50%), Gaps = 36/203 (17%)

Query: 108 LEDPDVNMLGIYGMGGIGKTMLAEEIA-RKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGD 166
           L + ++ +LG++GMGG+GKT L   I  R  +    FD V+++ VS+   I++IQ+EI +
Sbjct: 169 LMEDEIGILGLHGMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWE 228

Query: 167 KL---GLKFHEESESGRANSL----------------------------FTHGHKGCKVL 195
           KL     K+ +++E  +A+++                            F     GCK++
Sbjct: 229 KLRSDNEKWKQKTEDIKASNIYNVLKHKRFVLLLDDIWSKVDLTEVGVPFPSRENGCKIV 288

Query: 196 LTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS--EFQSIARDVAKECA 253
            T R +++  G+M    +  +  L  ++AW LF K  G+    S  E  ++AR VAK+C 
Sbjct: 289 FTTRLKEI-CGRMGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCR 347

Query: 254 GLPVSIVTIARALRNKRLF-EWK 275
           GLP+++  I   +  KR   EW+
Sbjct: 348 GLPLALNVIGETMAYKRTVQEWR 370

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVT3|DRL38_ARATH Probable disease resistance protein At5g47260 OS=Arabidopsis thaliana GN=At5g47260 PE=3 SV=2

 Score = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 61/199 (30%), Positives = 93/199 (46%), Gaps = 33/199 (16%)

Query: 108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK 167
           L D +V  LGIYG GG+GKT L  ++  K+  D  F  V+FV V   +++  IQ+EIG +
Sbjct: 164 LMDINVGTLGIYGRGGVGKTTLLTKLRNKLLVDA-FGLVIFVVVG-FEEVESIQDEIGKR 221

Query: 168 LGLKFHEESESGRANSL----------------------------FTHGHKGCKVLLTAR 199
           LGL++  E++  +A  +                            F     GCK++ T +
Sbjct: 222 LGLQWRRETKERKAAEILAVLKEKRFVLLLDGIQRELDLEEIGVPFPSRDNGCKIVFTTQ 281

Query: 200 SQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS--EFQSIARDVAKECAGLPV 257
           S +             I  L+ EEAW LF++  G+    S  +   +AR VA  C GLP+
Sbjct: 282 SLEACDESKWVDAKVEITCLSPEEAWDLFQETVGENTLRSHQDIPKLARVVASTCRGLPL 341

Query: 258 SIVTIARALRNKRLF-EWK 275
           ++  I  A+  KR   EW+
Sbjct: 342 ALNLIGEAMSGKRTVREWR 360

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LW09|DRL22_ARATH Putative disease resistance protein At3g15700 OS=Arabidopsis thaliana GN=At3g15700 PE=3 SV=1

 Score = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 110/226 (48%), Gaps = 37/226 (16%)

Query: 87  NFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL--FD 144
           N  +D+ T       G +   +   +  ++G+YG+ G+GKT +  ++  ++   KL  FD
Sbjct: 134 NVDRDDQTVGLEAVSGLVWRCMTVDNTGIIGLYGVEGVGKTTVLTQVNNRLLQHKLNGFD 193

Query: 145 QVVFVEVSQNQDIRKIQEEIGDKLGL---KFHEESESGRANSLF---------------- 185
            V++V VS+N ++ KIQ+ I +K+G     +  ++E  +A  +F                
Sbjct: 194 FVIWVFVSKNVNLEKIQDTIREKIGFLDRSWMSKTEEEKAGKIFEILSKRRFALFLDDVW 253

Query: 186 ------------THGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG 233
                         G    K++ T  S +V   +M ++    +  L  E AW LFK  AG
Sbjct: 254 EKVDLVKAGVPPPDGLNRSKIVFTTCSDEVCQ-EMGAQTKIKMEKLPWERAWDLFKMNAG 312

Query: 234 DYIEDS--EFQSIARDVAKECAGLPVSIVTIARALRNKRLF-EWKD 276
           + I  S  +   +A++VA +C GLP+++VTI RA+ +K+   EW+D
Sbjct: 313 EEIVKSHPDITKVAQEVAAKCDGLPLALVTIGRAMASKKTPQEWRD 358

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 59/198 (29%), Positives = 95/198 (47%), Gaps = 36/198 (18%)

Query: 113 VNMLGIYGMGGIGKTMLAEEIARK-VKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL- 170
           V ++G++GMGG+GKT L ++I  K  ++   FD V+++ VSQ   + K+QE+I +KL L 
Sbjct: 173 VGIMGLHGMGGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLC 232

Query: 171 --KFHEESESGRANSL----------------------------FTHGHKGCKVLLTARS 200
              +  ++ES +A  +                            +      CKV  T R 
Sbjct: 233 DDLWKNKNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRD 292

Query: 201 QDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYI--EDSEFQSIARDVAKECAGLPVS 258
           Q V  G+M       +  L  E+AW LFK   GD     D     +AR+VA++C GLP++
Sbjct: 293 QKV-CGQMGDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLA 351

Query: 259 IVTIARALRNKRLF-EWK 275
           +  I   + +K +  EW+
Sbjct: 352 LSCIGETMASKTMVQEWE 369

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 84.0 bits (206), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 59/198 (29%), Positives = 95/198 (47%), Gaps = 36/198 (18%)

Query: 113 VNMLGIYGMGGIGKTMLAEEIARKVKS-DKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL- 170
           V ++G++GMGG+GKT L ++I  K       FD V+++ VSQ   + K+QE+I +KL L 
Sbjct: 174 VGIMGLHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLC 233

Query: 171 --KFHEESESGRANSL----------------------------FTHGHKGCKVLLTARS 200
              +  ++ES +A  +                            +      CKV  T RS
Sbjct: 234 DDLWKNKNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRS 293

Query: 201 QDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYI--EDSEFQSIARDVAKECAGLPVS 258
           ++V  G+M       +  L  E+AW LFK   GD     D     +AR+VA++C GLP++
Sbjct: 294 REV-CGEMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVGLAREVAQKCRGLPLA 352

Query: 259 IVTIARALRNKRLF-EWK 275
           +  I   + +K +  EW+
Sbjct: 353 LNVIGETMASKTMVQEWE 370

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	276
359488027	1520	PREDICTED: disease resistance protein At	0.992	0.180	0.365	8e-55
147802546	1409	hypothetical protein VITISV_007222 [Viti	0.992	0.194	0.367	3e-54
358344899	1543	Cc-nbs resistance protein [Medicago trun	0.981	0.175	0.356	5e-50
255542484	2460	phosphoprotein phosphatase, putative [Ri	0.960	0.107	0.380	8e-49
359487992	1162	PREDICTED: disease resistance protein At	0.905	0.215	0.349	4e-43
449442431	1413	PREDICTED: probable disease resistance p	0.626	0.122	0.443	6e-43
147782989	1351	hypothetical protein VITISV_012099 [Viti	0.992	0.202	0.334	3e-42
358344919	1995	NBS/LRR resistance protein-like protein	0.981	0.135	0.341	3e-42
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.670	0.109	0.420	5e-42
147866716	454	hypothetical protein VITISV_025268 [Viti	0.670	0.407	0.420	8e-42

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

 Score =  219 bits (559), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 134/367 (36%), Positives = 189/367 (51%), Gaps = 93/367 (25%)

Query: 1   MAEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEA 60
           M EI+  I  +V + +V P  R   YL    Y SN+ +L+ +V+ L   R R E  VDEA
Sbjct: 1   MEEIVVTIAAKVAEYLVAPIGRSFGYL--FNYRSNIDDLRQQVEKLGDARARLERSVDEA 58

Query: 61  KRKGEEIEENVENWLARANNVIEAADNFTKDEATTNKRC--------------------- 99
            R G+EIE +V+ WL R +  +E A  F + E   N+ C                     
Sbjct: 59  IRNGDEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKR 118

Query: 100 -----------------------------FKGN------------ILSALEDPDVNMLGI 118
                                        FKG+            I+ AL D  VN++G+
Sbjct: 119 ARVVAEIQGDGKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGV 178

Query: 119 YGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESES 178
           +GM G+GKT L +++A++ + +KLFD+VV   +S   +++KIQ E+ D LGLKF EESE 
Sbjct: 179 WGMAGVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEM 238

Query: 179 GRANSL-----------------------------FTHGHKGCKVLLTARSQDVLSGKMD 209
           GRA  L                             F   HKGCK++LT+R++ +LS +M 
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHILSNEMG 298

Query: 210 SRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK 269
           ++ +F +  L EEEA  LFKKMAGD IE+ + QSIA DVAKECAGLP++IVT+A+AL+NK
Sbjct: 299 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 358

Query: 270 RLFEWKD 276
            L  W+D
Sbjct: 359 GLSIWED 365

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  218 bits (554), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 135/367 (36%), Positives = 191/367 (52%), Gaps = 93/367 (25%)

Query: 1   MAEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEA 60
           M EI+  I  +V + +V P  R   YL    Y SN+ +L+ +V+ L   R R E  VDEA
Sbjct: 1   MEEIVVTIAAKVAEYLVAPIGRSFGYL--FNYRSNIDDLRQQVEKLGDARARLERSVDEA 58

Query: 61  KRKGEEIEENVENWLARANNVIEAADNFTK-----DEATTNKRC---------------- 99
            R G+EIE +V+ WL R +  +E A  F +     +++  N  C                
Sbjct: 59  IRNGDEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKR 118

Query: 100 -----------------------------FKGN------------ILSALEDPDVNMLGI 118
                                        FKG+            I+ AL D  VN++G+
Sbjct: 119 ARVVAEIQGDGKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGV 178

Query: 119 YGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESES 178
           +GM G+GKT L +++A++V+ +KLFD+VV   +S   +++KIQ E+ D LGLKF EESE 
Sbjct: 179 WGMAGVGKTTLMKQVAKQVEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEM 238

Query: 179 GRANSL-----------------------------FTHGHKGCKVLLTARSQDVLSGKMD 209
           GRA  L                             F   HKGCK++LT+R++ VLS +M 
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHVLSNEMG 298

Query: 210 SRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK 269
           ++ +F +  L EEEA  LFKKMAGD IE+ + QSIA DVAKECAGLP++IVT+A+AL+NK
Sbjct: 299 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 358

Query: 270 RLFEWKD 276
            L  W+D
Sbjct: 359 GLSIWED 365

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358344899|ref|XP_003636523.1| Cc-nbs resistance protein [Medicago truncatula] gi|355502458|gb|AES83661.1| Cc-nbs resistance protein [Medicago truncatula]

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 127/356 (35%), Positives = 179/356 (50%), Gaps = 85/356 (23%)

Query: 3   EIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKR 62
           EI+  +V ++ +  + P  R+  YL    Y  N + LK  V+NL++ R R  H V+  +R
Sbjct: 2   EILTSVVGKITEYTIVPIGRQASYL--IFYKGNFKKLKDHVENLQAARERMLHSVERERR 59

Query: 63  KGEEIEENVENWLARANNVIEAADNFTKDEATTNKRC----------------------- 99
            G EIE++V NWL + N VIE A+    D    N RC                       
Sbjct: 60  NGREIEKDVLNWLEKVNEVIENANRLQNDPRRPNVRCSAWSFPNLILRHQLSRKATKITN 119

Query: 100 ---------------------------FKGNILSALEDPDVNMLGIYGMGGIGKTMLAEE 132
                                       K +I+ AL DP    +G+YG+GG+GKT L ++
Sbjct: 120 DVDQVQRKVGASSSSTRDGEKYDTRELLKEDIVKALADPTSRNIGVYGLGGVGKTTLVQK 179

Query: 133 IARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSL-------- 184
           +A      KLFD+VV  EVS+N DI+KIQ EI D L L+F EES  GRA  L        
Sbjct: 180 VAETANEHKLFDKVVITEVSKNPDIKKIQGEIADFLSLRFEEESNRGRAERLRQRIKMEK 239

Query: 185 ---------------------FTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGV--LNE 221
                                F + H GCK+L++ RSQ+VLS +MD   +F+  V  ++E
Sbjct: 240 SILIILDNIWTILDLKTVGIPFGNEHNGCKLLMSCRSQEVLS-QMDVPKDFTFKVELMSE 298

Query: 222 EEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFE-WKD 276
            E WSLF+ MAGD ++DS  + +   VA++CAGLP+ +VT+ARA++NKR  E WKD
Sbjct: 299 NETWSLFQFMAGDVVKDSNLKDLPFQVAQKCAGLPLRVVTVARAMKNKRDVESWKD 354

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542484|ref|XP_002512305.1| phosphoprotein phosphatase, putative [Ricinus communis] gi|223548266|gb|EEF49757.1| phosphoprotein phosphatase, putative [Ricinus communis]

 Score =  199 bits (507), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 119/313 (38%), Positives = 175/313 (55%), Gaps = 48/313 (15%)

Query: 8   IVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEI 67
           +V +V   +V   +R+I Y+    Y+SN+Q LKS+V+ LK+E+V   H+V+EA  KGEEI
Sbjct: 9   VVSKVTDQLVDSIWRQIGYIWN--YSSNIQGLKSKVEKLKAEKVSVMHRVEEAIAKGEEI 66

Query: 68  EENVENWLARANNVIEAADNFTKDEATTNKRCFK---------------GNILSALEDPD 112
           EE V  WL  A+  ++    F+        R F+                 I+ AL+D D
Sbjct: 67  EEIVSKWLTSADEAMKLQRLFSTKIMIEQTRKFEVAKDYETFDSRNQVLEEIIGALKDAD 126

Query: 113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF 172
           VN++G+YG+GG+GKT L +++  +VK   +F  V    V+ N D+ KIQ++I D LGLKF
Sbjct: 127 VNLIGVYGLGGVGKTTLLKQVTAQVKETGIFKVVATATVTDNPDLNKIQQDIADWLGLKF 186

Query: 173 HEESESGRANSL-----------------------------FTHGHKGCKVLLTARSQDV 203
             ES   RA  L                             + + HKGCK+L+T+R+ +V
Sbjct: 187 DVESTQVRAARLRARLKQDEKVLVILDNIWHKIALEELGIPYGNDHKGCKILMTSRNLNV 246

Query: 204 LSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIA 263
           L   MD + +F + VL +EEAW LF+K AG+ ++D     IA  +A++CAGLPV IV +A
Sbjct: 247 LLA-MDVQRHFLLRVLQDEEAWQLFEKKAGE-VKDPTLHPIATQIARKCAGLPVLIVAVA 304

Query: 264 RALRNKRLFEWKD 276
            AL+NK L EW+D
Sbjct: 305 TALKNKELCEWRD 317

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487992|ref|XP_002268678.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  181 bits (458), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 120/343 (34%), Positives = 173/343 (50%), Gaps = 93/343 (27%)

Query: 16  MVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWL 75
           +V P  R++ YL    Y SNL  L  +V+ L + R R +H VDEA R+G++IE +V +WL
Sbjct: 20  LVDPIVRQLGYL--FNYRSNLDELVEQVERLGNARERLQHDVDEANRQGDDIENDVRDWL 77

Query: 76  ARANNVIEAA------------------------------------------DNFTK--- 90
            R   +I+ A                                          +NFT+   
Sbjct: 78  TRTEEIIQRARELIQDENAENTSCLCFNLKLGYQRSRQAKELSEDIGELQEENNFTRVSY 137

Query: 91  --------------DEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARK 136
                          E   ++      I+ AL + D+ M+G++GMGG+GKT LA ++A+ 
Sbjct: 138 RPPLQGIWSPRLRDCEPLVSRASILNRIMEALRNDDIRMIGVWGMGGVGKTTLANQVAKN 197

Query: 137 VKSDKLFDQVVF-VEVSQNQDIRKIQEEIGDKLGLKFHEESESGRAN----SLFTH---- 187
            + DKLF++VV  + +SQ  ++ KIQE+I   LGLKF +E E  RA+    SL  H    
Sbjct: 198 AEEDKLFEKVVMALNISQIPNVTKIQEDIAGILGLKFEQEGELERAHRLRRSLNKHKTVL 257

Query: 188 ---------------------GHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWS 226
                                  +GCKVLLT+RSQ +LS  M ++ NF +  L EEEAWS
Sbjct: 258 VILDDIWGELLLEKIGIPCGDAQRGCKVLLTSRSQGLLSRSMGTQINFHVQHLCEEEAWS 317

Query: 227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK 269
           LFKK AGD +E  + +SIA  V +EC GLPV+IVT+A+AL+ +
Sbjct: 318 LFKKTAGDSVE--QLKSIAIKVLRECDGLPVAIVTVAKALKGE 358

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449442431|ref|XP_004138985.1| PREDICTED: probable disease resistance protein At4g27220-like [Cucumis sativus] gi|449477888|ref|XP_004155153.1| PREDICTED: probable disease resistance protein At4g27220-like [Cucumis sativus]

 Score =  180 bits (457), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 90/203 (44%), Positives = 124/203 (61%), Gaps = 30/203 (14%)

Query: 104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE 163
           I++AL D +V+ +G+YGMGG+GKTML +EI++     KLFD+V+   VSQ  D+R+IQ +
Sbjct: 160 IIAALMDDNVHTIGVYGMGGVGKTMLVQEISKLAMEQKLFDEVITSTVSQTPDLRRIQGQ 219

Query: 164 IGDKLGLKFHEESESGRANSLFTH------------------------------GHKGCK 193
           +GDKLGL+F +E+E GRA  L                                  H GCK
Sbjct: 220 LGDKLGLRFEQETEEGRALKLLNRLKMERQKILIVLDDVWKQIDLEKIGIPSIEDHSGCK 279

Query: 194 VLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECA 253
           +L T+R  DVL     +  NF I  L E+E W+LF+KMAG+ +E S+F+SIA ++ +ECA
Sbjct: 280 ILFTSRDNDVLFNDWRTYKNFEIKFLQEDETWNLFRKMAGEIVETSDFKSIAVEIVRECA 339

Query: 254 GLPVSIVTIARALRNKRLFEWKD 276
            LP++I TIARALRNK    WKD
Sbjct: 340 HLPIAITTIARALRNKPASIWKD 362

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147782989|emb|CAN68563.1| hypothetical protein VITISV_012099 [Vitis vinifera]

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 121/362 (33%), Positives = 179/362 (49%), Gaps = 88/362 (24%)

Query: 1   MAEIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEA 60
           M +I+  + VEV KC+V P  R++ YL    Y  N+ +L  +++NL+ ER   +  V+EA
Sbjct: 1   MVDIVISVAVEVAKCLVDPIKRQLGYLLN--YRRNITDLNQQIENLRRERDELQIPVNEA 58

Query: 61  KRKGE-----------------------------------------EIEENVENWLARAN 79
            R+G+                                         ++ +  E   A+  
Sbjct: 59  YRQGDEIFPRVQEWLTYAEGIILESNDFNEHERKASKSCFYLKSRYQLSKQAEKQAAKIV 118

Query: 80  NVIEAADNFT----------------KD-EATTNKRCFKGNILSALEDPDVNMLGIYGMG 122
           + I+ A NF                 KD EA  ++      I+ AL + D+ MLG++GMG
Sbjct: 119 DKIQEARNFGGRVSHRPPPFSSSASFKDYEAFQSRESTFNQIMEALRNEDMRMLGVWGMG 178

Query: 123 GIGKTMLAEEIARKVKSDKLFDQVVFV-EVSQNQDIRKIQEEIGDKLGLKFHE-ESESGR 180
           G+GKT L +++A++ + DKLF +VV V  +SQ  +I +IQE+I   LGLKF   E  +GR
Sbjct: 179 GVGKTTLVKQVAQQAEEDKLFHKVVMVLHISQTPNITEIQEKIARMLGLKFEAGEDRAGR 238

Query: 181 ANS--------------------------LFTHGHKGCKVLLTARSQDVLSGKMDSRPNF 214
                                         +   HKGCKVLLT+R + VLS  M ++  F
Sbjct: 239 LKQRLKGEEKILVILDDIWGKLDLGEIGIPYGDDHKGCKVLLTSRERQVLSKDMRTQKEF 298

Query: 215 SIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEW 274
            +  L+E+EAW+LFKK AGD +E  E + IA DVAK+C GLPV+IVTIA  LR + +  W
Sbjct: 299 HLQHLSEDEAWNLFKKTAGDSVEKPELRPIAVDVAKKCDGLPVAIVTIANTLRGESVHVW 358

Query: 275 KD 276
           K+
Sbjct: 359 KN 360

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358344919|ref|XP_003636533.1| NBS/LRR resistance protein-like protein [Medicago truncatula] gi|355502468|gb|AES83671.1| NBS/LRR resistance protein-like protein [Medicago truncatula]

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 126/369 (34%), Positives = 180/369 (48%), Gaps = 98/369 (26%)

Query: 3   EIIFIIVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKR 62
           EI+  IV ++ +  V P  R+  YL    Y  N + L + V +L++ R R  H V   + 
Sbjct: 2   EILISIVGKIAEYTVVPIGRQASYL--IFYKGNFKTLNNHVGDLEAARERMIHSVKSERE 59

Query: 63  KGEEIEENVENWLAR-------------------------------------------AN 79
            G+EIE++V NWL +                                           AN
Sbjct: 60  NGKEIEKDVLNWLEKVDGVIKEANQLQNDSHNANVRCSPWSFPNLILRHQLSRNATKIAN 119

Query: 80  NVIE-------------------AADNFTKD-EATTNKRCFKGNILSALEDPDVNMLGIY 119
           NV+E                   A+ + T+D E    +   K +I+ AL D     +GIY
Sbjct: 120 NVVEVQGKEKFNSFGHLPPLDVVASSSSTRDGEMYDTRESLKKDIVKALGDSTSCNIGIY 179

Query: 120 GMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESG 179
           G+GG+GKT L E++A+  K  KLFD+VV  EVS+  DIR+IQ EI D LGL+F EES  G
Sbjct: 180 GLGGVGKTTLVEKVAQIAKEHKLFDKVVKAEVSKKPDIRRIQGEIADFLGLRFEEESIPG 239

Query: 180 RANSL-----------------------------FTHGHKGCKVLLTARSQDVLSGKMDS 210
           RA  L                                 H GCK+L+T+R+QDVL  +MD 
Sbjct: 240 RAERLRQRIKMERSVLIILDNIWTILDLKEVGIPVGDEHNGCKLLMTSRNQDVLL-QMDV 298

Query: 211 RPNFSIGV--LNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRN 268
             +F+  V  + E E+WSLF+ MAGD ++DS  + +   VA++CAGLP+ +VT+ARA++N
Sbjct: 299 PKDFTFKVELMTENESWSLFQFMAGDVVKDSNLKDLPFKVARKCAGLPLRVVTVARAMKN 358

Query: 269 KR-LFEWKD 276
           KR +  WKD
Sbjct: 359 KRDVQSWKD 367

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  177 bits (448), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 90/214 (42%), Positives = 131/214 (61%), Gaps = 29/214 (13%)

Query: 92  EATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV 151
           EA  ++      ++ AL D ++N +G++GMGG+GK+ L +++A + + +KLF +VV V V
Sbjct: 149 EALESRMLTLNEVMEALRDANINRIGVWGMGGVGKSTLVKQVAEQAEQEKLFRKVVMVPV 208

Query: 152 SQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTH------------------------ 187
            Q  D + IQ++I DKLG+KF E SE GRA+ L                           
Sbjct: 209 IQTPDFKGIQQQIADKLGMKFEEVSEQGRADRLHQRIKQENTILIILDDLWAELELEKVG 268

Query: 188 -----GHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ 242
                 HKGCK++LT+R++ VLS +M ++ +F +  L E+E W LFK  AGD IE+ E Q
Sbjct: 269 IPSPDDHKGCKLVLTSRNKQVLSNEMSTQKDFRVQHLQEDETWILFKNTAGDSIENPELQ 328

Query: 243 SIARDVAKECAGLPVSIVTIARALRNKRLFEWKD 276
            IA DVAKECAGLP++IVT+A+AL+NK +  WKD
Sbjct: 329 PIAVDVAKECAGLPIAIVTVAKALKNKNVSIWKD 362

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147866716|emb|CAN80506.1| hypothetical protein VITISV_025268 [Vitis vinifera]

 Score =  176 bits (447), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 90/214 (42%), Positives = 129/214 (60%), Gaps = 29/214 (13%)

Query: 92  EATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV 151
           EA  ++      ++ AL D D+N +G++G+GG+GK+ L +++A   + +KLF +VV V V
Sbjct: 149 EALQSRMLTLNEVMEALRDADINRIGVWGLGGVGKSTLVKQVAELAEQEKLFRKVVMVPV 208

Query: 152 SQNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTH------------------------ 187
            Q  D + IQ++I DKLG+KF E SE GRA+ L                           
Sbjct: 209 FQTPDFKGIQQQIADKLGMKFEEVSEQGRADRLHQRIKQENTILIILDDLWAELELEKVG 268

Query: 188 -----GHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ 242
                 HKGCK++LT+R++ VLS +M ++ +F +  L E+E W LFK  AGD I++ E Q
Sbjct: 269 IPSPDDHKGCKLVLTSRNKQVLSNEMSTQKDFRVQHLQEDETWILFKNTAGDSIKNPELQ 328

Query: 243 SIARDVAKECAGLPVSIVTIARALRNKRLFEWKD 276
            IA DVAKECAGLP++IVT+A AL+NK L  WKD
Sbjct: 329 PIAVDVAKECAGLPIAIVTVATALKNKSLSIWKD 362

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	276
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.304	0.085	0.4	7.4e-19
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.307	0.092	0.413	1.1e-18
TAIR|locus:2093192	375	AT3G15700 [Arabidopsis thalian	0.550	0.405	0.254	6.9e-18
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.25	0.077	0.478	8.7e-18
TAIR|locus:2203881	893	AT1G62630 [Arabidopsis thalian	0.239	0.073	0.455	2.2e-17
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.282	0.088	0.414	2.3e-16
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.326	0.101	0.329	3e-16
TAIR|locus:2132741	892	AT4G10780 [Arabidopsis thalian	0.268	0.082	0.423	4.4e-16
TAIR|locus:2170892	848	AT5G43730 [Arabidopsis thalian	0.471	0.153	0.328	5e-16
TAIR|locus:2197739	762	AT1G61300 [Arabidopsis thalian	0.300	0.108	0.356	9.9e-16

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

 Score = 166 (63.5 bits), Expect = 7.4e-19, Sum P(3) = 7.4e-19
 Identities = 34/85 (40%), Positives = 53/85 (62%)

Query:   186 THGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIA 245
             T  +KG KV+LT+R  +V    M +  +  +  L EE+AW LF K AGD +     + IA
Sbjct:   270 TEENKGSKVILTSRFLEVCRS-MKTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIA 328

Query:   246 RDVAKECAGLPVSIVTIARALRNKR 270
             + V++EC GLP++I+T+  A+R K+
Sbjct:   329 KAVSQECGGLPLAIITVGTAMRGKK 353

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

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

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 166 (63.5 bits), Expect = 1.1e-18, Sum P(3) = 1.1e-18
 Identities = 36/87 (41%), Positives = 50/87 (57%)

Query:   190 KGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVA 249
             K  KV+LT+R  +V   +M +  N  +  L E+EAW LF    G+       + IA+DV+
Sbjct:   244 KDSKVVLTSRRLEVCQ-QMMTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVS 302

Query:   250 KECAGLPVSIVTIARALRNKRLFE-WK 275
              EC GLP++I+TI R LR K   E WK
Sbjct:   303 HECCGLPLAIITIGRTLRGKPQVEVWK 329

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2093192 AT3G15700 [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 6.9e-18, Sum P(2) = 6.9e-18
 Identities = 41/161 (25%), Positives = 81/161 (50%)

Query:    30 SKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARANNVIEAADNFT 89
             S  +SN  ++ S    L  +  +   +V E K +G   +  VEN    + +++    N  
Sbjct:    81 SSSSSNGSSMMS-FHKLDKKLCKKLKEVQEIKSRGT-FDVVVENSGIGSGSMM--ISNVD 136

Query:    90 KDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL--FDQVV 147
             +D+ T       G +   +   +  ++G+YG+ G+GKT +  ++  ++   KL  FD V+
Sbjct:   137 RDDQTVGLEAVSGLVWRCMTVDNTGIIGLYGVEGVGKTTVLTQVNNRLLQHKLNGFDFVI 196

Query:   148 FVEVSQNQDIRKIQEEIGDKLGL---KFHEESESGRANSLF 185
             +V VS+N ++ KIQ+ I +K+G     +  ++E  +A  +F
Sbjct:   197 WVFVSKNVNLEKIQDTIREKIGFLDRSWMSKTEEEKAGKIF 237

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 148 (57.2 bits), Expect = 8.7e-18, Sum P(2) = 8.7e-18
 Identities = 34/71 (47%), Positives = 47/71 (66%)

Query:   108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKV-KSDKLFDQVVFVEVSQNQDIRKIQEEIGD 166
             +ED    +LG+YGMGG+GKT L  +I  K  K D  FD V++V VS++  +RKIQ +I +
Sbjct:   172 MEDGS-GILGLYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAE 230

Query:   167 KLGLKFHEESE 177
             K+GL   E SE
Sbjct:   231 KVGLGGMEWSE 241

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

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

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

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008219 "cell death" evidence=IMP

GO:0038023 "signaling receptor activity" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IMP

GO:0005622 "intracellular" evidence=ISS

TAIR|locus:2203881 AT1G62630 [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 2.2e-17, Sum P(3) = 2.2e-17
 Identities = 31/68 (45%), Positives = 43/68 (63%)

Query:   108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL-FDQVVFVEVSQNQDIRKIQEEIGD 166
             +ED    ++G+YGMGG+GKT L  ++      DK  FD  ++V VSQ  ++ KIQ+EI  
Sbjct:   168 MED-GTGIMGMYGMGGVGKTTLLTQLFNMFNKDKCGFDIGIWVVVSQEVNVEKIQDEIAQ 226

Query:   167 KLGLKFHE 174
             KLGL  HE
Sbjct:   227 KLGLGGHE 234

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 144 (55.7 bits), Expect = 2.3e-16, Sum P(2) = 2.3e-16
 Identities = 34/82 (41%), Positives = 53/82 (64%)

Query:   104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV-KSDKLFDQVVFVEVSQNQDIRKIQE 162
             + + L +  V ++G+YGMGG+GKT L  +I  K  K    FD V++V VS+N  + KIQ+
Sbjct:   167 VWNCLMEDKVWIVGLYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQK 226

Query:   163 EIGDKLGL---KFHEESESGRA 181
              IG+KLGL    + E++++ RA
Sbjct:   227 SIGEKLGLVGKNWDEKNKNQRA 248

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009617 "response to bacterium" evidence=ISS

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

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

 Score = 142 (55.0 bits), Expect = 3.0e-16, Sum P(3) = 3.0e-16
 Identities = 31/94 (32%), Positives = 50/94 (53%)

Query:   185 FTHGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS--EFQ 242
             F     GCK++ T R +++  G+M    +  +  L  ++AW LF K  G+    S  E  
Sbjct:   278 FPSRENGCKIVFTTRLKEIC-GRMGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIP 336

Query:   243 SIARDVAKECAGLPVSIVTIARALRNKRLF-EWK 275
             ++AR VAK+C GLP+++  I   +  KR   EW+
Sbjct:   337 TVARTVAKKCRGLPLALNVIGETMAYKRTVQEWR 370

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 140 (54.3 bits), Expect = 4.4e-16, Sum P(3) = 4.4e-16
 Identities = 33/78 (42%), Positives = 49/78 (62%)

Query:   108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL-FDQVVFVEVSQNQDIRKIQEEIGD 166
             L D  V  +G+YGMGG+GKT L  +I   +   K   D V++V VS +  I KIQE+IG+
Sbjct:   168 LMDDGVGTMGLYGMGGVGKTTLLTQIHNTLHDTKNGVDIVIWVVVSSDLQIHKIQEDIGE 227

Query:   167 KLGL---KFHEESESGRA 181
             KLG    +++++ ES +A
Sbjct:   228 KLGFIGKEWNKKQESQKA 245

GO:0000166 "nucleotide binding" evidence=IEA

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

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 146 (56.5 bits), Expect = 5.0e-16, Sum P(2) = 5.0e-16
 Identities = 45/137 (32%), Positives = 74/137 (54%)

Query:    65 EEIEE--NVENWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMG 122
             EE++E  + +N+   A  +I  A+     + T       G    +L D ++  LG+YGMG
Sbjct:   123 EEVKELLSKKNFEVVAQKIIPKAEK-KHIQTTVGLDTMVGIAWESLIDDEIRTLGLYGMG 181

Query:   123 GIGKTMLAEEIARK-VKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKL--GLKFHEESESG 179
             GIGKT L E +  K V+ +  FD V++V VS++  +  IQ++I  +L    ++  E+ES 
Sbjct:   182 GIGKTTLLESLNNKFVELESEFDVVIWVVVSKDFQLEGIQDQILGRLRPDKEWERETESK 241

Query:   180 RANSLFTHGHKGCKVLL 196
             +A SL  +  K  K +L
Sbjct:   242 KA-SLINNNLKRKKFVL 257

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2197739 AT1G61300 [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 9.9e-16, Sum P(2) = 9.9e-16
 Identities = 31/87 (35%), Positives = 45/87 (51%)

Query:   192 CKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYI--EDSEFQSIARDVA 249
             CKV  T R Q V     D +P   +  L  E+AW LFK   GD     D     +AR+VA
Sbjct:   172 CKVAFTTRDQKVCGEMGDHKP-MQVKCLEPEDAWELFKNKVGDNTLRSDPVIVELAREVA 230

Query:   250 KECAGLPVSIVTIARALRNKRLF-EWK 275
             ++C GLP+++  I   + +K +  EW+
Sbjct:   231 QKCRGLPLALSVIGETMASKTMVQEWE 257

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00007117001 SubName- Full=Chromosome undetermined scaffold_183, whole genome shotgun sequence; (923 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	276
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	9e-26
pfam13401	124	pfam13401, AAA_22, AAA domain	0.001

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

 Score =  102 bits (256), Expect = 9e-26
 Identities = 52/202 (25%), Positives = 87/202 (43%), Gaps = 34/202 (16%)

Query: 109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKL 168
              ++ ++GI GMGG+GKT LA++I         FD V +V VS+     ++Q++I  +L
Sbjct: 15  MSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQEL 74

Query: 169 GL-----KFHEESESG--------RANSL------------------FTHGHKGCKVLLT 197
           GL         ESE          R   L                  F  G  G +V++T
Sbjct: 75  GLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKIGVPFPDGENGSRVIVT 134

Query: 198 ARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQSIARDVAKECAGL 255
            RS+ V      +     +  L  EE+W LF       +     E + +A+++ ++C GL
Sbjct: 135 TRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPELEEVAKEIVEKCKGL 194

Query: 256 PVSIVTIARALRNKR-LFEWKD 276
           P+++  +   L  K  + EW+ 
Sbjct: 195 PLALKVLGGLLAFKSTVQEWEH 216

Length = 285

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 4/60 (6%)

Query: 118 IYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESE 177
           + G  G GKT L   +AR++ +     +VV+VE       + +  +I   LGL     + 
Sbjct: 9   LTGESGSGKTTLLRRLARQLPN----RRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTT 64

Length = 124

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	276
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.96
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.94
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.99
PF05729	166	NACHT: NACHT domain	98.87
PRK04841	903	transcriptional regulator MalT; Provisional	98.7
PRK06893	229	DNA replication initiation factor; Validated	98.52
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.48
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.43
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.42
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.41
PRK13342	413	recombination factor protein RarA; Reviewed	98.4
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.35
KOG2028	554	consensus ATPase related to the helicase subunit o	98.29
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.29
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.28
cd01128	249	rho_factor Transcription termination factor rho is	98.25
PRK09376	416	rho transcription termination factor Rho; Provisio	98.19
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.18
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.16
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.14
PRK08084	235	DNA replication initiation factor; Provisional	98.11
COG3903	414	Predicted ATPase [General function prediction only	98.07
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.06
PRK12402	337	replication factor C small subunit 2; Reviewed	98.05
PLN03025	319	replication factor C subunit; Provisional	98.03
PF13173	128	AAA_14: AAA domain	98.03
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.01
PRK09087	226	hypothetical protein; Validated	98.0
PRK08118	167	topology modulation protein; Reviewed	97.97
PRK05642	234	DNA replication initiation factor; Validated	97.97
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.95
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.9
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.88
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.86
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.86
PRK13341	725	recombination factor protein RarA/unknown domain f	97.85
PRK08727	233	hypothetical protein; Validated	97.82
TIGR00767	415	rho transcription termination factor Rho. Members	97.82
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.82
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.82
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.79
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.79
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.74
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.68
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.68
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.64
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.62
PRK07261	171	topology modulation protein; Provisional	97.62
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.62
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.58
PRK04195	482	replication factor C large subunit; Provisional	97.57
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.56
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.56
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.55
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.55
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.54
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.53
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.53
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.5
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.48
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.48
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.48
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.46
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.46
PTZ00202	550	tuzin; Provisional	97.44
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.44
PRK08181	269	transposase; Validated	97.44
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.43
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.42
PRK06620	214	hypothetical protein; Validated	97.39
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.38
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.38
CHL00181	287	cbbX CbbX; Provisional	97.38
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.37
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.36
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.34
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.32
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.31
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.28
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.28
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.25
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.25
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.23
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	97.22
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.21
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.21
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.2
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.2
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.18
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.16
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.16
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.16
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.15
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.15
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.11
PRK05541	176	adenylylsulfate kinase; Provisional	97.1
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.08
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.08
PHA00729	226	NTP-binding motif containing protein	97.07
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.07
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.06
PF00004	132	AAA: ATPase family associated with various cellula	97.05
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.05
PRK06547	172	hypothetical protein; Provisional	97.05
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.04
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.04
PRK14974	336	cell division protein FtsY; Provisional	97.03
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	97.03
PRK08233	182	hypothetical protein; Provisional	97.01
PRK06762	166	hypothetical protein; Provisional	97.01
PRK05480	209	uridine/cytidine kinase; Provisional	97.0
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.0
CHL00195	489	ycf46 Ycf46; Provisional	97.0
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.99
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.98
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.97
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.96
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.95
smart00382	148	AAA ATPases associated with a variety of cellular	96.95
PTZ00301	210	uridine kinase; Provisional	96.94
PRK06696	223	uridine kinase; Validated	96.94
PHA02544	316	44 clamp loader, small subunit; Provisional	96.94
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.93
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.93
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.92
PRK12422	445	chromosomal replication initiation protein; Provis	96.92
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.91
PRK03839	180	putative kinase; Provisional	96.89
PRK10416	318	signal recognition particle-docking protein FtsY;	96.88
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.86
PRK08116	268	hypothetical protein; Validated	96.86
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.84
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.82
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.81
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.79
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.79
PRK04040	188	adenylate kinase; Provisional	96.78
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.78
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.77
CHL00176	638	ftsH cell division protein; Validated	96.77
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.75
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.75
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.75
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.74
PRK10867	433	signal recognition particle protein; Provisional	96.73
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.73
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.73
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.72
PRK00131	175	aroK shikimate kinase; Reviewed	96.71
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.71
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.7
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	96.7
PRK09183	259	transposase/IS protein; Provisional	96.69
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.68
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	96.67
PRK07667	193	uridine kinase; Provisional	96.65
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.65
PRK00625	173	shikimate kinase; Provisional	96.65
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.64
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.61
TIGR00959	428	ffh signal recognition particle protein. This mode	96.61
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.6
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	96.6
PRK06217	183	hypothetical protein; Validated	96.59
PF14516	331	AAA_35: AAA-like domain	96.59
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.59
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.58
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.58
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.58
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.57
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.57
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.56
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.55
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.54
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.53
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	96.53
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	96.53
PRK06526	254	transposase; Provisional	96.52
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.52
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.51
PRK06851	367	hypothetical protein; Provisional	96.51
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.51
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	96.5
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.49
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.49
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	96.48
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	96.47
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.47
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.47
PRK05439	311	pantothenate kinase; Provisional	96.47
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.47
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	96.47
PRK13949	169	shikimate kinase; Provisional	96.47
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	96.47
PRK13947	171	shikimate kinase; Provisional	96.46
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.43
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.43
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	96.43
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.43
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.43
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.43
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.42
PRK14530	215	adenylate kinase; Provisional	96.42
PRK07952	244	DNA replication protein DnaC; Validated	96.41
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.41
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.41
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.41
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.4
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	96.39
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.38
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.37
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	96.37
PF07726	131	AAA_3: ATPase family associated with various cellu	96.36
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.36
PRK00889	175	adenylylsulfate kinase; Provisional	96.36
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.35
PRK04182	180	cytidylate kinase; Provisional	96.35
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	96.35
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.35
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.35
PRK13975	196	thymidylate kinase; Provisional	96.33
PRK00300	205	gmk guanylate kinase; Provisional	96.32
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.32
PRK14527	191	adenylate kinase; Provisional	96.3
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.29
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	96.29
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.28
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.27
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	96.27
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.27
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.24
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	96.23
PRK12608	380	transcription termination factor Rho; Provisional	96.2
PRK14737	186	gmk guanylate kinase; Provisional	96.2
PRK03846	198	adenylylsulfate kinase; Provisional	96.19
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	96.19
TIGR00450	442	mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE	96.18
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.18
PRK05057	172	aroK shikimate kinase I; Reviewed	96.17
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.16
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.16
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.16
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.16
PF13245	76	AAA_19: Part of AAA domain	96.16
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.15
PRK12377	248	putative replication protein; Provisional	96.15
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	96.14
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	96.14
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.12
PLN02200	234	adenylate kinase family protein	96.12
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.11
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.11
COG4778	235	PhnL ABC-type phosphonate transport system, ATPase	96.1
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.1
PRK14738	206	gmk guanylate kinase; Provisional	96.09
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.09
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	96.09
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.09
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.09
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.08
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.07
PRK14531	183	adenylate kinase; Provisional	96.02
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	96.02
PRK13946	184	shikimate kinase; Provisional	96.02
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.0
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.99
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.98
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	95.98
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.98
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.97
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.97
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.96
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.96
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	95.95
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.95
PRK13948	182	shikimate kinase; Provisional	95.94
PRK14532	188	adenylate kinase; Provisional	95.94
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.93
PRK09825	176	idnK D-gluconate kinase; Provisional	95.92
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.92
cd03116	159	MobB Molybdenum is an essential trace element in t	95.91
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.91
COG3899	849	Predicted ATPase [General function prediction only	95.91
PRK13695	174	putative NTPase; Provisional	95.9
PRK00698	205	tmk thymidylate kinase; Validated	95.9
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.89
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	95.88
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.87
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.87
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	95.86
PRK06761	282	hypothetical protein; Provisional	95.86
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.86
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.85
PTZ00088	229	adenylate kinase 1; Provisional	95.84
PHA02530	300	pseT polynucleotide kinase; Provisional	95.83
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.83
PRK01184	184	hypothetical protein; Provisional	95.83
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	95.83
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.83
PRK08356	195	hypothetical protein; Provisional	95.83
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	95.81
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.81
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.81
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	95.8
PLN02348	395	phosphoribulokinase	95.8
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.78
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.77
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.77
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.77
PRK02496	184	adk adenylate kinase; Provisional	95.76
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.76
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	95.75
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	95.75
PRK04220	301	2-phosphoglycerate kinase; Provisional	95.75
COG4133	209	CcmA ABC-type transport system involved in cytochr	95.74
cd03269	210	ABC_putative_ATPase This subfamily is involved in	95.72
PRK08099	399	bifunctional DNA-binding transcriptional repressor	95.72
PLN02796	347	D-glycerate 3-kinase	95.71
PRK00279	215	adk adenylate kinase; Reviewed	95.71
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.7
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.7
PRK03731	171	aroL shikimate kinase II; Reviewed	95.7
PRK13236	296	nitrogenase reductase; Reviewed	95.69
PRK14528	186	adenylate kinase; Provisional	95.69
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	95.68
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.68
PRK13230	279	nitrogenase reductase-like protein; Reviewed	95.66
PLN02924	220	thymidylate kinase	95.66
PLN02165	334	adenylate isopentenyltransferase	95.65
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	95.63
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	95.62
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	95.61
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.61
PRK10536	262	hypothetical protein; Provisional	95.61
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	95.59
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	95.59
COG4136	213	ABC-type uncharacterized transport system, ATPase	95.58
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	95.58
cd03114	148	ArgK-like The function of this protein family is u	95.58
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	95.57
PF00142	273	Fer4_NifH: 4Fe-4S iron sulfur cluster binding prot	95.57
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	95.57
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	95.55
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	95.55
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	95.55
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	95.55
COG1100	219	GTPase SAR1 and related small G proteins [General	95.55
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.55
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	95.54
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.54
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	95.54
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	95.53
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	95.52
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	95.51
PRK15453	290	phosphoribulokinase; Provisional	95.51
cd02117	212	NifH_like This family contains the NifH (iron prot	95.51
cd02040	270	NifH NifH gene encodes component II (iron protein)	95.5
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	95.5
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	95.5
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	95.49
PRK12338	319	hypothetical protein; Provisional	95.48
PRK05973	237	replicative DNA helicase; Provisional	95.47
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	95.47
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	95.47
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	95.45
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	95.45
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	95.45
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	95.45
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	95.44
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	95.43
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.43
PRK06835	329	DNA replication protein DnaC; Validated	95.43
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	95.42
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	95.42
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	95.41
COG1127	263	Ttg2A ABC-type transport system involved in resist	95.41
PRK06067	234	flagellar accessory protein FlaH; Validated	95.41
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	95.4
PRK13973	213	thymidylate kinase; Provisional	95.4
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	95.4
PLN02318	656	phosphoribulokinase/uridine kinase	95.4
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.4
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	95.4
PRK09354	349	recA recombinase A; Provisional	95.39
PRK06851	367	hypothetical protein; Provisional	95.39
PRK13768	253	GTPase; Provisional	95.38
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.38
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	95.37
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	95.37
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	95.37
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	95.37
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	95.36
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.36
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	95.36
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	95.36
PRK05291	449	trmE tRNA modification GTPase TrmE; Reviewed	95.36
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	95.35
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	95.35
TIGR00101	199	ureG urease accessory protein UreG. This model rep	95.35
COG4619	223	ABC-type uncharacterized transport system, ATPase	95.35
PRK04328	249	hypothetical protein; Provisional	95.34
PRK07933	213	thymidylate kinase; Validated	95.34
cd03246	173	ABCC_Protease_Secretion This family represents the	95.34
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.33
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	95.32
PRK15455	644	PrkA family serine protein kinase; Provisional	95.31
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	95.31
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	95.3
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	95.3
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	95.3
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.3
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	95.3
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	95.3
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	95.3
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	95.3
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	95.3
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.3
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	95.3
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	95.29
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	95.28
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	95.28
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	95.28
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	95.28
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	95.27
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	95.27
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	95.27
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	95.27
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	95.27
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.25
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	95.25
COG3638	258	ABC-type phosphate/phosphonate transport system, A	95.24
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.24
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	95.23
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	95.23
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.23
COG2884	223	FtsE Predicted ATPase involved in cell division [C	95.22
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	95.22
PRK10908	222	cell division protein FtsE; Provisional	95.22
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	95.21
cd01673	193	dNK Deoxyribonucleoside kinase (dNK) catalyzes the	95.21
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	95.2
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	95.2
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	95.2
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	95.2
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	95.19
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	95.19
PLN03046	460	D-glycerate 3-kinase; Provisional	95.19
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	95.18
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	95.18
TIGR00972	247	3a0107s01c2 phosphate ABC transporter, ATP-binding	95.17
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	95.17
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	95.17
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	95.17
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.17
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	95.17
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	95.16
PRK13232	273	nifH nitrogenase reductase; Reviewed	95.16
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	95.16
PRK13976	209	thymidylate kinase; Provisional	95.15
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.15
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	95.15
TIGR02324	224	CP_lyasePhnL phosphonate C-P lyase system protein	95.15
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	95.15
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	95.14
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	95.13
COG0410	237	LivF ABC-type branched-chain amino acid transport	95.13
PTZ00035	337	Rad51 protein; Provisional	95.12
cd02032	267	Bchl_like This family of proteins contains bchL an	95.12
smart00178	184	SAR Sar1p-like members of the Ras-family of small	95.12
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	95.12
TIGR01281	268	DPOR_bchL light-independent protochlorophyllide re	95.11
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	95.11
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	95.11
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.1
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	95.1
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	95.1
PRK09984	262	phosphonate/organophosphate ester transporter subu	95.09
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	95.08
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	95.08
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	95.07
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	95.06
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	95.06
cd02034	116	CooC The accessory protein CooC, which contains a	95.06
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.06
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	95.06
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	95.05
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	95.05
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.05
PRK13531	498	regulatory ATPase RavA; Provisional	95.05
cd03234	226	ABCG_White The White subfamily represents ABC tran	95.04
COG1084	346	Predicted GTPase [General function prediction only	95.04
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	95.04
cd03215	182	ABC_Carb_Monos_II This family represents domain II	95.04
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.03
PF13479	213	AAA_24: AAA domain	95.03
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	95.02
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	95.02
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	95.01

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.4e-37  Score=290.68  Aligned_cols=238  Identities=31%  Similarity=0.517  Sum_probs=193.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHhhhhhhhhhhc-----------------cccc
Q 041612           38 NLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARANNVIEAADNFTKDEATTN-----------------KRCF  100 (276)
Q Consensus        38 ~l~~~l~~l~~~l~~i~~~~~~a~~~~~~~~~~~~~wl~~l~~~~~~~ed~ld~~~~~~-----------------~~~~  100 (276)
                      ..++.+..|++.+..++.+++|+++++.. ...+..|.+.+++++|+++++++.+....                 .-|+
T Consensus        25 ~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~-~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~c~  103 (889)
T KOG4658|consen   25 GKDNYILELKENLKALQSALEDLDAKRDD-LERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKANDLLSTRSVERQRLCL  103 (889)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhhcch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHhh
Confidence            44556777888888888888888888765 77888899999999999999887543211                 0011


Q ss_pred             hH---------------------------------------------------------------HHHHhhcCCCccEEE
Q 041612          101 KG---------------------------------------------------------------NILSALEDPDVNMLG  117 (276)
Q Consensus       101 ~~---------------------------------------------------------------~l~~~L~~~~~~vi~  117 (276)
                      .+                                                               ++.+.|.+++..+++
T Consensus       104 ~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~~~~VG~e~~~~kl~~~L~~d~~~iv~  183 (889)
T KOG4658|consen  104 CGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSESDVGLETMLEKLWNRLMEDDVGIVG  183 (889)
T ss_pred             hhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCccccccHHHHHHHHHHHhccCCCCEEE
Confidence            11                                                               677777777789999


Q ss_pred             EEcCCCCcHHHHHHHHHHhcc-cCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcccc---cchhhhhhccc-------
Q 041612          118 IYGMGGIGKTMLAEEIARKVK-SDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEE---SESGRANSLFT-------  186 (276)
Q Consensus       118 I~G~gGiGKTtLa~~v~~~~~-~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~l~~-------  186 (276)
                      |+||||+||||||++++|+.. ..++|+.++||++|+.++...++++|+..++......   ........+.+       
T Consensus       184 i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krf  263 (889)
T KOG4658|consen  184 IYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRF  263 (889)
T ss_pred             EECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCce
Confidence            999999999999999999998 8899999999999999999999999999888743322   11222222222       


Q ss_pred             ---------------------cCCCCcEEEEEeccccccccCCCCCCceeCCCCCHHHHHHHHHHhhCC--CCCChhHHH
Q 041612          187 ---------------------HGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGD--YIEDSEFQS  243 (276)
Q Consensus       187 ---------------------~~~~gs~IivTTR~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~~  243 (276)
                                           ....||+|++|||+..|+...++....+++++|.++|||.||.+.+|.  ....+.+.+
T Consensus       264 llvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~  343 (889)
T KOG4658|consen  264 LLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEE  343 (889)
T ss_pred             EEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccccccccHHH
Confidence                                 345679999999999998776888889999999999999999999983  334455899


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHh-CCCccccCC
Q 041612          244 IARDVAKECAGLPVSIVTIARALR-NKRLFEWKD  276 (276)
Q Consensus       244 ~~~~i~~~c~G~PLai~~i~~~L~-~~~~~~W~~  276 (276)
                      ++++|+++|+|+|||+.+||+.|+ +.+++||++
T Consensus       344 lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~  377 (889)
T KOG4658|consen  344 LAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRR  377 (889)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHH
Confidence            999999999999999999999999 999999973

>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=99.96  E-value=5.6e-30  Score=217.82  Aligned_cols=173  Identities=32%  Similarity=0.511  Sum_probs=132.1

Q ss_pred             HHHHhhcC--CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcccc----c
Q 041612          103 NILSALED--PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEE----S  176 (276)
Q Consensus       103 ~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~----~  176 (276)
                      +|.+.|..  ++.++|+|+|+||+||||||..++++...+.+|+.++|++++...+...++..|+.+++......    .
T Consensus         7 ~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~   86 (287)
T PF00931_consen    7 KLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKD   86 (287)
T ss_dssp             HHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSS
T ss_pred             HHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            66677766  78999999999999999999999999666777999999999999999999999999998773321    1


Q ss_pred             chhhhhhccc----------------------------cCCCCcEEEEEeccccccccCCCCCCceeCCCCCHHHHHHHH
Q 041612          177 ESGRANSLFT----------------------------HGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLF  228 (276)
Q Consensus       177 ~~~~~~~l~~----------------------------~~~~gs~IivTTR~~~va~~~~~~~~~~~l~~L~~~ea~~Lf  228 (276)
                      .......+..                            ....||+||||||+..++.........+++++|++++|++||
T Consensus        87 ~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~  166 (287)
T PF00931_consen   87 IEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELF  166 (287)
T ss_dssp             HHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHH
T ss_pred             cccccccchhhhccccceeeeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            1111111111                            345689999999999987543333678999999999999999


Q ss_pred             HHhhCCC--CCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh-CCCccccC
Q 041612          229 KKMAGDY--IEDSEFQSIARDVAKECAGLPVSIVTIARALR-NKRLFEWK  275 (276)
Q Consensus       229 ~~~~~~~--~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~-~~~~~~W~  275 (276)
                      .+.++..  ..++.+.+.+++|+++|+|+|||++++|++|+ +.++.+|+
T Consensus       167 ~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~  216 (287)
T PF00931_consen  167 KKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWE  216 (287)
T ss_dssp             HHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            9999833  24455667899999999999999999999997 44788886

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=99.94  E-value=1.4e-25  Score=221.54  Aligned_cols=234  Identities=19%  Similarity=0.337  Sum_probs=151.7

Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHH------------------HHHHHHhhhhhh
Q 041612           30 SKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARAN------------------NVIEAADNFTKD   91 (276)
Q Consensus        30 ~~~~~~~~~l~~~l~~l~~~l~~i~~~~~~a~~~~~~~~~~~~~wl~~l~------------------~~~~~~ed~ld~   91 (276)
                      .-|..+..+++.+...+...+.....       .  ...+.++.|...+.                  -+.+.++|+++.
T Consensus       104 vfy~v~p~~v~~~~g~f~~~f~~~~~-------~--~~~~~~~~w~~al~~~~~~~g~~~~~~~~E~~~i~~Iv~~v~~~  174 (1153)
T PLN03210        104 VFYGLDPSHVRKQTGDFGEAFEKTCQ-------N--KTEDEKIQWKQALTDVANILGYHSQNWPNEAKMIEEIANDVLGK  174 (1153)
T ss_pred             EEecccHHHHhhccchHHHHHHHHhc-------c--cchhHHHHHHHHHHHHhCcCceecCCCCCHHHHHHHHHHHHHHh
Confidence            55555666666666666555443211       0  11233445554444                  444455555554


Q ss_pred             hhhhcc---ccchH------HHHHhh--cCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe---cCc---
Q 041612           92 EATTNK---RCFKG------NILSAL--EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV---SQN---  154 (276)
Q Consensus        92 ~~~~~~---~~~~~------~l~~~L--~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~---~~~---  154 (276)
                      ......   ..+.|      ++..+|  ..++.++|+|+||||+||||||+.+|+....+  |+..+|+..   +..   
T Consensus       175 l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~--F~g~vfv~~~~v~~~~~~  252 (1153)
T PLN03210        175 LNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQ--FQSSVFIDRAFISKSMEI  252 (1153)
T ss_pred             hccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhc--CCeEEEeeccccccchhh
Confidence            432221   22222      555554  34678999999999999999999999988765  998888742   111   


Q ss_pred             --------CC-HHHHHHHHHHHh----CCCc-------------------ccccchhhhhhcc---ccCCCCcEEEEEec
Q 041612          155 --------QD-IRKIQEEIGDKL----GLKF-------------------HEESESGRANSLF---THGHKGCKVLLTAR  199 (276)
Q Consensus       155 --------~~-~~~l~~~i~~~l----~~~~-------------------~~~~~~~~~~~l~---~~~~~gs~IivTTR  199 (276)
                              ++ ...+...++..+    +...                   ++.+....+..+.   ...++||+||||||
T Consensus       253 ~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTr  332 (1153)
T PLN03210        253 YSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITK  332 (1153)
T ss_pred             cccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeC
Confidence                    01 122333333322    1111                   1111111122221   14578999999999


Q ss_pred             cccccccCCCCCCceeCCCCCHHHHHHHHHHhhC-CCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCccccC
Q 041612          200 SQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG-DYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWK  275 (276)
Q Consensus       200 ~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~-~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~~~~~~~W~  275 (276)
                      +..++.. .+..+.|+++.|++++||+||+++|| ...+++++.+++++|+++|+|+|||++++|++|+.++..+|+
T Consensus       333 d~~vl~~-~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~  408 (1153)
T PLN03210        333 DKHFLRA-HGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWM  408 (1153)
T ss_pred             cHHHHHh-cCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHH
Confidence            9999753 45668999999999999999999998 344556788999999999999999999999999988889996

syringae 6; Provisional

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

Probab=98.99  E-value=2.5e-08  Score=83.97  Aligned_cols=154  Identities=15%  Similarity=0.203  Sum_probs=93.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcccccchhhhhhcc----
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEESESGRANSLF----  185 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~----  185 (276)
                      ..+...+.|+|++|+|||||++.+++...... + ..+|+ .....+..+++..|+..++.+............+.    
T Consensus        40 ~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~-~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~  116 (269)
T TIGR03015        40 SQREGFILITGEVGAGKTTLIRNLLKRLDQER-V-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLI  116 (269)
T ss_pred             hcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCC-e-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHH
Confidence            34456899999999999999999998876431 1 22333 23344667788888888876543221111111110    


Q ss_pred             ----c------------------------------cCCCCcEEEEEeccccc--ccc-C-----CCCCCceeCCCCCHHH
Q 041612          186 ----T------------------------------HGHKGCKVLLTARSQDV--LSG-K-----MDSRPNFSIGVLNEEE  223 (276)
Q Consensus       186 ----~------------------------------~~~~gs~IivTTR~~~v--a~~-~-----~~~~~~~~l~~L~~~e  223 (276)
                          .                              .......|++|....-.  ... .     ......+++++|+.+|
T Consensus       117 ~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e  196 (269)
T TIGR03015       117 EQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREE  196 (269)
T ss_pred             HHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHH
Confidence                0                              11122244555433211  000 0     0112357899999999


Q ss_pred             HHHHHHHhhCC--CC-CChhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 041612          224 AWSLFKKMAGD--YI-EDSEFQSIARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       224 a~~Lf~~~~~~--~~-~~~~~~~~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      ...++...+..  .. ...-..+..+.|++.++|.|..+..++..+
T Consensus       197 ~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       197 TREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            99999877641  11 112234678899999999999999999887

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.

>PF05729 NACHT: NACHT domain

Probab=98.87  E-value=2e-08  Score=77.91  Aligned_cols=119  Identities=20%  Similarity=0.310  Sum_probs=74.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCC----CCeEEEEEecCcCCHH---HHHHHHHHHhCCCc--------------
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKL----FDQVVFVEVSQNQDIR---KIQEEIGDKLGLKF--------------  172 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----f~~~~wv~~~~~~~~~---~l~~~i~~~l~~~~--------------  172 (276)
                      |++.|+|.+|+||||+++.++........    +...+|.+.+......   .+...|..+.....              
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKN   80 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcC
Confidence            57899999999999999999988876643    3456777666543322   23333322221110              


Q ss_pred             ----------ccccc--h--------hhhhhccc-cCCCCcEEEEEeccccc--cccCCCCCCceeCCCCCHHHHHHHHH
Q 041612          173 ----------HEESE--S--------GRANSLFT-HGHKGCKVLLTARSQDV--LSGKMDSRPNFSIGVLNEEEAWSLFK  229 (276)
Q Consensus       173 ----------~~~~~--~--------~~~~~l~~-~~~~gs~IivTTR~~~v--a~~~~~~~~~~~l~~L~~~ea~~Lf~  229 (276)
                                ++...  .        .....+.. ...+++++|||+|....  ..........+.+++|++++..++++
T Consensus        81 ~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  160 (166)
T PF05729_consen   81 KRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLR  160 (166)
T ss_pred             CceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHH
Confidence                      00000  0        00111111 34678999999998766  22233444689999999999999998


Q ss_pred             Hhh
Q 041612          230 KMA  232 (276)
Q Consensus       230 ~~~  232 (276)
                      +..
T Consensus       161 ~~f  163 (166)
T PF05729_consen  161 KYF  163 (166)
T ss_pred             HHh
Confidence            764

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.70  E-value=2.8e-07  Score=90.46  Aligned_cols=155  Identities=15%  Similarity=0.216  Sum_probs=99.3

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-CCHHHHHHHHHHHhCCCcccc-----
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-QDIRKIQEEIGDKLGLKFHEE-----  175 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~~-----  175 (276)
                      .|...|.. ...+++.|+|++|.||||++..+..+      ++.++|+++... .++..+...++..++......     
T Consensus        21 rl~~~l~~~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~   94 (903)
T PRK04841         21 RLLAKLSGANNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSE   94 (903)
T ss_pred             HHHHHHhcccCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhh
Confidence            66666654 35789999999999999999998742      236899999744 455666666655553111000     


Q ss_pred             --------cc-hhhh----hh-----------------------------ccccCCCCcEEEEEeccccccc--cCCCCC
Q 041612          176 --------SE-SGRA----NS-----------------------------LFTHGHKGCKVLLTARSQDVLS--GKMDSR  211 (276)
Q Consensus       176 --------~~-~~~~----~~-----------------------------l~~~~~~gs~IivTTR~~~va~--~~~~~~  211 (276)
                              .. ....    ..                             +.....++.++|||||...-..  ......
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~  174 (903)
T PRK04841         95 ALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRD  174 (903)
T ss_pred             hhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcC
Confidence                    00 0000    00                             0003466788999999853211  001112


Q ss_pred             CceeCC----CCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          212 PNFSIG----VLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       212 ~~~~l~----~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ....+.    +|+.+|+..||....+....    .+....|.+.|+|.|+++..++..++
T Consensus       175 ~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~----~~~~~~l~~~t~Gwp~~l~l~~~~~~  230 (903)
T PRK04841        175 QLLEIGSQQLAFDHQEAQQFFDQRLSSPIE----AAESSRLCDDVEGWATALQLIALSAR  230 (903)
T ss_pred             cceecCHHhCCCCHHHHHHHHHhccCCCCC----HHHHHHHHHHhCChHHHHHHHHHHHh
Confidence            345555    89999999999887653222    23467899999999999999987775

>PRK06893 DNA replication initiation factor; Validated

Probab=98.52  E-value=1e-06  Score=72.39  Aligned_cols=144  Identities=14%  Similarity=0.161  Sum_probs=81.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC----cccc---cchhh----h
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK----FHEE---SESGR----A  181 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~----~~~~---~~~~~----~  181 (276)
                      .+.+.++|++|+|||+|++.+++....+  ...+.|+++.....   ....+.+.+...    .++.   .....    .
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~~~~~--~~~~~y~~~~~~~~---~~~~~~~~~~~~dlLilDDi~~~~~~~~~~~~l  113 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNHYLLN--QRTAIYIPLSKSQY---FSPAVLENLEQQDLVCLDDLQAVIGNEEWELAI  113 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEeeHHHhhh---hhHHHHhhcccCCEEEEeChhhhcCChHHHHHH
Confidence            3578999999999999999999987554  33456776642211   111222222110    0000   00011    1


Q ss_pred             hhccc-cCCCCcEEEEEeccc----------cccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 041612          182 NSLFT-HGHKGCKVLLTARSQ----------DVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAK  250 (276)
Q Consensus       182 ~~l~~-~~~~gs~IivTTR~~----------~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~  250 (276)
                      -.+.. ....|+.+|++|.+.          .+.. .+.....++++++++++.++++.+.+..... .--+++..-|++
T Consensus       114 ~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~s-Rl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l-~l~~~v~~~L~~  191 (229)
T PRK06893        114 FDLFNRIKEQGKTLLLISADCSPHALSIKLPDLAS-RLTWGEIYQLNDLTDEQKIIVLQRNAYQRGI-ELSDEVANFLLK  191 (229)
T ss_pred             HHHHHHHHHcCCcEEEEeCCCChHHccccchhHHH-HHhcCCeeeCCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHH
Confidence            11111 223456666555443          2222 1334457899999999999999988862221 122356778888


Q ss_pred             HcCCCcHHHHHHH
Q 041612          251 ECAGLPVSIVTIA  263 (276)
Q Consensus       251 ~c~G~PLai~~i~  263 (276)
                      ++.|-.-.+..+-
T Consensus       192 ~~~~d~r~l~~~l  204 (229)
T PRK06893        192 RLDRDMHTLFDAL  204 (229)
T ss_pred             hccCCHHHHHHHH
Confidence            8887665554443

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

Probab=98.48  E-value=1.3e-06  Score=75.15  Aligned_cols=123  Identities=23%  Similarity=0.308  Sum_probs=78.0

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC----HHHHHHHHHHHhCC--------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD----IRKIQEEIGDKLGL--------  170 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~----~~~l~~~i~~~l~~--------  170 (276)
                      -|...+....+.-.-+||++|+||||||+.+.......  |     ..++...+    +..++..--+..+.        
T Consensus        38 ~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~--f-----~~~sAv~~gvkdlr~i~e~a~~~~~~gr~tiLfl  110 (436)
T COG2256          38 PLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAA--F-----EALSAVTSGVKDLREIIEEARKNRLLGRRTILFL  110 (436)
T ss_pred             hHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhCCc--e-----EEeccccccHHHHHHHHHHHHHHHhcCCceEEEE
Confidence            45555667788888999999999999999999866544  3     33333332    33333222222221        


Q ss_pred             CcccccchhhhhhccccCCCCcEEEE--Eecccccc--ccCCCCCCceeCCCCCHHHHHHHHHHhh
Q 041612          171 KFHEESESGRANSLFTHGHKGCKVLL--TARSQDVL--SGKMDSRPNFSIGVLNEEEAWSLFKKMA  232 (276)
Q Consensus       171 ~~~~~~~~~~~~~l~~~~~~gs~Iiv--TTR~~~va--~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  232 (276)
                      +....-+..+.+.+...-..|.-|+|  ||.|+...  ........++.+++|+.++..+++.+-+
T Consensus       111 DEIHRfnK~QQD~lLp~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~  176 (436)
T COG2256         111 DEIHRFNKAQQDALLPHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRAL  176 (436)
T ss_pred             ehhhhcChhhhhhhhhhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHH
Confidence            11112333444455557778887777  77777642  2234455689999999999999998843

>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=98.43  E-value=1.2e-06  Score=71.66  Aligned_cols=51  Identities=16%  Similarity=0.169  Sum_probs=31.0

Q ss_pred             CCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          211 RPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       211 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      ...+.+++|+.+++++++...+.....-+.-.+..++|...++|+|..|..
T Consensus       183 ~~~~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  183 FSHIELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             --EEEE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT-HHHHHH
T ss_pred             cceEEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCCHHHHhc
Confidence            345999999999999999987643211012244568999999999998764

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

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.42  E-value=1.4e-05  Score=71.05  Aligned_cols=156  Identities=20%  Similarity=0.164  Sum_probs=87.5

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC-cccc--cc---------
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK-FHEE--SE---------  177 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~-~~~~--~~---------  177 (276)
                      ......+.|+|++|+|||++++.++++.......-..++++.....+...++..|+.++... .+..  ..         
T Consensus        52 ~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~  131 (394)
T PRK00411         52 GSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAE  131 (394)
T ss_pred             CCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHH
Confidence            34456788999999999999999999886553223456666666666677777777766531 1000  00         


Q ss_pred             ------------hhhhhhcc------------c--cCCCCcE--EEEEeccccccccC------CCCCCceeCCCCCHHH
Q 041612          178 ------------SGRANSLF------------T--HGHKGCK--VLLTARSQDVLSGK------MDSRPNFSIGVLNEEE  223 (276)
Q Consensus       178 ------------~~~~~~l~------------~--~~~~gs~--IivTTR~~~va~~~------~~~~~~~~l~~L~~~e  223 (276)
                                  .+..+.+.            .  ...++++  +|.++....+....      .-....+.+++++.++
T Consensus       132 ~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e  211 (394)
T PRK00411        132 YLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADE  211 (394)
T ss_pred             HHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHH
Confidence                        00011111            0  1122334  56666554432210      0012357899999999


Q ss_pred             HHHHHHHhhC----CCCCChhH-HHHHHHHHHHcCCCcHHHHHHHHH
Q 041612          224 AWSLFKKMAG----DYIEDSEF-QSIARDVAKECAGLPVSIVTIARA  265 (276)
Q Consensus       224 a~~Lf~~~~~----~~~~~~~~-~~~~~~i~~~c~G~PLai~~i~~~  265 (276)
                      ..+++...+.    ....+++. ..+++......|..+.|+.++-..
T Consensus       212 ~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a  258 (394)
T PRK00411        212 IFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRA  258 (394)
T ss_pred             HHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            9999987763    11223332 222332323356678888776543

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.41  E-value=6e-06  Score=70.87  Aligned_cols=148  Identities=18%  Similarity=0.118  Sum_probs=80.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc----c--cccchhhhhhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF----H--EESESGRANSLF  185 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~----~--~~~~~~~~~~l~  185 (276)
                      .+..+.++|++|+|||+||+.+.+.....  +   .....+.......+ ...+..++...    +  +.-.......+.
T Consensus        29 ~~~~~ll~Gp~G~GKT~la~~ia~~~~~~--~---~~~~~~~~~~~~~l-~~~l~~~~~~~vl~iDEi~~l~~~~~e~l~  102 (305)
T TIGR00635        29 ALDHLLLYGPPGLGKTTLAHIIANEMGVN--L---KITSGPALEKPGDL-AAILTNLEEGDVLFIDEIHRLSPAVEELLY  102 (305)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhCCC--E---EEeccchhcCchhH-HHHHHhcccCCEEEEehHhhhCHHHHHHhh
Confidence            35568899999999999999999887543  2   11221111122222 12222222111    0  000000111111


Q ss_pred             c----------------------cCCCCcEEEEEeccccccccC-CCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHH
Q 041612          186 T----------------------HGHKGCKVLLTARSQDVLSGK-MDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ  242 (276)
Q Consensus       186 ~----------------------~~~~gs~IivTTR~~~va~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~  242 (276)
                      .                      ..++.+-|..||+...+.... ......+.+++++.++..+++.+.+..... .-..
T Consensus       103 ~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~-~~~~  181 (305)
T TIGR00635       103 PAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNV-EIEP  181 (305)
T ss_pred             HHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCC-CcCH
Confidence            0                      123345555667765443221 112346789999999999999988752111 1123


Q ss_pred             HHHHHHHHHcCCCcHHHHHHHHHH
Q 041612          243 SIARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      +....|++.|+|.|-.+..+...+
T Consensus       182 ~al~~ia~~~~G~pR~~~~ll~~~  205 (305)
T TIGR00635       182 EAALEIARRSRGTPRIANRLLRRV  205 (305)
T ss_pred             HHHHHHHHHhCCCcchHHHHHHHH
Confidence            456789999999997766555443

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.40  E-value=7.6e-06  Score=73.21  Aligned_cols=155  Identities=20%  Similarity=0.260  Sum_probs=85.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC----CHHHHHHHHHHHhC--CC----c
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ----DIRKIQEEIGDKLG--LK----F  172 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~----~~~~l~~~i~~~l~--~~----~  172 (276)
                      .+...+..+..+.+.++|++|+||||||+.+.+.....  |     +.++...    +...++........  ..    .
T Consensus        26 ~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~--~-----~~l~a~~~~~~~ir~ii~~~~~~~~~g~~~vL~I   98 (413)
T PRK13342         26 PLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP--F-----EALSAVTSGVKDLREVIEEARQRRSAGRRTILFI   98 (413)
T ss_pred             HHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhCCC--E-----EEEecccccHHHHHHHHHHHHHhhhcCCceEEEE
Confidence            35566666677788999999999999999999876543  3     2222211    22223222221111  00    0


Q ss_pred             cc--ccchhhhhhccccCCCCcEEEEE--ecccc--ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCC-CCC-hhHHHH
Q 041612          173 HE--ESESGRANSLFTHGHKGCKVLLT--ARSQD--VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDY-IED-SEFQSI  244 (276)
Q Consensus       173 ~~--~~~~~~~~~l~~~~~~gs~IivT--TR~~~--va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~-~~~-~~~~~~  244 (276)
                      ++  ..+......+......|..++|.  |.+..  +..........+.+.+++.++...++.+.+... ... .-..+.
T Consensus        99 DEi~~l~~~~q~~LL~~le~~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~a  178 (413)
T PRK13342         99 DEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEA  178 (413)
T ss_pred             echhhhCHHHHHHHHHHhhcCcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHH
Confidence            00  01111222222333345555553  44432  211122333578999999999999998876421 111 222456


Q ss_pred             HHHHHHHcCCCcHHHHHHHH
Q 041612          245 ARDVAKECAGLPVSIVTIAR  264 (276)
Q Consensus       245 ~~~i~~~c~G~PLai~~i~~  264 (276)
                      ...|++.|+|-|..+.-+..
T Consensus       179 l~~l~~~s~Gd~R~aln~Le  198 (413)
T PRK13342        179 LDALARLANGDARRALNLLE  198 (413)
T ss_pred             HHHHHHhCCCCHHHHHHHHH
Confidence            77889999999877654443

>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=98.35  E-value=1.2e-05  Score=64.70  Aligned_cols=150  Identities=19%  Similarity=0.160  Sum_probs=77.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC------cccccchhhhhhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK------FHEESESGRANSL  184 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~------~~~~~~~~~~~~l  184 (276)
                      +.+.-+.++|++|+||||||..+.+.....  |.   +.+.+......++ ..++..+...      ....-+....+.+
T Consensus        48 ~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~--~~---~~sg~~i~k~~dl-~~il~~l~~~~ILFIDEIHRlnk~~qe~L  121 (233)
T PF05496_consen   48 EALDHMLFYGPPGLGKTTLARIIANELGVN--FK---ITSGPAIEKAGDL-AAILTNLKEGDILFIDEIHRLNKAQQEIL  121 (233)
T ss_dssp             S---EEEEESSTTSSHHHHHHHHHHHCT----EE---EEECCC--SCHHH-HHHHHT--TT-EEEECTCCC--HHHHHHH
T ss_pred             CCcceEEEECCCccchhHHHHHHHhccCCC--eE---eccchhhhhHHHH-HHHHHhcCCCcEEEEechhhccHHHHHHH
Confidence            457789999999999999999999998865  42   3333221122222 2334443321      1111111111111


Q ss_pred             cc----------------------cCCCCcEEEEEeccccccccCCCCCC-ceeCCCCCHHHHHHHHHHhhCCCCCChhH
Q 041612          185 FT----------------------HGHKGCKVLLTARSQDVLSGKMDSRP-NFSIGVLNEEEAWSLFKKMAGDYIEDSEF  241 (276)
Q Consensus       185 ~~----------------------~~~~gs~IivTTR~~~va~~~~~~~~-~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~  241 (276)
                      ..                      ..++-+-|=-|||...+......-.. ..+++..+.+|-.++..+.+.--. .+-.
T Consensus       122 lpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~-i~i~  200 (233)
T PF05496_consen  122 LPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILN-IEID  200 (233)
T ss_dssp             HHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT--EE-
T ss_pred             HHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhC-CCcC
Confidence            11                      12223334458888766433222222 458999999999999988774111 1122


Q ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          242 QSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       242 ~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      .+.+.+|+.+|.|-|--+.-+-+..+
T Consensus       201 ~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  201 EDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            35688999999999976665554443

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.

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

Probab=98.29  E-value=5e-06  Score=70.84  Aligned_cols=125  Identities=18%  Similarity=0.224  Sum_probs=83.4

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc----------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF----------  172 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~----------  172 (276)
                      -|.+.++.+.++.+.+||++|+||||||+.+.+..+...    .+||..+-......-.+.|.++-....          
T Consensus       152 llrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq~~~~l~krkTilF  227 (554)
T KOG2028|consen  152 LLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQNEKSLTKRKTILF  227 (554)
T ss_pred             HHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHHHHHhhhcceeEEE
Confidence            666777778899999999999999999999998887653    677877766554444455544432110          


Q ss_pred             ---ccccchhhhhhccccCCCCcEEEE--Eecccccc--ccCCCCCCceeCCCCCHHHHHHHHHHh
Q 041612          173 ---HEESESGRANSLFTHGHKGCKVLL--TARSQDVL--SGKMDSRPNFSIGVLNEEEAWSLFKKM  231 (276)
Q Consensus       173 ---~~~~~~~~~~~l~~~~~~gs~Iiv--TTR~~~va--~~~~~~~~~~~l~~L~~~ea~~Lf~~~  231 (276)
                         ....+..+.+.+...-.+|+-++|  ||.|.+.-  ........++-|+.|+.++-..++.+-
T Consensus       228 iDEiHRFNksQQD~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~ra  293 (554)
T KOG2028|consen  228 IDEIHRFNKSQQDTFLPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRA  293 (554)
T ss_pred             eHHhhhhhhhhhhcccceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHH
Confidence               011122222333335667777776  78777642  223444567899999999999988763

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.29  E-value=1.5e-05  Score=69.12  Aligned_cols=148  Identities=17%  Similarity=0.051  Sum_probs=80.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc----c--cccchhhhhhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF----H--EESESGRANSLF  185 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~----~--~~~~~~~~~~l~  185 (276)
                      ..+.+.++|++|+|||+||+.+.+.....  +   .+.+.+.. .....+..++..+....    +  +.-.......+.
T Consensus        50 ~~~~~ll~GppG~GKT~la~~ia~~l~~~--~---~~~~~~~~-~~~~~l~~~l~~l~~~~vl~IDEi~~l~~~~~e~l~  123 (328)
T PRK00080         50 ALDHVLLYGPPGLGKTTLANIIANEMGVN--I---RITSGPAL-EKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILY  123 (328)
T ss_pred             CCCcEEEECCCCccHHHHHHHHHHHhCCC--e---EEEecccc-cChHHHHHHHHhcccCCEEEEecHhhcchHHHHHHH
Confidence            45678899999999999999999987543  2   11221111 11122223333332211    0  000000000110


Q ss_pred             c----------------------cCCCCcEEEEEeccccccccC-CCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHH
Q 041612          186 T----------------------HGHKGCKVLLTARSQDVLSGK-MDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ  242 (276)
Q Consensus       186 ~----------------------~~~~gs~IivTTR~~~va~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~  242 (276)
                      .                      ..++.+-|..||+...+.... ......+.++++++++..+++.+.+..... .--.
T Consensus       124 ~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~-~~~~  202 (328)
T PRK00080        124 PAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGV-EIDE  202 (328)
T ss_pred             HHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCC-CcCH
Confidence            0                      112334455666655442211 112346899999999999999988762211 1123


Q ss_pred             HHHHHHHHHcCCCcHHHHHHHHHH
Q 041612          243 SIARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      +....|++.|+|.|-.+..+...+
T Consensus       203 ~~~~~ia~~~~G~pR~a~~~l~~~  226 (328)
T PRK00080        203 EGALEIARRSRGTPRIANRLLRRV  226 (328)
T ss_pred             HHHHHHHHHcCCCchHHHHHHHHH
Confidence            468899999999997666555543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.28  E-value=5.4e-06  Score=67.86  Aligned_cols=156  Identities=13%  Similarity=0.159  Sum_probs=86.8

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC----cccc---
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK----FHEE---  175 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~----~~~~---  175 (276)
                      .+..++.....+.+.|+|.+|+|||+||+.+++.....  ....++++++.-.+..   ..++..+...    .++.   
T Consensus        28 ~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~--~~~~~~i~~~~~~~~~---~~~~~~~~~~~lLvIDdi~~l  102 (226)
T TIGR03420        28 ALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER--GKSAIYLPLAELAQAD---PEVLEGLEQADLVCLDDVEAI  102 (226)
T ss_pred             HHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc--CCcEEEEeHHHHHHhH---HHHHhhcccCCEEEEeChhhh
Confidence            45555445556789999999999999999999887543  3345566554332210   1222222110    0010   


Q ss_pred             cch-hhhhhccc----cCCCCcEEEEEecccccccc--------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHH
Q 041612          176 SES-GRANSLFT----HGHKGCKVLLTARSQDVLSG--------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ  242 (276)
Q Consensus       176 ~~~-~~~~~l~~----~~~~gs~IivTTR~~~va~~--------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~  242 (276)
                      ... .....+..    ....+.++|+||+.......        .......+.+.++++++...++...+.... .+--.
T Consensus       103 ~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~-~~~~~  181 (226)
T TIGR03420       103 AGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAARRG-LQLPD  181 (226)
T ss_pred             cCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHHcC-CCCCH
Confidence            000 00111111    12234578888875431110        111235688999999999999887653111 11122


Q ss_pred             HHHHHHHHHcCCCcHHHHHHHH
Q 041612          243 SIARDVAKECAGLPVSIVTIAR  264 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai~~i~~  264 (276)
                      +..+.++..+.|.|..+.-+-.
T Consensus       182 ~~l~~L~~~~~gn~r~L~~~l~  203 (226)
T TIGR03420       182 EVADYLLRHGSRDMGSLMALLD  203 (226)
T ss_pred             HHHHHHHHhccCCHHHHHHHHH
Confidence            4567788889999988776643

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.

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

Probab=98.25  E-value=2.8e-06  Score=70.39  Aligned_cols=52  Identities=17%  Similarity=0.190  Sum_probs=45.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc--CCHHHHHHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN--QDIRKIQEEI  164 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i  164 (276)
                      .-..++|.|++|+|||||++.++++.... +|+..+|+.+.+.  .+..++++.+
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I   68 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSV   68 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHh
Confidence            34589999999999999999999998766 7999999997776  6889998888

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=98.19  E-value=2.7e-06  Score=74.01  Aligned_cols=52  Identities=17%  Similarity=0.204  Sum_probs=45.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC--CHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ--DIRKIQEEIG  165 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~  165 (276)
                      -...+|+|++|+|||||++.++++...+ +|+.++|+.+.+..  ...++++.+.
T Consensus       169 GQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIl  222 (416)
T PRK09376        169 GQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVK  222 (416)
T ss_pred             CceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhc
Confidence            4478999999999999999999999876 79999999998887  6777777775

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.18  E-value=9.7e-05  Score=65.01  Aligned_cols=149  Identities=15%  Similarity=0.156  Sum_probs=84.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCC-CC---CeEEEEEecCcCCHHHHHHHHHHHh---CCCcccc--cchh--
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDK-LF---DQVVFVEVSQNQDIRKIQEEIGDKL---GLKFHEE--SESG--  179 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~f---~~~~wv~~~~~~~~~~l~~~i~~~l---~~~~~~~--~~~~--  179 (276)
                      ...+.+.|+|++|+|||++++.++++..... ..   -..+|++.....+...++..|++++   +...+..  ....  
T Consensus        38 ~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  117 (365)
T TIGR02928        38 SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVF  117 (365)
T ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHH
Confidence            4456899999999999999999998764321 01   2456777666667777888888777   2221110  0000  


Q ss_pred             -------------------hhhhc-----------ccc----CC--CCcEEEEEeccccccccC-----CCC-CCceeCC
Q 041612          180 -------------------RANSL-----------FTH----GH--KGCKVLLTARSQDVLSGK-----MDS-RPNFSIG  217 (276)
Q Consensus       180 -------------------~~~~l-----------~~~----~~--~gs~IivTTR~~~va~~~-----~~~-~~~~~l~  217 (276)
                                         ..+.+           ...    ..  ....+|.+|.........     ... ...+.++
T Consensus       118 ~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~  197 (365)
T TIGR02928       118 RRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFP  197 (365)
T ss_pred             HHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeC
Confidence                               00011           001    11  223344455433221110     011 2457899


Q ss_pred             CCCHHHHHHHHHHhhC----CCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          218 VLNEEEAWSLFKKMAG----DYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       218 ~L~~~ea~~Lf~~~~~----~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      +++.++..+++..++.    ....+++..+.+..++..+.|-|-.+
T Consensus       198 p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~a  243 (365)
T TIGR02928       198 PYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKA  243 (365)
T ss_pred             CCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHH
Confidence            9999999999988763    22234444455666777777887544

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.16  E-value=5.2e-05  Score=71.19  Aligned_cols=158  Identities=18%  Similarity=0.254  Sum_probs=107.7

Q ss_pred             HHHHhhcCC-CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-CHHHHHHHHHHHhCCCcccccchh-
Q 041612          103 NILSALEDP-DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-DIRKIQEEIGDKLGLKFHEESESG-  179 (276)
Q Consensus       103 ~l~~~L~~~-~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~~~~~~~-  179 (276)
                      .|++.|... +.|.+.|..+.|.|||||+.........   =..+.|+++.+.. ++..+++.++..++.-.+...+.. 
T Consensus        26 rL~~~L~~~~~~RL~li~APAGfGKttl~aq~~~~~~~---~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~  102 (894)
T COG2909          26 RLLDRLRRANDYRLILISAPAGFGKTTLLAQWRELAAD---GAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQ  102 (894)
T ss_pred             HHHHHHhcCCCceEEEEeCCCCCcHHHHHHHHHHhcCc---ccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHH
Confidence            788888775 7999999999999999999999874333   3579999988654 677777777776653322211111 


Q ss_pred             ----------------------------------------------hhhhccccCCCCcEEEEEecccccccc-CCC-CC
Q 041612          180 ----------------------------------------------RANSLFTHGHKGCKVLLTARSQDVLSG-KMD-SR  211 (276)
Q Consensus       180 ----------------------------------------------~~~~l~~~~~~gs~IivTTR~~~va~~-~~~-~~  211 (276)
                                                                    ....+.++.+++-..|+|||+..-..- .+. .+
T Consensus       103 ~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lRlr~  182 (894)
T COG2909         103 TLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLARLRLRD  182 (894)
T ss_pred             HHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccceeehh
Confidence                                                          111222277889999999998753110 011 11


Q ss_pred             CceeCC----CCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          212 PNFSIG----VLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       212 ~~~~l~----~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ..++++    .|+.+|+-++|....+..-+..+    .+.+.+..+|-+-|+..++=.++
T Consensus       183 ~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld~~~----~~~L~~~teGW~~al~L~aLa~~  238 (894)
T COG2909         183 ELLEIGSEELRFDTEEAAAFLNDRGSLPLDAAD----LKALYDRTEGWAAALQLIALALR  238 (894)
T ss_pred             hHHhcChHhhcCChHHHHHHHHHcCCCCCChHH----HHHHHhhcccHHHHHHHHHHHcc
Confidence            234443    48999999999988653333333    56788899999999988887776

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.14  E-value=8.6e-05  Score=64.01  Aligned_cols=152  Identities=18%  Similarity=0.216  Sum_probs=91.5

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcc----cCCCCCeEEEEE-ecCcCCHHHHHHHHHHHhCCCcc---
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVK----SDKLFDQVVFVE-VSQNQDIRKIQEEIGDKLGLKFH---  173 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~----~~~~f~~~~wv~-~~~~~~~~~l~~~i~~~l~~~~~---  173 (276)
                      .+.+.+..+. .+...++|+.|+||||+|+.++...-    ...|+|...|.. -+.....+++ +.+.+.+.....   
T Consensus        15 ~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~i-r~~~~~~~~~p~~~~   93 (313)
T PRK05564         15 RIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDI-RNIIEEVNKKPYEGD   93 (313)
T ss_pred             HHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHH-HHHHHHHhcCcccCC
Confidence            4555555544 45778999999999999999988652    235677766655 3344455554 344454432211   


Q ss_pred             ---------cccchhh---hhhccccCCCCcEEEEEecccccc-ccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChh
Q 041612          174 ---------EESESGR---ANSLFTHGHKGCKVLLTARSQDVL-SGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSE  240 (276)
Q Consensus       174 ---------~~~~~~~---~~~l~~~~~~gs~IivTTR~~~va-~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  240 (276)
                               +.-+...   +.+..+..++++.+|++|.+.+.. .........+++.++++++....+.+....  .+  
T Consensus        94 ~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~~--~~--  169 (313)
T PRK05564         94 KKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYND--IK--  169 (313)
T ss_pred             ceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhcC--CC--
Confidence                     1111111   222333667788999888765432 222233457889999999998877665421  11  


Q ss_pred             HHHHHHHHHHHcCCCcHHHH
Q 041612          241 FQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~PLai~  260 (276)
                       .+.+..++..++|.|..+.
T Consensus       170 -~~~~~~l~~~~~g~~~~a~  188 (313)
T PRK05564        170 -EEEKKSAIAFSDGIPGKVE  188 (313)
T ss_pred             -HHHHHHHHHHcCCCHHHHH
Confidence             1235678888899886443

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.11  E-value=5.8e-05  Score=62.28  Aligned_cols=149  Identities=13%  Similarity=0.140  Sum_probs=82.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-HHHHHHHHHHHhCCC-cccc---cchhh----
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-IRKIQEEIGDKLGLK-FHEE---SESGR----  180 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-~~~l~~~i~~~l~~~-~~~~---~~~~~----  180 (276)
                      ....+.+.|+|++|+|||+|++.+++....+  -..+.|+++..... ..++.+.+ .+...- .++.   .....    
T Consensus        42 ~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~--~~~v~y~~~~~~~~~~~~~~~~~-~~~dlliiDdi~~~~~~~~~~~~  118 (235)
T PRK08084         42 QEHSGYIYLWSREGAGRSHLLHAACAELSQR--GRAVGYVPLDKRAWFVPEVLEGM-EQLSLVCIDNIECIAGDELWEMA  118 (235)
T ss_pred             CCCCCeEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEEHHHHhhhhHHHHHHh-hhCCEEEEeChhhhcCCHHHHHH
Confidence            3445688999999999999999999876643  23556766654221 22222222 111100 0110   00011    


Q ss_pred             hhhccc-cCCCC-cEEEEEecccccccc--------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 041612          181 ANSLFT-HGHKG-CKVLLTARSQDVLSG--------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAK  250 (276)
Q Consensus       181 ~~~l~~-~~~~g-s~IivTTR~~~va~~--------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~  250 (276)
                      ...+.. ....| .++|+||++..-...        .+.....+.++++++++-.+++.+.+.... -.--+++..-|++
T Consensus       119 lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~-~~l~~~v~~~L~~  197 (235)
T PRK08084        119 IFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRARLRG-FELPEDVGRFLLK  197 (235)
T ss_pred             HHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHH
Confidence            111111 11233 479999986532211        123345789999999999999987664221 1122456778888


Q ss_pred             HcCCCcHHHHHH
Q 041612          251 ECAGLPVSIVTI  262 (276)
Q Consensus       251 ~c~G~PLai~~i  262 (276)
                      .+.|-.-++..+
T Consensus       198 ~~~~d~r~l~~~  209 (235)
T PRK08084        198 RLDREMRTLFMT  209 (235)
T ss_pred             hhcCCHHHHHHH
Confidence            888665544433

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.07  E-value=8.9e-06  Score=70.45  Aligned_cols=149  Identities=22%  Similarity=0.318  Sum_probs=97.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCC-CeEEEEEecCcCCHHHHHHHHHHHhCCCccc-ccch-hhhhhccc--
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLF-DQVVFVEVSQNQDIRKIQEEIGDKLGLKFHE-ESES-GRANSLFT--  186 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f-~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-~~~~-~~~~~l~~--  186 (276)
                      ..+.+.++|.|||||||++..+.. ....  | +.+.++......+...+.-.....++....+ .+.. ........  
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~~~--~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~g~~~~~~~~~~~~~rr   89 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AASE--YADGVAFVDLAPITDPALVFPTLAGALGLHVQPGDSAVDTLVRRIGDRR   89 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-Hhhh--cccceeeeeccccCchhHhHHHHHhhcccccccchHHHHHHHHHHhhhh
Confidence            468999999999999999999988 4433  5 5666777766667666666666656554433 1111 01111000  


Q ss_pred             -----------------------cCCCCcEEEEEeccccccccCCCCCCceeCCCCCHH-HHHHHHHHhhC----CCCCC
Q 041612          187 -----------------------HGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEE-EAWSLFKKMAG----DYIED  238 (276)
Q Consensus       187 -----------------------~~~~gs~IivTTR~~~va~~~~~~~~~~~l~~L~~~-ea~~Lf~~~~~----~~~~~  238 (276)
                                             .+.+.-.|+.|+|....    +.....+.+..|+.. ++.++|...+.    .-...
T Consensus        90 ~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l----~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~  165 (414)
T COG3903          90 ALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAIL----VAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLT  165 (414)
T ss_pred             HHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhc----ccccccccCCccccCCchhHHHHHHHHHhccceeec
Confidence                                   55666778888887744    233445667776655 68888877764    11112


Q ss_pred             hhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          239 SEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ..-.....+|.++..|.||+|...++..+
T Consensus       166 ~~~~a~v~~icr~ldg~~laielaaarv~  194 (414)
T COG3903         166 DDNAAAVAEICRRLDGIPLAIELAAARVR  194 (414)
T ss_pred             CCchHHHHHHHHHhhcchHHHHHHHHHHH
Confidence            22234578899999999999999998776

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.06  E-value=0.0013  Score=61.75  Aligned_cols=38  Identities=26%  Similarity=0.360  Sum_probs=30.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++..+.......+.|+|++|+||||||+.+++..+..
T Consensus       165 ~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~  202 (615)
T TIGR02903       165 ALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKL  202 (615)
T ss_pred             HHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhc
Confidence            45555555566789999999999999999998877543

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.05  E-value=0.00019  Score=62.43  Aligned_cols=157  Identities=12%  Similarity=0.130  Sum_probs=83.8

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcC-------------------------C
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQ-------------------------D  156 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~-------------------------~  156 (276)
                      .+..++..+..+.+.++|++|+||||+|+.+.+...... +. ..+.++++...                         .
T Consensus        26 ~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (337)
T PRK12402         26 RLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDP-WENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSS  104 (337)
T ss_pred             HHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCcc-cccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccc
Confidence            455555556556788999999999999999988765331 22 23444433210                         0


Q ss_pred             HHHHHHHHHHHhCC--C--c-------cc--ccchh---hhhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCC
Q 041612          157 IRKIQEEIGDKLGL--K--F-------HE--ESESG---RANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVL  219 (276)
Q Consensus       157 ~~~l~~~i~~~l~~--~--~-------~~--~~~~~---~~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L  219 (276)
                      ....++.++.....  +  .       ++  .-...   .+..+.......+++|+||.+.. +..........+.+.++
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~  184 (337)
T PRK12402        105 KIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAP  184 (337)
T ss_pred             hHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCCceEEEecCC
Confidence            12233333322110  0  0       00  00111   11122223445678888875433 22222222346888999


Q ss_pred             CHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          220 NEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       220 ~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      +.++...++.+.+...... --.+....+++.++|.+-.+..
T Consensus       185 ~~~~~~~~l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        185 TDDELVDVLESIAEAEGVD-YDDDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             CHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            9999998888876421111 1234567788888876555433

>PLN03025 replication factor C subunit; Provisional

Probab=98.03  E-value=9e-05  Score=64.06  Aligned_cols=153  Identities=12%  Similarity=0.084  Sum_probs=80.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcCCHHHHHHHHHHHhCC-------Cccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQDIRKIQEEIGDKLGL-------KFHE  174 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l~~-------~~~~  174 (276)
                      .|..++..+..+.+.++|++|+||||+|..+.+...... |. ..+-++.+...+... .+.++..+..       ....
T Consensus        24 ~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~-~~~~~~eln~sd~~~~~~-vr~~i~~~~~~~~~~~~~~~k  101 (319)
T PLN03025         24 RLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPN-YKEAVLELNASDDRGIDV-VRNKIKMFAQKKVTLPPGRHK  101 (319)
T ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccc-CccceeeecccccccHHH-HHHHHHHHHhccccCCCCCeE
Confidence            344444455556678999999999999999998864321 32 222233333333332 2333222110       0000


Q ss_pred             c--------cchhh---hhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHH
Q 041612          175 E--------SESGR---ANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ  242 (276)
Q Consensus       175 ~--------~~~~~---~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~  242 (276)
                      .        -....   +.+..+.....+++|++|.... +..........++++++++++....+...+......- ..
T Consensus       102 viiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~i-~~  180 (319)
T PLN03025        102 IVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPY-VP  180 (319)
T ss_pred             EEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCCC-CH
Confidence            0        00011   1111223445677777765432 2221122234789999999999998888775211111 12


Q ss_pred             HHHHHHHHHcCCCcHH
Q 041612          243 SIARDVAKECAGLPVS  258 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLa  258 (276)
                      +....|+..++|-.-.
T Consensus       181 ~~l~~i~~~~~gDlR~  196 (319)
T PLN03025        181 EGLEAIIFTADGDMRQ  196 (319)
T ss_pred             HHHHHHHHHcCCCHHH
Confidence            3467788888876533

>PF13173 AAA_14: AAA domain

Probab=98.03  E-value=2.3e-05  Score=58.26  Aligned_cols=109  Identities=18%  Similarity=0.221  Sum_probs=63.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHH----HHHHHHHHhCC--C---cccccchhhhhh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRK----IQEEIGDKLGL--K---FHEESESGRANS  183 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~----l~~~i~~~l~~--~---~~~~~~~~~~~~  183 (276)
                      .+++.|.|+.|+|||||+++++.+..   ....+++++.........    +.+.+.+....  .   .++......+..
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~~~~~~   78 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYLPDWED   78 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhhccHHH
Confidence            36899999999999999999998876   145677777765543221    22333333211  1   011111111111


Q ss_pred             ccc---cCCCCcEEEEEecccccccc-----CCCCCCceeCCCCCHHHH
Q 041612          184 LFT---HGHKGCKVLLTARSQDVLSG-----KMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       184 l~~---~~~~gs~IivTTR~~~va~~-----~~~~~~~~~l~~L~~~ea  224 (276)
                      ..+   +..+..+|++|+.+......     ..+....+++.||+-.|.
T Consensus        79 ~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   79 ALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             HHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            111   44467899999987765422     223334688899987763

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.01  E-value=0.0001  Score=64.97  Aligned_cols=142  Identities=19%  Similarity=0.190  Sum_probs=73.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc--CCHHHHHHHHHHHhCCCcc------c--------
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN--QDIRKIQEEIGDKLGLKFH------E--------  174 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i~~~l~~~~~------~--------  174 (276)
                      ..++-+.++|++|+|||++|+.+++.....  |-.+....+...  .......+.+++......+      +        
T Consensus       154 ~~p~gvLL~GppGtGKT~lakaia~~l~~~--~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~  231 (364)
T TIGR01242       154 EPPKGVLLYGPPGTGKTLLAKAVAHETNAT--FIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKR  231 (364)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHhCCCC--EEecchHHHHHHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhcccc
Confidence            346679999999999999999999887543  322110000000  0111222233222111000      0        


Q ss_pred             --c---cch---hhhhhccc-----cCCCCcEEEEEecccccccc-C---CCCCCceeCCCCCHHHHHHHHHHhhCCCCC
Q 041612          175 --E---SES---GRANSLFT-----HGHKGCKVLLTARSQDVLSG-K---MDSRPNFSIGVLNEEEAWSLFKKMAGDYIE  237 (276)
Q Consensus       175 --~---~~~---~~~~~l~~-----~~~~gs~IivTTR~~~va~~-~---~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~  237 (276)
                        .   .+.   .....+..     ....+..||.||........ .   ......+.++..+.++..++|..++.....
T Consensus       232 ~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l  311 (364)
T TIGR01242       232 TDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKL  311 (364)
T ss_pred             ccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCC
Confidence              0   000   01111111     12346778888875432221 1   123457889999999999999988753222


Q ss_pred             ChhHHHHHHHHHHHcCCCc
Q 041612          238 DSEFQSIARDVAKECAGLP  256 (276)
Q Consensus       238 ~~~~~~~~~~i~~~c~G~P  256 (276)
                      .++.  -...++..+.|+.
T Consensus       312 ~~~~--~~~~la~~t~g~s  328 (364)
T TIGR01242       312 AEDV--DLEAIAKMTEGAS  328 (364)
T ss_pred             CccC--CHHHHHHHcCCCC
Confidence            2111  1346777787764

Many proteins may score above the trusted cutoff because an internal

>PRK09087 hypothetical protein; Validated

Probab=98.00  E-value=7.2e-05  Score=61.26  Aligned_cols=139  Identities=13%  Similarity=0.084  Sum_probs=75.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH-hCCCcccc--cchhhhhhccc-cC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK-LGLKFHEE--SESGRANSLFT-HG  188 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~-l~~~~~~~--~~~~~~~~l~~-~~  188 (276)
                      .+.+.|+|.+|+|||+|++.++.....       .|++.. .+.. .+...+.+. +-.+..+.  .....+-.+.. ..
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~~~-------~~i~~~-~~~~-~~~~~~~~~~l~iDDi~~~~~~~~~lf~l~n~~~  114 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKSDA-------LLIHPN-EIGS-DAANAAAEGPVLIEDIDAGGFDETGLFHLINSVR  114 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhcCC-------EEecHH-Hcch-HHHHhhhcCeEEEECCCCCCCCHHHHHHHHHHHH
Confidence            456899999999999999998866422       133332 1111 111111100 00000000  01111111111 23


Q ss_pred             CCCcEEEEEecccccc-----cc---CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          189 HKGCKVLLTARSQDVL-----SG---KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       189 ~~gs~IivTTR~~~va-----~~---~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      ..|..||+|++...-.     ..   .+.....++++++++++-..++.+.+..... .--+++..-|++++.|-+-++.
T Consensus       115 ~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~-~l~~ev~~~La~~~~r~~~~l~  193 (226)
T PRK09087        115 QAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADRQL-YVDPHVVYYLVSRMERSLFAAQ  193 (226)
T ss_pred             hCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhhhhHHHHH
Confidence            4467899998743211     11   1244468999999999999999988752211 1123567778888877766665


Q ss_pred             H
Q 041612          261 T  261 (276)
Q Consensus       261 ~  261 (276)
                      .
T Consensus       194 ~  194 (226)
T PRK09087        194 T  194 (226)
T ss_pred             H
Confidence            4

>PRK08118 topology modulation protein; Reviewed

Probab=97.97  E-value=5.5e-06  Score=64.59  Aligned_cols=36  Identities=25%  Similarity=0.479  Sum_probs=29.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC-CCCCeEEEE
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD-KLFDQVVFV  149 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~f~~~~wv  149 (276)
                      +.|.|+|++|+||||||+.+++..... -+||..+|-
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~   38 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWK   38 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcc
Confidence            468999999999999999999997654 347777753

>PRK05642 DNA replication initiation factor; Validated

Probab=97.97  E-value=7.8e-05  Score=61.45  Aligned_cols=147  Identities=12%  Similarity=0.196  Sum_probs=80.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-HHHHHHHHHHHhCCC-cccc---cchhh-hhhccc-
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-IRKIQEEIGDKLGLK-FHEE---SESGR-ANSLFT-  186 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-~~~l~~~i~~~l~~~-~~~~---~~~~~-~~~l~~-  186 (276)
                      ..+.|+|.+|+|||+|++.+++....+  -..++|++...-.. ...+.+.+. ....- .++.   ..... ...++. 
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~--~~~v~y~~~~~~~~~~~~~~~~~~-~~d~LiiDDi~~~~~~~~~~~~Lf~l  122 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQR--GEPAVYLPLAELLDRGPELLDNLE-QYELVCLDDLDVIAGKADWEEALFHL  122 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEeeHHHHHhhhHHHHHhhh-hCCEEEEechhhhcCChHHHHHHHHH
Confidence            578999999999999999998876543  23566776543221 112221111 11000 0000   00011 111222 


Q ss_pred             ---cCCCCcEEEEEecccccccc--------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCC
Q 041612          187 ---HGHKGCKVLLTARSQDVLSG--------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGL  255 (276)
Q Consensus       187 ---~~~~gs~IivTTR~~~va~~--------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~  255 (276)
                         ....|..||+|++...-...        .+.....+.++++++++-..++...+..... .--+++..-|++++.|-
T Consensus       123 ~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~~~~-~l~~ev~~~L~~~~~~d  201 (234)
T PRK05642        123 FNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASRRGL-HLTDEVGHFILTRGTRS  201 (234)
T ss_pred             HHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhcCCC
Confidence               23356789998875432111        0122346889999999999999866642211 11146778888888877


Q ss_pred             cHHHHHHHH
Q 041612          256 PVSIVTIAR  264 (276)
Q Consensus       256 PLai~~i~~  264 (276)
                      .-.+..+-.
T Consensus       202 ~r~l~~~l~  210 (234)
T PRK05642        202 MSALFDLLE  210 (234)
T ss_pred             HHHHHHHHH
Confidence            555544433

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.95  E-value=0.00031  Score=55.82  Aligned_cols=147  Identities=17%  Similarity=0.170  Sum_probs=84.1

Q ss_pred             HHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          104 ILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       104 l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      |.+.+..+.. +.+.++|+.|+|||++|+.+.......                    .+.+..+..........+.+ +
T Consensus         4 l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i-~   82 (188)
T TIGR00678         4 LKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQV-R   82 (188)
T ss_pred             HHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHH-H
Confidence            4445555544 678999999999999999988876432                    23333332222223344443 3


Q ss_pred             HHHHHhCCCcc------------cccchh---hhhhccccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH------------EESESG---RANSLFTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~------------~~~~~~---~~~~l~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+.+.+.....            +.-...   .+....+...+.+.+|++|++. .+..........+.+.+++.++..+
T Consensus        83 ~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~  162 (188)
T TIGR00678        83 ELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQ  162 (188)
T ss_pred             HHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHH
Confidence            34444332110            001111   1122222445566777777654 2222222233579999999999988


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      .+.+. +   .+   .+.+..|+..++|.|..
T Consensus       163 ~l~~~-g---i~---~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       163 WLIRQ-G---IS---EEAAELLLALAGGSPGA  187 (188)
T ss_pred             HHHHc-C---CC---HHHHHHHHHHcCCCccc
Confidence            88777 2   11   34578899999998853

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.

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

Probab=97.90  E-value=2.3e-05  Score=58.24  Aligned_cols=63  Identities=29%  Similarity=0.473  Sum_probs=47.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCC---CCCeEEEEEecCcCCHHHHHHHHHHHhCCCccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDK---LFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~  174 (276)
                      +.+.+.|+|.+|+|||+++..+.+......   .-..++|+.++...+...+...|++.++.....
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~   68 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKS   68 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccc
Confidence            346899999999999999999999875310   024567999988889999999999999887665

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.88  E-value=0.00025  Score=62.97  Aligned_cols=136  Identities=18%  Similarity=0.210  Sum_probs=71.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-----CCHHHHHHHHHHHhCCCc-------------
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-----QDIRKIQEEIGDKLGLKF-------------  172 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-----~~~~~l~~~i~~~l~~~~-------------  172 (276)
                      ..++-|.++|++|+|||++|+.+++.....  |-   .+..+.-     .......+.+++......             
T Consensus       163 ~~p~gvLL~GppGtGKT~lAkaia~~~~~~--~i---~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~  237 (389)
T PRK03992        163 EPPKGVLLYGPPGTGKTLLAKAVAHETNAT--FI---RVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA  237 (389)
T ss_pred             CCCCceEEECCCCCChHHHHHHHHHHhCCC--EE---EeehHHHhHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhh
Confidence            456779999999999999999999876532  21   1111110     011233333333221100             


Q ss_pred             ---ccc--c-chh---hhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHhhCC
Q 041612          173 ---HEE--S-ESG---RANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKMAGD  234 (276)
Q Consensus       173 ---~~~--~-~~~---~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~  234 (276)
                         .+.  . +..   ....+..     ....+..||.||........ ..   .....+.++..+.++-.++|+.+...
T Consensus       238 ~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~  317 (389)
T PRK03992        238 AKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRK  317 (389)
T ss_pred             cccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhcc
Confidence               000  0 000   0111111     12235567777765433221 11   23457899999999999999988753


Q ss_pred             CCC--ChhHHHHHHHHHHHcCCC
Q 041612          235 YIE--DSEFQSIARDVAKECAGL  255 (276)
Q Consensus       235 ~~~--~~~~~~~~~~i~~~c~G~  255 (276)
                      ...  +.+    ...++..+.|+
T Consensus       318 ~~~~~~~~----~~~la~~t~g~  336 (389)
T PRK03992        318 MNLADDVD----LEELAELTEGA  336 (389)
T ss_pred             CCCCCcCC----HHHHHHHcCCC
Confidence            222  223    34566666665

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.86  E-value=0.00055  Score=64.53  Aligned_cols=160  Identities=14%  Similarity=0.179  Sum_probs=90.4

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+++..+. .+.+.++|..|+||||+|+.+.+...-.                   +.|...++++.+......++ +
T Consensus        27 ~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas~rgVDdI-R  105 (830)
T PRK07003         27 ALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAASNRGVDEM-A  105 (830)
T ss_pred             HHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccccccHHHH-H
Confidence            5555565555 4456899999999999999888765321                   11223455555444444433 3


Q ss_pred             HHHHHhCCC-c---------cc--ccchhhhhhccc---cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLK-F---------HE--ESESGRANSLFT---HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~-~---------~~--~~~~~~~~~l~~---~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+++.+... .         ++  .-.....+.+.+   ......++|+||.+.. +......-...++++.++.++..+
T Consensus       106 eLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~  185 (830)
T PRK07003        106 ALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVS  185 (830)
T ss_pred             HHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHH
Confidence            344432111 0         00  011111122222   4455788888877654 332333344579999999999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCc-HHHHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLP-VSIVTIAR  264 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~P-Lai~~i~~  264 (276)
                      .+.+....... .--.+....|++.++|.. -|+..+-.
T Consensus       186 ~L~~Il~~EgI-~id~eAL~lIA~~A~GsmRdALsLLdQ  223 (830)
T PRK07003        186 HLERILGEERI-AFEPQALRLLARAAQGSMRDALSLTDQ  223 (830)
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            99887752111 112345678888998854 45555433

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.86  E-value=0.00026  Score=67.83  Aligned_cols=157  Identities=17%  Similarity=0.202  Sum_probs=86.5

Q ss_pred             HHHHhhcCCCccE-EEEEcCCCCcHHHHHHHHHHhcccCC-------------------CCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDVNM-LGIYGMGGIGKTMLAEEIARKVKSDK-------------------LFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~~v-i~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+.+..+.+.- +.++|++|+||||+|+.+.+......                   .|...+++.......+.. ++
T Consensus        27 ~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas~~kVDd-IR  105 (944)
T PRK14949         27 ALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAASRTKVDD-TR  105 (944)
T ss_pred             HHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEeccccccCHHH-HH
Confidence            4555555555444 58999999999999999998875321                   122234443332223333 34


Q ss_pred             HHHHHhCCCcc----cc--------cchhhhhhccc---cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH----EE--------SESGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~----~~--------~~~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .|.+.+.....    ..        -.....+.+++   ......++|++|.+ ..+..........|++++|+.++...
T Consensus       106 eLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~  185 (944)
T PRK14949        106 ELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGT  185 (944)
T ss_pred             HHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHH
Confidence            45443321110    00        11111122222   34455666665544 43433323334679999999999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      .+.+.+..... .--.+....|++.++|.|--+..
T Consensus       186 ~L~~il~~EgI-~~edeAL~lIA~~S~Gd~R~ALn  219 (944)
T PRK14949        186 QLNHILTQEQL-PFEAEALTLLAKAANGSMRDALS  219 (944)
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHH
Confidence            99887642111 11234567889999998754443

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

Probab=97.85  E-value=0.00016  Score=68.74  Aligned_cols=148  Identities=20%  Similarity=0.274  Sum_probs=77.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec--CcCCHHHHHHHHHHHhCC--C-----cc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS--QNQDIRKIQEEIGDKLGL--K-----FH  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~--~~~~~~~l~~~i~~~l~~--~-----~~  173 (276)
                      .+...+..+....+.++|++|+||||||+.+++.....  |.   .++..  ...+....+..+...+..  .     .+
T Consensus        42 ~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~~~--f~---~lna~~~~i~dir~~i~~a~~~l~~~~~~~IL~ID  116 (725)
T PRK13341         42 LLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRAH--FS---SLNAVLAGVKDLRAEVDRAKERLERHGKRTILFID  116 (725)
T ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhcCc--ce---eehhhhhhhHHHHHHHHHHHHHhhhcCCceEEEEe
Confidence            34455566677788999999999999999999876533  42   11111  111222222222221111  0     00


Q ss_pred             c--ccchhhhhhccccCCCCcEEEEE--ecccc--ccccCCCCCCceeCCCCCHHHHHHHHHHhhCC------CCCChhH
Q 041612          174 E--ESESGRANSLFTHGHKGCKVLLT--ARSQD--VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGD------YIEDSEF  241 (276)
Q Consensus       174 ~--~~~~~~~~~l~~~~~~gs~IivT--TR~~~--va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~------~~~~~~~  241 (276)
                      +  ..+......+......|+.++|+  |.+..  +..........+.+++|+.++...++.+.+..      .....--
T Consensus       117 EIh~Ln~~qQdaLL~~lE~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~  196 (725)
T PRK13341        117 EVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLE  196 (725)
T ss_pred             ChhhCCHHHHHHHHHHhcCceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCC
Confidence            0  01111222233333446656653  44431  21112222457899999999999999876531      1111112


Q ss_pred             HHHHHHHHHHcCCC
Q 041612          242 QSIARDVAKECAGL  255 (276)
Q Consensus       242 ~~~~~~i~~~c~G~  255 (276)
                      .+....|++.+.|-
T Consensus       197 deaL~~La~~s~GD  210 (725)
T PRK13341        197 PEAEKHLVDVANGD  210 (725)
T ss_pred             HHHHHHHHHhCCCC
Confidence            34566777777775

>PRK08727 hypothetical protein; Validated

Probab=97.82  E-value=0.0002  Score=58.96  Aligned_cols=140  Identities=14%  Similarity=0.103  Sum_probs=78.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC----cccc---c-chhhhhhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK----FHEE---S-ESGRANSLF  185 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~----~~~~---~-~~~~~~~l~  185 (276)
                      ..+.|+|.+|+|||+|++.+++....+  ...+.|+++.....   -+..+++.+...    .++.   . .......++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~--~~~~~y~~~~~~~~---~~~~~~~~l~~~dlLiIDDi~~l~~~~~~~~~lf  116 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQA--GRSSAYLPLQAAAG---RLRDALEALEGRSLVALDGLESIAGQREDEVALF  116 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEeHHHhhh---hHHHHHHHHhcCCEEEEeCcccccCChHHHHHHH
Confidence            469999999999999999999887655  23566776544221   111222222111    0010   0 000111111


Q ss_pred             c----cCCCCcEEEEEeccccccc-----c---CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcC
Q 041612          186 T----HGHKGCKVLLTARSQDVLS-----G---KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECA  253 (276)
Q Consensus       186 ~----~~~~gs~IivTTR~~~va~-----~---~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~  253 (276)
                      .    ....|..||+||+...-..     .   .+.....+++++++.++-..++.+++..... .--.+...-|++.+.
T Consensus       117 ~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l-~l~~e~~~~La~~~~  195 (233)
T PRK08727        117 DFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRGL-ALDEAAIDWLLTHGE  195 (233)
T ss_pred             HHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhCC
Confidence            1    2234667999998642211     1   1122447899999999999999987642111 112345667888887


Q ss_pred             CCcHHH
Q 041612          254 GLPVSI  259 (276)
Q Consensus       254 G~PLai  259 (276)
                      |-.-.+
T Consensus       196 rd~r~~  201 (233)
T PRK08727        196 RELAGL  201 (233)
T ss_pred             CCHHHH
Confidence            554444

>TIGR00767 rho transcription termination factor Rho

Probab=97.82  E-value=5.3e-05  Score=66.32  Aligned_cols=53  Identities=17%  Similarity=0.198  Sum_probs=45.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc--CCHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN--QDIRKIQEEIGD  166 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i~~  166 (276)
                      -..++|+|++|+|||||++.+++....+ +|+..+|+.+.+.  .++.++++.+..
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg  222 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKG  222 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhc
Confidence            4468999999999999999999998766 7999999999866  688888888843

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

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.82  E-value=0.00013  Score=59.88  Aligned_cols=149  Identities=10%  Similarity=0.139  Sum_probs=77.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH---hCCCcccccchhhhhhccc--
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK---LGLKFHEESESGRANSLFT--  186 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~---l~~~~~~~~~~~~~~~l~~--  186 (276)
                      ..+.+.|+|.+|+|||+||+.+++.....+  ....+++.......   .. ....   +-.+.-+.........+..  
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~~~~~~--~~~~~i~~~~~~~~---~~-~~~~~~~liiDdi~~l~~~~~~~L~~~~  114 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVADASYGG--RNARYLDAASPLLA---FD-FDPEAELYAVDDVERLDDAQQIALFNLF  114 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEEehHHhHHH---Hh-hcccCCEEEEeChhhcCchHHHHHHHHH
Confidence            345789999999999999999998864331  23344444332111   00 0000   0000000000111111111  


Q ss_pred             --cCCCCc-EEEEEecccccccc-------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCc
Q 041612          187 --HGHKGC-KVLLTARSQDVLSG-------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLP  256 (276)
Q Consensus       187 --~~~~gs-~IivTTR~~~va~~-------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~P  256 (276)
                        ....+. .+|+|++.......       .+.....+.++++++++-..++.+.+.... ..--.+....+++.+.|.|
T Consensus       115 ~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~~~~-v~l~~~al~~L~~~~~gn~  193 (227)
T PRK08903        115 NRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAAAERG-LQLADEVPDYLLTHFRRDM  193 (227)
T ss_pred             HHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHhccCCH
Confidence              122344 36666664332111       111235788999999887777766543111 1112346777888899999


Q ss_pred             HHHHHHHHHHh
Q 041612          257 VSIVTIARALR  267 (276)
Q Consensus       257 Lai~~i~~~L~  267 (276)
                      ..+..+-..|.
T Consensus       194 ~~l~~~l~~l~  204 (227)
T PRK08903        194 PSLMALLDALD  204 (227)
T ss_pred             HHHHHHHHHHH
Confidence            98877766553

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.82  E-value=0.00079  Score=58.00  Aligned_cols=157  Identities=13%  Similarity=0.145  Sum_probs=82.4

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCe-EEEEEecCcCCHH---HHHHHHHHHhCCC-c-----
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQ-VVFVEVSQNQDIR---KIQEEIGDKLGLK-F-----  172 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~-~~wv~~~~~~~~~---~l~~~i~~~l~~~-~-----  172 (276)
                      .+..++.....+.+.++|.+|+||||+++.+.+...... +.. .+-++.+......   ..+..+....... .     
T Consensus        28 ~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~vv  106 (319)
T PRK00440         28 RLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-WRENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKII  106 (319)
T ss_pred             HHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-cccceEEeccccccchHHHHHHHHHHHhcCCCCCCCceEE
Confidence            455555555556689999999999999999998875432 221 1222222222222   2222222221111 0     


Q ss_pred             --cccc--chh---hhhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHH
Q 041612          173 --HEES--ESG---RANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSI  244 (276)
Q Consensus       173 --~~~~--~~~---~~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  244 (276)
                        ++..  ...   .+..+.......+.+|+++.... +..........+++.++++++....+...+...... -..+.
T Consensus       107 iiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~-i~~~a  185 (319)
T PRK00440        107 FLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIE-ITDDA  185 (319)
T ss_pred             EEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCC-CCHHH
Confidence              0000  010   11122224445577777764332 211111123367889999999988888877521111 11235


Q ss_pred             HHHHHHHcCCCcHHHHH
Q 041612          245 ARDVAKECAGLPVSIVT  261 (276)
Q Consensus       245 ~~~i~~~c~G~PLai~~  261 (276)
                      ...+++.++|-+--+..
T Consensus       186 l~~l~~~~~gd~r~~~~  202 (319)
T PRK00440        186 LEAIYYVSEGDMRKAIN  202 (319)
T ss_pred             HHHHHHHcCCCHHHHHH
Confidence            67788899887765433

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

Probab=97.79  E-value=0.00043  Score=62.04  Aligned_cols=29  Identities=31%  Similarity=0.479  Sum_probs=24.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...+-+.++|++|+|||++|+.+.+....
T Consensus       215 ~~p~gVLL~GPPGTGKT~LAraIA~el~~  243 (438)
T PTZ00361        215 KPPKGVILYGPPGTGKTLLAKAVANETSA  243 (438)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhhCC
Confidence            45667889999999999999999997654

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.79  E-value=0.00027  Score=65.62  Aligned_cols=158  Identities=15%  Similarity=0.191  Sum_probs=88.0

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC------------------------CCCCeEEEEEecCcCCH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD------------------------KLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~------------------------~~f~~~~wv~~~~~~~~  157 (276)
                      .|.+.+..+.+ +.+.++|..|+||||+|+.+.+...-.                        +.|...++++..+...+
T Consensus        27 ~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~~gV  106 (700)
T PRK12323         27 ALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGV  106 (700)
T ss_pred             HHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccccCCH
Confidence            55556666554 456889999999999999998776421                        01222445554444444


Q ss_pred             HHHHHHHHHHhCCCc-c-----------cccchhhhhhccc---cCCCCcEEEEEec-cccccccCCCCCCceeCCCCCH
Q 041612          158 RKIQEEIGDKLGLKF-H-----------EESESGRANSLFT---HGHKGCKVLLTAR-SQDVLSGKMDSRPNFSIGVLNE  221 (276)
Q Consensus       158 ~~l~~~i~~~l~~~~-~-----------~~~~~~~~~~l~~---~~~~gs~IivTTR-~~~va~~~~~~~~~~~l~~L~~  221 (276)
                      .++ +++++.+.... .           +.-+....+.+.+   ....++.+|++|. ...+......-...++++.++.
T Consensus       107 DdI-ReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~  185 (700)
T PRK12323        107 DEM-AQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPP  185 (700)
T ss_pred             HHH-HHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCCh
Confidence            443 33433322110 0           0011111222222   3344556555554 4444433333345789999999


Q ss_pred             HHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          222 EEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       222 ~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      ++..+.+.+.+....... -.+....|++.++|.|.....+
T Consensus       186 eei~~~L~~Il~~Egi~~-d~eAL~~IA~~A~Gs~RdALsL  225 (700)
T PRK12323        186 GHIVSHLDAILGEEGIAH-EVNALRLLAQAAQGSMRDALSL  225 (700)
T ss_pred             HHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            999998887764211111 1234577899999988655443

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.74  E-value=0.00084  Score=61.03  Aligned_cols=40  Identities=20%  Similarity=0.328  Sum_probs=28.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      ...+++|+|.+|+||||++..+......+.....+..++.
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdt  388 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTT  388 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEec
Confidence            3579999999999999999998876544321233444443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.0014  Score=57.75  Aligned_cols=155  Identities=15%  Similarity=0.181  Sum_probs=83.5

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC-------------------CCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK-------------------LFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .+.+.+..+. .+.+.++|++|+||||+|+.+.+......                   .+....++..+....... .+
T Consensus        27 ~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~~~~v~~-ir  105 (363)
T PRK14961         27 AISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTKVEE-MR  105 (363)
T ss_pred             HHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccccCCHHH-HH
Confidence            3444444444 45678999999999999999988764211                   111223333332233333 34


Q ss_pred             HHHHHhCCCcc----------c--ccchhhhhhcc---ccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH----------E--ESESGRANSLF---THGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~----------~--~~~~~~~~~l~---~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+.+.+.....          +  .-.......+.   ...+...++|++|.+. .+..........+++.+++.++..+
T Consensus       106 ~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~  185 (363)
T PRK14961        106 EILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFN  185 (363)
T ss_pred             HHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHH
Confidence            55444321110          0  00111111222   2445566777776543 2322222234578999999999998


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      .+.+.+..... .--.+....|+..++|-|-.+
T Consensus       186 ~L~~~~~~~g~-~i~~~al~~ia~~s~G~~R~a  217 (363)
T PRK14961        186 FLKYILIKESI-DTDEYALKLIAYHAHGSMRDA  217 (363)
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHH
Confidence            88876642111 111234667888999977543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.68  E-value=0.0014  Score=59.97  Aligned_cols=155  Identities=17%  Similarity=0.200  Sum_probs=83.8

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccCCCC------------------CeEEEEEecCcCCHHHHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSDKLF------------------DQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f------------------~~~~wv~~~~~~~~~~l~~~  163 (276)
                      .|...+..+.. +.+.++|++|+||||+|+.+.+.....+.+                  ..+.+++.+....... .++
T Consensus        25 ~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~~~~vd~-iR~  103 (504)
T PRK14963         25 VLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVED-VRD  103 (504)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccccCCHHH-HHH
Confidence            34444444443 456999999999999999998877432111                  1234444443333333 234


Q ss_pred             HHHHhCCC-c---------c--cccchhhhhhccc---cCCCCcEEEEEec-cccccccCCCCCCceeCCCCCHHHHHHH
Q 041612          164 IGDKLGLK-F---------H--EESESGRANSLFT---HGHKGCKVLLTAR-SQDVLSGKMDSRPNFSIGVLNEEEAWSL  227 (276)
Q Consensus       164 i~~~l~~~-~---------~--~~~~~~~~~~l~~---~~~~gs~IivTTR-~~~va~~~~~~~~~~~l~~L~~~ea~~L  227 (276)
                      +...+... .         +  +.........+.+   .....+.+|++|. ...+..........+++.+++.++....
T Consensus       104 l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~  183 (504)
T PRK14963        104 LREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGK  183 (504)
T ss_pred             HHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHH
Confidence            43333211 0         0  0011111222222   3334455555554 3334222233345799999999999999


Q ss_pred             HHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          228 FKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       228 f~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      +.+.+......- -.+....|++.++|.+--+
T Consensus       184 L~~i~~~egi~i-~~~Al~~ia~~s~GdlR~a  214 (504)
T PRK14963        184 LRRLLEAEGREA-EPEALQLVARLADGAMRDA  214 (504)
T ss_pred             HHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            988775211111 2245678899999987544

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

Probab=97.68  E-value=0.00071  Score=60.06  Aligned_cols=29  Identities=34%  Similarity=0.487  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..++-+.++|++|+|||+||+.+.+....
T Consensus       177 ~~pkgvLL~GppGTGKT~LAkalA~~l~~  205 (398)
T PTZ00454        177 DPPRGVLLYGPPGTGKTMLAKAVAHHTTA  205 (398)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHhcCC
Confidence            45678999999999999999999987654

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.64  E-value=0.0016  Score=57.74  Aligned_cols=140  Identities=17%  Similarity=0.129  Sum_probs=78.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEe-cCcCCHHHHHHHHHHHhCCCc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEV-SQNQDIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~-~~~~~~~~l~~~i~~~l~~~~  172 (276)
                      .+-+.++|++|+|||++|+.+....--.                   .|.|.. ++.. +......++ +.+.+.+....
T Consensus        36 ~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~-~i~~~~~~i~i~~i-R~l~~~~~~~p  113 (394)
T PRK07940         36 THAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPDVR-VVAPEGLSIGVDEV-RELVTIAARRP  113 (394)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEE-EeccccccCCHHHH-HHHHHHHHhCc
Confidence            4568899999999999999987654221                   233332 3322 222334333 34444432211


Q ss_pred             c------------cccchhhhh---hccccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCC
Q 041612          173 H------------EESESGRAN---SLFTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYI  236 (276)
Q Consensus       173 ~------------~~~~~~~~~---~l~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~  236 (276)
                      .            +.-+....+   +..+...++..+|++|.+. .+..........+.+.+++.++..+.+....+   
T Consensus       114 ~~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~---  190 (394)
T PRK07940        114 STGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDG---  190 (394)
T ss_pred             ccCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcC---
Confidence            1            001111112   2222445566677776664 34333333346899999999999988875432   


Q ss_pred             CChhHHHHHHHHHHHcCCCcHHHH
Q 041612          237 EDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       237 ~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      .+   .+.+..++..++|.|....
T Consensus       191 ~~---~~~a~~la~~s~G~~~~A~  211 (394)
T PRK07940        191 VD---PETARRAARASQGHIGRAR  211 (394)
T ss_pred             CC---HHHHHHHHHHcCCCHHHHH
Confidence            11   2346778899999887553

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.62  E-value=0.0016  Score=60.00  Aligned_cols=159  Identities=14%  Similarity=0.173  Sum_probs=84.1

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|...+..+.. +.+.++|+.|+||||+|+.+.+...-.                   +.|...+++.........++ +
T Consensus        27 ~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~~gvd~i-r  105 (546)
T PRK14957         27 SLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRTGVEET-K  105 (546)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecccccCHHHH-H
Confidence            45555555443 457889999999999999998765321                   11233444444333333332 3


Q ss_pred             HHHHHhCCC-c---------c--cccchhhhhhc---cccCCCCcEEEEEec-cccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLK-F---------H--EESESGRANSL---FTHGHKGCKVLLTAR-SQDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~-~---------~--~~~~~~~~~~l---~~~~~~gs~IivTTR-~~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+++.+... .         +  +.-+......+   .+.....+.+|++|- ...+..........+++++++.++...
T Consensus       106 ~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~  185 (546)
T PRK14957        106 EILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKD  185 (546)
T ss_pred             HHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHH
Confidence            333332211 0         0  00111112222   224445566665553 333432223334679999999999888


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCc-HHHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLP-VSIVTIA  263 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~P-Lai~~i~  263 (276)
                      .+.+.+..... .--......|+..++|-+ .|+..+-
T Consensus       186 ~L~~il~~egi-~~e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        186 QLKIILAKENI-NSDEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            88776542111 112234567888888855 4544443

>PRK07261 topology modulation protein; Provisional

Probab=97.62  E-value=0.00017  Score=56.50  Aligned_cols=54  Identities=24%  Similarity=0.368  Sum_probs=35.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC-CCCCeEEEEEecCcCCHHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD-KLFDQVVFVEVSQNQDIRKIQEEIGDKL  168 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~f~~~~wv~~~~~~~~~~l~~~i~~~l  168 (276)
                      .|.|+|++|+||||||+.+....... -+.|...|-......+...+...+...+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~   56 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPNWQERDDDDMIADISNFL   56 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccccccCCHHHHHHHHHHHH
Confidence            58999999999999999998775432 1356666754333334445544444333

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

Probab=97.62  E-value=0.0021  Score=53.48  Aligned_cols=148  Identities=17%  Similarity=0.118  Sum_probs=80.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC------cccccchhhhhhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK------FHEESESGRANSL  184 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~------~~~~~~~~~~~~l  184 (276)
                      +.+--+.++|++|.||||||..+.+...++  +.    +.-+.......-+..|+..+...      .....+....+.+
T Consensus        50 e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn--~k----~tsGp~leK~gDlaaiLt~Le~~DVLFIDEIHrl~~~vEE~L  123 (332)
T COG2255          50 EALDHVLLFGPPGLGKTTLAHIIANELGVN--LK----ITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEEVL  123 (332)
T ss_pred             CCcCeEEeeCCCCCcHHHHHHHHHHHhcCC--eE----ecccccccChhhHHHHHhcCCcCCeEEEehhhhcChhHHHHh
Confidence            446689999999999999999999998776  21    11111111111111222221110      0000000000000


Q ss_pred             cc----------------------cCCCCcEEEEEeccccccccC-CCCCCceeCCCCCHHHHHHHHHHhhC--CCCCCh
Q 041612          185 FT----------------------HGHKGCKVLLTARSQDVLSGK-MDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDS  239 (276)
Q Consensus       185 ~~----------------------~~~~gs~IivTTR~~~va~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~  239 (276)
                      ..                      +.++-.-|=-|||...+.... ....-+.+++.-+.+|-.++..+.+.  +-..++
T Consensus       124 YpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~  203 (332)
T COG2255         124 YPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEIDE  203 (332)
T ss_pred             hhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCCh
Confidence            00                      223333344589977664321 12234678889999999999988774  222222


Q ss_pred             hHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          240 EFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       240 ~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                         +-+.+|+++.+|-|--..-+-+..+
T Consensus       204 ---~~a~eIA~rSRGTPRIAnRLLrRVR  228 (332)
T COG2255         204 ---EAALEIARRSRGTPRIANRLLRRVR  228 (332)
T ss_pred             ---HHHHHHHHhccCCcHHHHHHHHHHH
Confidence               3477899999999976555444443

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.58  E-value=0.0041  Score=52.74  Aligned_cols=61  Identities=15%  Similarity=0.226  Sum_probs=36.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-CCHHHHHHHHHHHhCCCc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-QDIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~  172 (276)
                      ..++++++|++|+||||++..+......+..-..+..++.... ......+......++.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~  254 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPV  254 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCce
Confidence            4569999999999999999998877654310124455554321 122333334445555444

>PRK04195 replication factor C large subunit; Provisional

Probab=97.57  E-value=0.0015  Score=59.79  Aligned_cols=141  Identities=17%  Similarity=0.206  Sum_probs=74.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC-------Cc-----ccccc---
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL-------KF-----HEESE---  177 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~-------~~-----~~~~~---  177 (276)
                      .+.+.|+|++|+||||+|+.+++...    |+. +-++.+...+...+ ..++.....       ..     ++.+.   
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~el~----~~~-ielnasd~r~~~~i-~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~  112 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALANDYG----WEV-IELNASDQRTADVI-ERVAGEAATSGSLFGARRKLILLDEVDGIHG  112 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcC----CCE-EEEcccccccHHHH-HHHHHHhhccCcccCCCCeEEEEecCccccc
Confidence            57899999999999999999998874    322 23344433333322 222221110       00     00000   


Q ss_pred             ---hhhhhhccc-cCCCCcEEEEEecccc-ccc-cCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 041612          178 ---SGRANSLFT-HGHKGCKVLLTARSQD-VLS-GKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKE  251 (276)
Q Consensus       178 ---~~~~~~l~~-~~~~gs~IivTTR~~~-va~-~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~  251 (276)
                         ......+.. ....++.||+|+-+.. ... ........+.+.+++.++....+.+.+......- -.+....|++.
T Consensus       113 ~~d~~~~~aL~~~l~~~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i-~~eaL~~Ia~~  191 (482)
T PRK04195        113 NEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIEC-DDEALKEIAER  191 (482)
T ss_pred             ccchhHHHHHHHHHHcCCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHH
Confidence               001111111 1234455777664432 111 1122345788999999999888887764211111 12456778888


Q ss_pred             cCCCcHHHH
Q 041612          252 CAGLPVSIV  260 (276)
Q Consensus       252 c~G~PLai~  260 (276)
                      ++|-.-.+.
T Consensus       192 s~GDlR~ai  200 (482)
T PRK04195        192 SGGDLRSAI  200 (482)
T ss_pred             cCCCHHHHH
Confidence            877554443

>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=97.56  E-value=0.00045  Score=56.33  Aligned_cols=144  Identities=19%  Similarity=0.233  Sum_probs=75.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHH------------HhCCC----ccc--
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGD------------KLGLK----FHE--  174 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~------------~l~~~----~~~--  174 (276)
                      ...+-|+|..|+|||+|.+.+++.......=..++|++..      ++...+..            .+...    .++  
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~------~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~  107 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAE------EFIREFADALRDGEIEEFKDRLRSADLLIIDDIQ  107 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHH------HHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGG
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHH------HHHHHHHHHHHcccchhhhhhhhcCCEEEEecch
Confidence            3468899999999999999999987653111245565432      22222221            11110    000  


Q ss_pred             -ccchh-hhhhccc----cCCCCcEEEEEecccccc-cc-------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChh
Q 041612          175 -ESESG-RANSLFT----HGHKGCKVLLTARSQDVL-SG-------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSE  240 (276)
Q Consensus       175 -~~~~~-~~~~l~~----~~~~gs~IivTTR~~~va-~~-------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  240 (276)
                       ..... ....++.    ....|.+||+|++...-. ..       .+...-.+.++++++++-..++.+.+...... -
T Consensus       108 ~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~-l  186 (219)
T PF00308_consen  108 FLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAKERGIE-L  186 (219)
T ss_dssp             GGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT---S
T ss_pred             hhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhCCC-C
Confidence             00101 0111111    334567899999655321 11       12233478999999999999999888521111 2


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHH
Q 041612          241 FQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                      -+++..-|++.+.+..-.+..+-
T Consensus       187 ~~~v~~~l~~~~~~~~r~L~~~l  209 (219)
T PF00308_consen  187 PEEVIEYLARRFRRDVRELEGAL  209 (219)
T ss_dssp             -HHHHHHHHHHTTSSHHHHHHHH
T ss_pred             cHHHHHHHHHhhcCCHHHHHHHH
Confidence            23567778888876665554443

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.

>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=97.56  E-value=7.2e-05  Score=54.80  Aligned_cols=23  Identities=39%  Similarity=0.600  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|.|.|++|+||||+|+.+....
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            68999999999999999999876

...

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.55  E-value=0.0008  Score=60.82  Aligned_cols=148  Identities=18%  Similarity=0.168  Sum_probs=82.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC--------------C----ccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL--------------K----FHE  174 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~--------------~----~~~  174 (276)
                      ..-+.|+|..|+|||+|++.+.+.......--.+++++..      .+...+...++.              .    .++
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~------~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDD  214 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGD------EFARKAVDILQKTHKEIEQFKNEICQNDVLIIDD  214 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHH------HHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEec
Confidence            3458899999999999999999876543212344555442      222222211111              0    000


Q ss_pred             c---cc-hhhhhhccc----cCCCCcEEEEEeccccc-ccc-------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCC-
Q 041612          175 E---SE-SGRANSLFT----HGHKGCKVLLTARSQDV-LSG-------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIE-  237 (276)
Q Consensus       175 ~---~~-~~~~~~l~~----~~~~gs~IivTTR~~~v-a~~-------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~-  237 (276)
                      .   .. ......++.    ....|..||+|+....- ...       .+...-...+++++.++-..++.+.+..... 
T Consensus       215 iq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~  294 (450)
T PRK14087        215 VQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQNIK  294 (450)
T ss_pred             cccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHhcCCC
Confidence            0   00 011111211    23345578888754321 110       1233446779999999999999988752211 


Q ss_pred             ChhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 041612          238 DSEFQSIARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       238 ~~~~~~~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      ..-.+++..-|+..+.|.|-.+.-+...+
T Consensus       295 ~~l~~evl~~Ia~~~~gd~R~L~gaL~~l  323 (450)
T PRK14087        295 QEVTEEAINFISNYYSDDVRKIKGSVSRL  323 (450)
T ss_pred             CCCCHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            12224577888888988887776655433

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.55  E-value=0.0034  Score=55.07  Aligned_cols=62  Identities=18%  Similarity=0.250  Sum_probs=39.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~  173 (276)
                      .-.++.++|+.|+||||++..+......+.....+..++... .....+-++...+.++.+..
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~  198 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVH  198 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceE
Confidence            356999999999999999999988764331123455554332 22344455555666665543

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

Probab=97.54  E-value=0.00029  Score=52.73  Aligned_cols=51  Identities=31%  Similarity=0.365  Sum_probs=36.4

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      .+...+..+..+.+.|+|.+|+|||++++.+++.....  -..++++......
T Consensus         9 ~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~   59 (151)
T cd00009           9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASDLL   59 (151)
T ss_pred             HHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhh
Confidence            34444445456789999999999999999999988533  2346666665543

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

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.53  E-value=0.0027  Score=57.72  Aligned_cols=163  Identities=18%  Similarity=0.235  Sum_probs=86.3

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccCCC-------------------CCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSDKL-------------------FDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|...+..+.. +.+.++|++|+||||+|+.+.+.......                   +.....++.+.......+ +
T Consensus        25 ~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~~~gid~i-R  103 (472)
T PRK14962         25 LIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAASNRGIDEI-R  103 (472)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcccCCHHHH-H
Confidence            44444555554 45789999999999999999887543110                   112334444433334433 3


Q ss_pred             HHHHHhCCCcc----cc---cc-----hhhhhhccc---cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH----EE---SE-----SGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~----~~---~~-----~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+.+.......    ..   ++     ......+..   ..+....+|++|.+ ..+..........+.+.+++.++...
T Consensus       104 ~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~  183 (472)
T PRK14962        104 KIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIK  183 (472)
T ss_pred             HHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHH
Confidence            44443321100    00   11     111111222   32333444444443 33433333344578999999999988


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcC-CCcHHHHHHHHHHh
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECA-GLPVSIVTIARALR  267 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~-G~PLai~~i~~~L~  267 (276)
                      .+.+.+..... .-..+....|+..++ +++.++..+-.+..
T Consensus       184 ~L~~i~~~egi-~i~~eal~~Ia~~s~GdlR~aln~Le~l~~  224 (472)
T PRK14962        184 RLQEVAEAEGI-EIDREALSFIAKRASGGLRDALTMLEQVWK  224 (472)
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            88887642111 111245667888775 56777777766543

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

Probab=97.53  E-value=0.0026  Score=53.64  Aligned_cols=66  Identities=26%  Similarity=0.299  Sum_probs=53.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCC----CeEEEEEecCcCCHHHHHHHHHHHhCCCccccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLF----DQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEES  176 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f----~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~  176 (276)
                      ...+.+.|+|.+|.|||++++.+...+-....-    -.++.+.....++...+...|+.+++.+.....
T Consensus        59 ~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~  128 (302)
T PF05621_consen   59 HRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRD  128 (302)
T ss_pred             cCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCC
Confidence            346789999999999999999999877543111    157788888999999999999999999876543

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

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.50  E-value=0.0018  Score=60.71  Aligned_cols=157  Identities=15%  Similarity=0.179  Sum_probs=84.6

Q ss_pred             HHHHhhcCCCcc-EEEEEcCCCCcHHHHHHHHHHhcccCC-------------------CCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDVN-MLGIYGMGGIGKTMLAEEIARKVKSDK-------------------LFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+.+..+... .+.++|..|+||||+|+.+.+...-..                   .|...+.++.......++ .+
T Consensus        27 ~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas~~~Vdd-iR  105 (647)
T PRK07994         27 ALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAASRTKVED-TR  105 (647)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccccCCHHH-HH
Confidence            445555555543 468899999999999999877754311                   121223344333233333 34


Q ss_pred             HHHHHhCCCcc----c--------ccchhhhhhccc---cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH----E--------ESESGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~----~--------~~~~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+.+.+.....    .        .-+....+.+.+   ......++|++|.+ ..+......-...+++++|+.++...
T Consensus       106 ~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~  185 (647)
T PRK07994        106 ELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQ  185 (647)
T ss_pred             HHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHH
Confidence            44444321110    0        011111222222   44455566655544 44433333335689999999999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      .+.+........ --......|++.++|.|--+..
T Consensus       186 ~L~~il~~e~i~-~e~~aL~~Ia~~s~Gs~R~Al~  219 (647)
T PRK07994        186 QLEHILQAEQIP-FEPRALQLLARAADGSMRDALS  219 (647)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            988776311111 1123456788899997764433

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

Probab=97.48  E-value=0.0002  Score=63.73  Aligned_cols=57  Identities=25%  Similarity=0.306  Sum_probs=43.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .++..|..  .+.+.++|++|+|||++|+.+++......+|+.+.|+.+++..+..+++
T Consensus       186 ~l~~~L~~--~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI  242 (459)
T PRK11331        186 TILKRLTI--KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFI  242 (459)
T ss_pred             HHHHHHhc--CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHh
Confidence            44444443  3478889999999999999999988766668889999988776655543

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.48  E-value=0.0033  Score=57.51  Aligned_cols=155  Identities=16%  Similarity=0.198  Sum_probs=83.8

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCCC-----------------------CCeEEEEEecCcCCHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDKL-----------------------FDQVVFVEVSQNQDIR  158 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-----------------------f~~~~wv~~~~~~~~~  158 (276)
                      .|.+.+..+. .+.+.++|++|+||||+|+.+++.......                       ...++.++..+.....
T Consensus        32 ~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd  111 (507)
T PRK06645         32 VLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVD  111 (507)
T ss_pred             HHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHH
Confidence            3333344443 457889999999999999999887643210                       0123334444444444


Q ss_pred             HHHHHHHHHhC-CCcc---------c--ccchhhhhhcc---ccCCCCcEEEE-EeccccccccCCCCCCceeCCCCCHH
Q 041612          159 KIQEEIGDKLG-LKFH---------E--ESESGRANSLF---THGHKGCKVLL-TARSQDVLSGKMDSRPNFSIGVLNEE  222 (276)
Q Consensus       159 ~l~~~i~~~l~-~~~~---------~--~~~~~~~~~l~---~~~~~gs~Iiv-TTR~~~va~~~~~~~~~~~l~~L~~~  222 (276)
                      ++ +.+++... .+..         +  .-.......+.   ....+.+.+|+ ||+...+..........+.+++++.+
T Consensus       112 ~I-r~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~  190 (507)
T PRK06645        112 DI-RRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFE  190 (507)
T ss_pred             HH-HHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHH
Confidence            44 33443331 1110         0  00111112222   24445566655 44544443332333457889999999


Q ss_pred             HHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          223 EAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       223 ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      +....+.+.+......- -.+....|+..++|.+--+
T Consensus       191 el~~~L~~i~~~egi~i-e~eAL~~Ia~~s~GslR~a  226 (507)
T PRK06645        191 EIFKLLEYITKQENLKT-DIEALRIIAYKSEGSARDA  226 (507)
T ss_pred             HHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            99999988875211111 1234567888898876443

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

Probab=97.48  E-value=0.0092  Score=51.28  Aligned_cols=38  Identities=26%  Similarity=0.419  Sum_probs=32.2

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++...+.-+.++=|.+||++|+|||-||+++.++-...
T Consensus       175 ElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~At  212 (406)
T COG1222         175 ELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDAT  212 (406)
T ss_pred             HHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCce
Confidence            66666666778889999999999999999999887644

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.46  E-value=0.0063  Score=55.60  Aligned_cols=35  Identities=23%  Similarity=0.358  Sum_probs=27.3

Q ss_pred             HhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          106 SALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       106 ~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ....-..++-+.++|++|+|||++|+.+++.....
T Consensus       209 ~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~  243 (512)
T TIGR03689       209 REYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQR  243 (512)
T ss_pred             HhccCCCCcceEEECCCCCcHHHHHHHHHHhhccc
Confidence            33333446679999999999999999999987543

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.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.46  E-value=0.0023  Score=59.65  Aligned_cols=156  Identities=15%  Similarity=0.170  Sum_probs=86.9

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+++..+. .+.+.++|+.|+||||+|+.+.+...-.                   +.|...+.++.++......+ +
T Consensus        26 ~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~~~VddI-R  104 (702)
T PRK14960         26 ALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDT-R  104 (702)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEecccccCCHHHH-H
Confidence            5556666555 4577899999999999999988775321                   11223444555444444443 3


Q ss_pred             HHHHHhCCCcc----c--------ccchhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH----E--------ESESGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~----~--------~~~~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .++..+.....    .        .-+......+   .+....+.++|++|.+.. +..........+++++++.++...
T Consensus       105 eli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k  184 (702)
T PRK14960        105 ELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITK  184 (702)
T ss_pred             HHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHH
Confidence            44443311100    0        0011111112   224445667887776533 322222334578999999999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      .+.+.+...... --.+....|++.++|-+-.+.
T Consensus       185 ~L~~Il~kEgI~-id~eAL~~IA~~S~GdLRdAL  217 (702)
T PRK14960        185 HLGAILEKEQIA-ADQDAIWQIAESAQGSLRDAL  217 (702)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHH
Confidence            888877521111 112346678888888764443

>PTZ00202 tuzin; Provisional

Probab=97.44  E-value=0.0022  Score=56.93  Aligned_cols=54  Identities=24%  Similarity=0.371  Sum_probs=41.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  172 (276)
                      ..++++.|.|++|+|||||++.+.....    + ...+++..   +..+++..++.+||.+.
T Consensus       284 ~~privvLtG~~G~GKTTLlR~~~~~l~----~-~qL~vNpr---g~eElLr~LL~ALGV~p  337 (550)
T PTZ00202        284 AHPRIVVFTGFRGCGKSSLCRSAVRKEG----M-PAVFVDVR---GTEDTLRSVVKALGVPN  337 (550)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhcCC----c-eEEEECCC---CHHHHHHHHHHHcCCCC
Confidence            3467999999999999999999986654    1 13333333   67999999999999743

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.44  E-value=0.0044  Score=51.97  Aligned_cols=27  Identities=30%  Similarity=0.332  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+.++|++|+||||+|+.+.+...
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~l~   67 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKLFK   67 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHHH
Confidence            456788999999999999999987753

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.

>PRK08181 transposase; Validated

Probab=97.44  E-value=0.0026  Score=53.41  Aligned_cols=37  Identities=27%  Similarity=0.276  Sum_probs=28.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      ..-+.++|++|+|||+||..+.+....+  ...+.|+++
T Consensus       106 ~~nlll~Gp~GtGKTHLa~Aia~~a~~~--g~~v~f~~~  142 (269)
T PRK08181        106 GANLLLFGPPGGGKSHLAAAIGLALIEN--GWRVLFTRT  142 (269)
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHc--CCceeeeeH
Confidence            3469999999999999999999876544  234555554

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.43  E-value=0.0077  Score=51.16  Aligned_cols=26  Identities=27%  Similarity=0.332  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -+.++|++|+|||++|+.+.......
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~   85 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRL   85 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            68899999999999998887776543

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.42  E-value=0.008  Score=53.93  Aligned_cols=38  Identities=18%  Similarity=0.306  Sum_probs=27.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc-cCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK-SDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~f~~~~wv~~  151 (276)
                      .+++.++|++|+||||++..+..... ... -..+..++.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~-g~~V~li~~  259 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYG-KKKVALITL  259 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEEC
Confidence            46899999999999999988877664 221 234555554

>PRK06620 hypothetical protein; Validated

Probab=97.39  E-value=0.00093  Score=54.24  Aligned_cols=132  Identities=17%  Similarity=0.011  Sum_probs=69.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC---Ccccccchhhhhhccc-cCC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL---KFHEESESGRANSLFT-HGH  189 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~---~~~~~~~~~~~~~l~~-~~~  189 (276)
                      +.+-|+|++|+|||+|++.+.+....       .++.  ......    ....+...   +.-+.......-.+.. ...
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~-------~~~~--~~~~~~----~~~~~~d~lliDdi~~~~~~~lf~l~N~~~e  111 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNA-------YIIK--DIFFNE----EILEKYNAFIIEDIENWQEPALLHIFNIINE  111 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCC-------EEcc--hhhhch----hHHhcCCEEEEeccccchHHHHHHHHHHHHh
Confidence            56899999999999999987766531       1111  000001    11111100   0000000001111111 224


Q ss_pred             CCcEEEEEecccccccc------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          190 KGCKVLLTARSQDVLSG------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       190 ~gs~IivTTR~~~va~~------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      .|..||+|++...-.-.      .+...-.+.++++++++-..++.+.+.... -.--+++..-|++++.|---.+
T Consensus       112 ~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~-l~l~~ev~~~L~~~~~~d~r~l  186 (214)
T PRK06620        112 KQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS-VTISRQIIDFLLVNLPREYSKI  186 (214)
T ss_pred             cCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHccCCHHHH
Confidence            57789999875533110      122334789999999998888887765211 1122456777888777654433

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.38  E-value=0.0019  Score=58.23  Aligned_cols=155  Identities=15%  Similarity=0.161  Sum_probs=81.9

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-------------------eEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-------------------QVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-------------------~~~wv~~~~~~~~~~l~~  162 (276)
                      .|...+..+.. +.+.++|+.|+||||+|+.+.+...-....+                   ..+.++......... .+
T Consensus        29 ~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas~~gVd~-IR  107 (484)
T PRK14956         29 ALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASNRGIEN-IR  107 (484)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhhcccHHH-HH
Confidence            45555666654 4579999999999999999988765321000                   112222222222222 23


Q ss_pred             HHHHHhCCCcc------------cccchhhhhhccc---cCCCCcEEEE-EeccccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFH------------EESESGRANSLFT---HGHKGCKVLL-TARSQDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~------------~~~~~~~~~~l~~---~~~~gs~Iiv-TTR~~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+.+.+.....            +.-.......+.+   .......+|+ ||....+..........|.+.+++.++..+
T Consensus       108 eL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~  187 (484)
T PRK14956        108 ELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQD  187 (484)
T ss_pred             HHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHH
Confidence            33333221100            0001111222222   3334455444 444444433333444578999999999988


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      .+.+.+...... --.+....|++.++|-|--+
T Consensus       188 ~L~~i~~~Egi~-~e~eAL~~Ia~~S~Gd~RdA  219 (484)
T PRK14956        188 YSEKLCKIENVQ-YDQEGLFWIAKKGDGSVRDM  219 (484)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCChHHHH
Confidence            888876421111 11345678899999887443

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.38  E-value=0.0032  Score=58.83  Aligned_cols=157  Identities=14%  Similarity=0.175  Sum_probs=85.2

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC------------------------CCCCeEEEEEecCcCCH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD------------------------KLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~------------------------~~f~~~~wv~~~~~~~~  157 (276)
                      .|.+.+..+.. +.+.++|..|+||||+|+.+.+...-.                        +.+...++++......+
T Consensus        27 ~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~~~V  106 (618)
T PRK14951         27 ALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAASNRGV  106 (618)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCcccccCH
Confidence            55666666554 566899999999999999986654311                        01222344444444444


Q ss_pred             HHHHHHHHHHhCCCcc----------c--ccchhhhhhccc---cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCH
Q 041612          158 RKIQEEIGDKLGLKFH----------E--ESESGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNE  221 (276)
Q Consensus       158 ~~l~~~i~~~l~~~~~----------~--~~~~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~  221 (276)
                      ..+ +++++.+.....          +  .-+....+.+.+   .....+++|++|.+ ..+..........++++.++.
T Consensus       107 d~i-Reli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~  185 (618)
T PRK14951        107 DEV-QQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAP  185 (618)
T ss_pred             HHH-HHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCH
Confidence            443 344444321110          0  001111122222   34455666665543 434333333346789999999


Q ss_pred             HHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          222 EEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       222 ~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      ++....+.+.+......- -.+....|++.++|-+--+..
T Consensus       186 eei~~~L~~i~~~egi~i-e~~AL~~La~~s~GslR~al~  224 (618)
T PRK14951        186 ETVLEHLTQVLAAENVPA-EPQALRLLARAARGSMRDALS  224 (618)
T ss_pred             HHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHH
Confidence            999988887764211111 123466788888886644433

>CHL00181 cbbX CbbX; Provisional

Probab=97.38  E-value=0.0061  Score=51.80  Aligned_cols=26  Identities=27%  Similarity=0.312  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+.++|++|+|||++|+.++.....
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~   85 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYK   85 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            35888999999999999999887543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.37  E-value=0.0093  Score=52.14  Aligned_cols=74  Identities=12%  Similarity=0.126  Sum_probs=46.1

Q ss_pred             cCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHH
Q 041612          187 HGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       187 ~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                      .......+|++| +...+..........+++.+++.++..+++.+.......+   .+....++..++|.|.....+.
T Consensus       167 Epp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~~~---~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        167 EPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQGSD---GEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             cCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccCCC---HHHHHHHHHHcCCCHHHHHHHH
Confidence            333445555544 4333433333334589999999999999998753321111   2346788999999998665544

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.36  E-value=0.01  Score=52.18  Aligned_cols=72  Identities=13%  Similarity=0.081  Sum_probs=47.4

Q ss_pred             cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHH
Q 041612          187 HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       187 ~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                      ....++.+|++|.+.+ +..........+.+.+++.++..+++......  ...   .....++..++|.|+.+..+.
T Consensus       167 epp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~--~~~---~~~~~l~~~s~Gsp~~Al~ll  239 (365)
T PRK07471        167 EPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPD--LPD---DPRAALAALAEGSVGRALRLA  239 (365)
T ss_pred             cCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhccc--CCH---HHHHHHHHHcCCCHHHHHHHh
Confidence            4445667777777654 33333344558999999999999999876431  111   112578899999998665443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.34  E-value=0.004  Score=56.61  Aligned_cols=155  Identities=13%  Similarity=0.146  Sum_probs=85.0

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhccc-------------------CCCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKS-------------------DKLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~-------------------~~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+.+..+.. +-+.++|+.|+||||+|+.+.....-                   ...+..++.++.++..+..++ +
T Consensus        24 ~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~~vddI-R  102 (491)
T PRK14964         24 ILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDDI-K  102 (491)
T ss_pred             HHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCCCHHHH-H
Confidence            44444445554 47889999999999999998764311                   011223455566555555554 3


Q ss_pred             HHHHHhC-CCcc---------c--ccchh---hhhhccccCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLG-LKFH---------E--ESESG---RANSLFTHGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~-~~~~---------~--~~~~~---~~~~l~~~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+++... .+..         +  .-...   .+.+..+...+.+++|++|.+ ..+..........+.+.+++.++...
T Consensus       103 ~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~  182 (491)
T PRK14964        103 VILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVE  182 (491)
T ss_pred             HHHHHHHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHH
Confidence            4444331 1110         0  00111   112222245566777766633 33433223334578899999999998


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      .+.+.+...... --.+....|++.++|-+-.+
T Consensus       183 ~L~~ia~~Egi~-i~~eAL~lIa~~s~GslR~a  214 (491)
T PRK14964        183 HLVDIAKKENIE-HDEESLKLIAENSSGSMRNA  214 (491)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHH
Confidence            888877521111 11234667888888876533

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.32  E-value=0.0096  Score=52.15  Aligned_cols=158  Identities=15%  Similarity=0.167  Sum_probs=83.9

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .+.+.+.... .+.+.++|++|+|||++|+.+.......                    .+++. .++.......... .
T Consensus        25 ~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~~~~~~~~~~~~-~  102 (355)
T TIGR02397        25 TLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IEIDAASNNGVDD-I  102 (355)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEeeccccCCHHH-H
Confidence            4444444444 3467889999999999999988775321                    12333 3343332222222 2


Q ss_pred             HHHHHHhCCCc----------cc--ccchhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKF----------HE--ESESGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~----------~~--~~~~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +.+.+.+....          ++  .-.......+   .....+.+.+|++|.+.. +..........+++.++++++..
T Consensus       103 ~~l~~~~~~~p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~  182 (355)
T TIGR02397       103 REILDNVKYAPSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIV  182 (355)
T ss_pred             HHHHHHHhcCcccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHH
Confidence            33433322110          00  0011111122   224445667677765443 22222222346788899999998


Q ss_pred             HHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHH
Q 041612          226 SLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       226 ~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                      ..+...+...... --.+....++..++|-|..+....
T Consensus       183 ~~l~~~~~~~g~~-i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       183 ERLKKILDKEGIK-IEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             HHHHHHHHHcCCC-CCHHHHHHHHHHcCCChHHHHHHH
Confidence            8888776421111 112457788899999886554443

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.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.31  E-value=0.0041  Score=57.12  Aligned_cols=156  Identities=12%  Similarity=0.147  Sum_probs=86.5

Q ss_pred             HHHHhhcCCCcc-EEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDVN-MLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+.+..+..+ ...++|++|+||||+|+.+.+...-.                   +.|.-.+.+..++....+++ +
T Consensus        27 ~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~~v~~i-R  105 (509)
T PRK14958         27 ALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDT-R  105 (509)
T ss_pred             HHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccCCHHHH-H
Confidence            566666665544 56899999999999999988876422                   11223455555555555554 4


Q ss_pred             HHHHHhCCCccc------------ccchhhhh---hccccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKFHE------------ESESGRAN---SLFTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~~~------------~~~~~~~~---~l~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+++.+......            .-.....+   +..+.....+++|++|.+. .+..........+++.+++.++...
T Consensus       106 ~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~  185 (509)
T PRK14958        106 ELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAA  185 (509)
T ss_pred             HHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHH
Confidence            455543221110            00111111   2222445567777665443 3322222233468899999998887


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      .+.+.+......- -.+....|++.++|-|--+.
T Consensus       186 ~l~~il~~egi~~-~~~al~~ia~~s~GslR~al  218 (509)
T PRK14958        186 HCQHLLKEENVEF-ENAALDLLARAANGSVRDAL  218 (509)
T ss_pred             HHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHH
Confidence            7766654211111 12345678888888775443

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

Probab=97.28  E-value=0.012  Score=51.72  Aligned_cols=65  Identities=23%  Similarity=0.314  Sum_probs=51.4

Q ss_pred             HHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          105 LSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       105 ~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      ...+....+.-+.|+|.+|+|||+.++.++.+......=...++++.....+..+++..|+++++
T Consensus        34 ~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~   98 (366)
T COG1474          34 APALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLG   98 (366)
T ss_pred             HHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcC
Confidence            33344455556999999999999999999999876521122788998889999999999999886

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.28  E-value=0.0049  Score=56.93  Aligned_cols=158  Identities=15%  Similarity=0.189  Sum_probs=83.8

Q ss_pred             HHHHhhcCCCcc-EEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDVN-MLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+.+..+... .+.++|++|+||||+|+.+.....-.                   +.|...+++..+.......+ +
T Consensus        27 ~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~~~~vd~i-r  105 (527)
T PRK14969         27 ALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAASNTQVDAM-R  105 (527)
T ss_pred             HHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccccCCHHHH-H
Confidence            445555555544 56899999999999999997776321                   11223344544433344433 3


Q ss_pred             HHHHHhCCC-cc-----------cccchhhhhhc---cccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLK-FH-----------EESESGRANSL---FTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~-~~-----------~~~~~~~~~~l---~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+++..... ..           +.-.....+.+   .+.....+.+|++|.+. .+..........++++.++.++...
T Consensus       106 ~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~  185 (527)
T PRK14969        106 ELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVS  185 (527)
T ss_pred             HHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHH
Confidence            454433211 10           00011111122   22444556666665443 3321112223478899999999988


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcH-HHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPV-SIVTI  262 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PL-ai~~i  262 (276)
                      .+.+.+...... --.+....|++.++|.+- |+..+
T Consensus       186 ~L~~il~~egi~-~~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        186 HLQHILEQENIP-FDATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            887766411111 112345678888898764 44443

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.25  E-value=0.0036  Score=55.82  Aligned_cols=152  Identities=13%  Similarity=0.113  Sum_probs=80.2

Q ss_pred             HHHHhhcCCCcc-EEEEEcCCCCcHHHHHHHHHHhcccCC----------------------------CCCeEEEEEecC
Q 041612          103 NILSALEDPDVN-MLGIYGMGGIGKTMLAEEIARKVKSDK----------------------------LFDQVVFVEVSQ  153 (276)
Q Consensus       103 ~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~----------------------------~f~~~~wv~~~~  153 (276)
                      .|.+.+..+..+ .+.++|++|+||||+|+.+.+...-..                            +++...+ ..+.
T Consensus        27 ~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~~~n~~~~-~~~~  105 (397)
T PRK14955         27 TIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLNISEF-DAAS  105 (397)
T ss_pred             HHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCCCCCeEee-cccc
Confidence            455556655544 588999999999999999887764311                            2222222 2222


Q ss_pred             cCCHHHHHHHHHHHhCCCcc------------cccchhh---hhhccccCCCCcEEEEEe-ccccccccCCCCCCceeCC
Q 041612          154 NQDIRKIQEEIGDKLGLKFH------------EESESGR---ANSLFTHGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIG  217 (276)
Q Consensus       154 ~~~~~~l~~~i~~~l~~~~~------------~~~~~~~---~~~l~~~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~  217 (276)
                      .....++ +++.+.+.....            +.-....   ..+..+...+.+.+|++| +...+..........+++.
T Consensus       106 ~~~id~I-r~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~  184 (397)
T PRK14955        106 NNSVDDI-RLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFK  184 (397)
T ss_pred             cCCHHHH-HHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcC
Confidence            2223333 344444421110            0001111   112222444566666655 3333322211123468899


Q ss_pred             CCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcH
Q 041612          218 VLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPV  257 (276)
Q Consensus       218 ~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PL  257 (276)
                      ++++++....+...+..... .--.+.+..++..++|.+-
T Consensus       185 ~l~~~ei~~~l~~~~~~~g~-~i~~~al~~l~~~s~g~lr  223 (397)
T PRK14955        185 RIPLEEIQQQLQGICEAEGI-SVDADALQLIGRKAQGSMR  223 (397)
T ss_pred             CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHH
Confidence            99999998888776631110 1112356788899998664

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.25  E-value=0.0054  Score=54.86  Aligned_cols=142  Identities=20%  Similarity=0.223  Sum_probs=71.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH--------HHHHh---CCC-ccccc---c
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE--------IGDKL---GLK-FHEES---E  177 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~--------i~~~l---~~~-~~~~~---~  177 (276)
                      ...+.|+|.+|+|||+|++.+++....+..-..++|++...-  ...+...        +.+.+   ..- .++..   .
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~--~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~  213 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKF--TNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAG  213 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHH--HHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcC
Confidence            356889999999999999999998765411124556653321  0111111        11111   000 00000   0


Q ss_pred             h-hhhhhccc----cCCCCcEEEEEeccccc-ccc-------CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHH
Q 041612          178 S-GRANSLFT----HGHKGCKVLLTARSQDV-LSG-------KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSI  244 (276)
Q Consensus       178 ~-~~~~~l~~----~~~~gs~IivTTR~~~v-a~~-------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  244 (276)
                      . .....+..    ....+..+|+||....- ...       .+.....+.+++.+.++-..++.+.+...... --+++
T Consensus       214 ~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~-l~~e~  292 (405)
T TIGR00362       214 KERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEEEGLE-LPDEV  292 (405)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCC-CCHHH
Confidence            0 00011111    11235568888764321 110       12223468899999999999998887521111 11345


Q ss_pred             HHHHHHHcCCCcH
Q 041612          245 ARDVAKECAGLPV  257 (276)
Q Consensus       245 ~~~i~~~c~G~PL  257 (276)
                      ..-|++.+.|.+-
T Consensus       293 l~~ia~~~~~~~r  305 (405)
T TIGR00362       293 LEFIAKNIRSNVR  305 (405)
T ss_pred             HHHHHHhcCCCHH
Confidence            5566666665443

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).

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.23  E-value=0.0048  Score=58.01  Aligned_cols=157  Identities=13%  Similarity=0.187  Sum_probs=84.3

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+++..+. .+.+.++|+.|+||||+|+.+.+...-.                   +.|...+.++......... ++
T Consensus        27 ~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaAs~~gVd~-IR  105 (709)
T PRK08691         27 ALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDN-IR  105 (709)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEeccccCCHHH-HH
Confidence            5555566555 3467999999999999999987764321                   1121223444444444433 33


Q ss_pred             HHHHHhCC-----C-----ccc--ccchhhhhhccc---cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGL-----K-----FHE--ESESGRANSLFT---HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~-----~-----~~~--~~~~~~~~~l~~---~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+++....     .     .++  .-+......+.+   .....+++|++|.+.. +..........+++..++.++...
T Consensus       106 elle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~  185 (709)
T PRK08691        106 EVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVAD  185 (709)
T ss_pred             HHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHH
Confidence            44432211     0     000  011111112222   3445667777765432 322222223467888999999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      .+.+.+...... --.+....|++.++|-+.-+..
T Consensus       186 ~L~~Il~kEgi~-id~eAL~~Ia~~A~GslRdAln  219 (709)
T PRK08691        186 HLAHVLDSEKIA-YEPPALQLLGRAAAGSMRDALS  219 (709)
T ss_pred             HHHHHHHHcCCC-cCHHHHHHHHHHhCCCHHHHHH
Confidence            888877521111 1123567888999888754433

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

Probab=97.22  E-value=0.0091  Score=55.08  Aligned_cols=34  Identities=26%  Similarity=0.367  Sum_probs=29.0

Q ss_pred             hhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          107 ALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       107 ~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+.-+.++=|.++|+||+|||++|+.+.+.....
T Consensus       462 r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~n  495 (693)
T KOG0730|consen  462 RFGISPPKGVLLYGPPGCGKTLLAKALANEAGMN  495 (693)
T ss_pred             HhcCCCCceEEEECCCCcchHHHHHHHhhhhcCC
Confidence            3444567889999999999999999999998766

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.21  E-value=0.0068  Score=56.84  Aligned_cols=155  Identities=14%  Similarity=0.178  Sum_probs=81.2

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC----------------------------CCCCeEEEEEecC
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD----------------------------KLFDQVVFVEVSQ  153 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~----------------------------~~f~~~~wv~~~~  153 (276)
                      .|.+.+..+.. +.+.++|+.|+||||+|+.+.+...-.                            .+|+...+ ....
T Consensus        27 ~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~-d~~s  105 (620)
T PRK14954         27 TIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLNISEF-DAAS  105 (620)
T ss_pred             HHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhccCCCCeEEe-cccc
Confidence            45555555544 458899999999999999988776321                            12332222 2222


Q ss_pred             cCCHHHHHHHHHHHhCCCcc------------cccchhhhhhccc---cCCCCcEEEEEe-ccccccccCCCCCCceeCC
Q 041612          154 NQDIRKIQEEIGDKLGLKFH------------EESESGRANSLFT---HGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIG  217 (276)
Q Consensus       154 ~~~~~~l~~~i~~~l~~~~~------------~~~~~~~~~~l~~---~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~  217 (276)
                      .....++. .+.+.+.....            +.-.....+.+.+   .....+.+|++| +...+..........+++.
T Consensus       106 ~~~vd~Ir-~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~  184 (620)
T PRK14954        106 NNSVDDIR-QLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFK  184 (620)
T ss_pred             cCCHHHHH-HHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhhceEEecC
Confidence            22333333 34444421100            0011111222222   333455555555 3333432223334578999


Q ss_pred             CCCHHHHHHHHHHhhCC-C-CCChhHHHHHHHHHHHcCCCc-HHHHHH
Q 041612          218 VLNEEEAWSLFKKMAGD-Y-IEDSEFQSIARDVAKECAGLP-VSIVTI  262 (276)
Q Consensus       218 ~L~~~ea~~Lf~~~~~~-~-~~~~~~~~~~~~i~~~c~G~P-Lai~~i  262 (276)
                      +++.++....+.+.+.. . ..+   .+.+..|+..++|-+ .|+..+
T Consensus       185 ~l~~~ei~~~L~~i~~~egi~I~---~eal~~La~~s~Gdlr~al~eL  229 (620)
T PRK14954        185 RIPLDEIQSQLQMICRAEGIQID---ADALQLIARKAQGSMRDAQSIL  229 (620)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHhCCCHHHHHHHH
Confidence            99999988888776541 1 122   234677888888844 344433

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

Probab=97.21  E-value=0.00073  Score=53.16  Aligned_cols=32  Identities=22%  Similarity=0.284  Sum_probs=22.2

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .....+.+.|+|.+|+|||+|.+.++......
T Consensus        20 ~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen   20 QSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             SS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             HcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            34457899999999999999999999888776

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.20  E-value=0.0065  Score=57.09  Aligned_cols=152  Identities=11%  Similarity=0.160  Sum_probs=83.4

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcc---------------------cCCCCCeEEEEEecCcCCHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVK---------------------SDKLFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~---------------------~~~~f~~~~wv~~~~~~~~~~l  160 (276)
                      .|...+..+.. +.+.++|+.|+||||+|+.+.....                     ...+|+.. .++.++..+...+
T Consensus        28 ~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~-~ld~~~~~~vd~I  106 (614)
T PRK14971         28 TLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIH-ELDAASNNSVDDI  106 (614)
T ss_pred             HHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceE-EecccccCCHHHH
Confidence            55555655554 4578999999999999998877653                     11245533 3344433344444


Q ss_pred             HHHHHHHhCCCcc------------cccchhhhhhc---cccCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHHH
Q 041612          161 QEEIGDKLGLKFH------------EESESGRANSL---FTHGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       161 ~~~i~~~l~~~~~------------~~~~~~~~~~l---~~~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                      . .+++++.....            +.-+......+   .+.....+.+|++| ....+..........+++.++++++.
T Consensus       107 r-~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei  185 (614)
T PRK14971        107 R-NLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADI  185 (614)
T ss_pred             H-HHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHH
Confidence            3 33333321110            00111112222   22444556666554 44445433333456799999999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcH
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPV  257 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PL  257 (276)
                      ...+.+.+...... --.+.+..|+..++|-+-
T Consensus       186 ~~~L~~ia~~egi~-i~~~al~~La~~s~gdlr  217 (614)
T PRK14971        186 VNHLQYVASKEGIT-AEPEALNVIAQKADGGMR  217 (614)
T ss_pred             HHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHH
Confidence            98888766421111 112346678888887554

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.20  E-value=0.008  Score=58.19  Aligned_cols=152  Identities=12%  Similarity=0.124  Sum_probs=82.3

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC----------------------CCCCeEEEEEecCcCCHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD----------------------KLFDQVVFVEVSQNQDIRK  159 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~----------------------~~f~~~~wv~~~~~~~~~~  159 (276)
                      .|.+.+..+.+ +.+.++|..|+||||+|+.+.+.+.-.                      .+++ +++++......+.+
T Consensus        26 ~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~d-v~eidaas~~~Vd~  104 (824)
T PRK07764         26 PLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLD-VTEIDAASHGGVDD  104 (824)
T ss_pred             HHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCc-EEEecccccCCHHH
Confidence            45555666554 457899999999999999998776421                      1122 23444333333444


Q ss_pred             HHHHHHHHhCCC----cc--------cccchhh---hhhccccCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHH
Q 041612          160 IQEEIGDKLGLK----FH--------EESESGR---ANSLFTHGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEE  223 (276)
Q Consensus       160 l~~~i~~~l~~~----~~--------~~~~~~~---~~~l~~~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~e  223 (276)
                      + +.+.+.+...    ..        +.-....   +.+..+.....+.+|++|.+ ..+..........|.+..++.++
T Consensus       105 i-R~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~  183 (824)
T PRK07764        105 A-RELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEV  183 (824)
T ss_pred             H-HHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHH
Confidence            3 2333322111    00        0011111   22222344456666665543 33433333345678999999999


Q ss_pred             HHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcH
Q 041612          224 AWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPV  257 (276)
Q Consensus       224 a~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PL  257 (276)
                      ....+.+.+...... --.+....|+..++|-+.
T Consensus       184 l~~~L~~il~~EGv~-id~eal~lLa~~sgGdlR  216 (824)
T PRK07764        184 MRGYLERICAQEGVP-VEPGVLPLVIRAGGGSVR  216 (824)
T ss_pred             HHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHH
Confidence            988887765311111 112345678888888773

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.18  E-value=0.0096  Score=51.58  Aligned_cols=142  Identities=15%  Similarity=0.189  Sum_probs=81.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEec---CcCCHHHHHHHHHHHhC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVS---QNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~---~~~~~~~l~~~i~~~l~  169 (276)
                      .+-+.++|+.|+|||++|..+....--.                    .|.| ..|+.-.   +...++++ +++.+.+.
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~~~~~~~~i~id~i-R~l~~~~~   99 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPD-NFVLEPEEADKTIKVDQV-RELVSFVV   99 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccCCCCCCCHHHH-HHHHHHHh
Confidence            5568899999999999999987775321                    1333 2344221   22344444 33444443


Q ss_pred             CCccc------------ccchhhhhhccc---cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhC
Q 041612          170 LKFHE------------ESESGRANSLFT---HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG  233 (276)
Q Consensus       170 ~~~~~------------~~~~~~~~~l~~---~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~  233 (276)
                      .....            .-+....+.+.+   ..+.++.+|+||.+.. +......-...+.+.+++.+++.+.+.....
T Consensus       100 ~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~  179 (328)
T PRK05707        100 QTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALP  179 (328)
T ss_pred             hccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhcc
Confidence            32111            111112222222   4446778888887754 3333333445789999999999988876532


Q ss_pred             CCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          234 DYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       234 ~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      . ..    .+.+..++..++|.|+.+..
T Consensus       180 ~-~~----~~~~~~~l~la~Gsp~~A~~  202 (328)
T PRK05707        180 E-SD----ERERIELLTLAGGSPLRALQ  202 (328)
T ss_pred             c-CC----hHHHHHHHHHcCCCHHHHHH
Confidence            1 11    22345678899999975543

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.015  Score=51.23  Aligned_cols=160  Identities=16%  Similarity=0.199  Sum_probs=81.3

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC------CCCCeE-EEEEecCcCCHHHHHHHHHHHhCC-Ccc
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD------KLFDQV-VFVEVSQNQDIRKIQEEIGDKLGL-KFH  173 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~------~~f~~~-~wv~~~~~~~~~~l~~~i~~~l~~-~~~  173 (276)
                      .+.+.+..+. .+.+.++|++|+|||++|+.+.+.....      ..|... +-+......+...+ ..+.+.+.. +..
T Consensus        28 ~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i-~~l~~~~~~~p~~  106 (367)
T PRK14970         28 TLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDI-RNLIDQVRIPPQT  106 (367)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHHH-HHHHHHHhhcccc
Confidence            4555555544 4588899999999999999998876431      113222 22222222223333 333333221 100


Q ss_pred             ---------c--ccchhhhhhc---cccCCCCcEEEEEec-cccccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCC
Q 041612          174 ---------E--ESESGRANSL---FTHGHKGCKVLLTAR-SQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIED  238 (276)
Q Consensus       174 ---------~--~~~~~~~~~l---~~~~~~gs~IivTTR-~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  238 (276)
                               +  .-.......+   .......+.+|++|. ...+.........+++..++++++....+...+......
T Consensus       107 ~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~  186 (367)
T PRK14970        107 GKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIK  186 (367)
T ss_pred             CCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCCC
Confidence                     0  0011111122   123334455665553 333322222233478899999999988888766421110


Q ss_pred             hhHHHHHHHHHHHcCCCcH-HHHHHHH
Q 041612          239 SEFQSIARDVAKECAGLPV-SIVTIAR  264 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G~PL-ai~~i~~  264 (276)
                       -..+....++..++|-+- ++..+-.
T Consensus       187 -i~~~al~~l~~~~~gdlr~~~~~lek  212 (367)
T PRK14970        187 -FEDDALHIIAQKADGALRDALSIFDR  212 (367)
T ss_pred             -CCHHHHHHHHHhCCCCHHHHHHHHHH
Confidence             112456778888887544 4444433

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.16  E-value=0.011  Score=54.45  Aligned_cols=28  Identities=29%  Similarity=0.309  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++-+.++|++|+|||+||+.+.+....
T Consensus        87 ~~~giLL~GppGtGKT~la~alA~~~~~  114 (495)
T TIGR01241        87 IPKGVLLVGPPGTGKTLLAKAVAGEAGV  114 (495)
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHcCC
Confidence            3456889999999999999999987643

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.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.16  E-value=0.00056  Score=51.97  Aligned_cols=46  Identities=26%  Similarity=0.392  Sum_probs=35.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  172 (276)
                      .+|.|.|++|+||||+|+.+.++..-.             ..+...++++++...|.+.
T Consensus         1 m~ItIsG~pGsG~TTva~~lAe~~gl~-------------~vsaG~iFR~~A~e~gmsl   46 (179)
T COG1102           1 MVITISGLPGSGKTTVARELAEHLGLK-------------LVSAGTIFREMARERGMSL   46 (179)
T ss_pred             CEEEeccCCCCChhHHHHHHHHHhCCc-------------eeeccHHHHHHHHHcCCCH
Confidence            378999999999999999999988654             1244567778877777653

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.15  E-value=0.0061  Score=55.07  Aligned_cols=134  Identities=20%  Similarity=0.267  Sum_probs=69.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcCCHHHHHHHHHHHhC--------------CC---ccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQDIRKIQEEIGDKLG--------------LK---FHE  174 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l~--------------~~---~~~  174 (276)
                      ..-+.|+|.+|+|||+|++.+.+...... ++ .++|++...      ++..+...+.              .+   .++
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~-~~~~v~yi~~~~------f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDD  202 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNE-PDLRVMYITSEK------FLNDLVDSMKEGKLNEFREKYRKKVDVLLIDD  202 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEEHHH------HHHHHHHHHhcccHHHHHHHHHhcCCEEEEec
Confidence            44699999999999999999999876541 33 456665432      2222222111              00   000


Q ss_pred             cc---c-hhhhhhccc----cCCCCcEEEEEecc-ccccc----c---CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCC
Q 041612          175 ES---E-SGRANSLFT----HGHKGCKVLLTARS-QDVLS----G---KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIED  238 (276)
Q Consensus       175 ~~---~-~~~~~~l~~----~~~~gs~IivTTR~-~~va~----~---~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  238 (276)
                      ..   . ......++.    ....|..||+||.. ..-..    .   .+.......+++.+.+.-..++.+.+......
T Consensus       203 i~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~  282 (440)
T PRK14088        203 VQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHGE  282 (440)
T ss_pred             hhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhcCCC
Confidence            00   0 000011111    22335578888753 22111    1   12334477899999999999998887521110


Q ss_pred             hhHHHHHHHHHHHcCC
Q 041612          239 SEFQSIARDVAKECAG  254 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G  254 (276)
                       --+++..-|++.+.|
T Consensus       283 -l~~ev~~~Ia~~~~~  297 (440)
T PRK14088        283 -LPEEVLNFVAENVDD  297 (440)
T ss_pred             -CCHHHHHHHHhcccc
Confidence             112345555555544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.15  E-value=0.0084  Score=56.06  Aligned_cols=158  Identities=13%  Similarity=0.160  Sum_probs=86.4

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCCC------------------------CCeEEEEEecCcCCH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDKL------------------------FDQVVFVEVSQNQDI  157 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~------------------------f~~~~wv~~~~~~~~  157 (276)
                      .|.+.+..+. .+-+.++|+.|+||||+|+.+.+...-...                        ..-++++...+...+
T Consensus        35 ~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gv  114 (598)
T PRK09111         35 TLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGV  114 (598)
T ss_pred             HHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcCCCCceEEecccccCCH
Confidence            5555555554 446889999999999999999887542210                        011234443433344


Q ss_pred             HHHHHHHHHHhCCCcc----------c--ccchhh---hhhccccCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCH
Q 041612          158 RKIQEEIGDKLGLKFH----------E--ESESGR---ANSLFTHGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNE  221 (276)
Q Consensus       158 ~~l~~~i~~~l~~~~~----------~--~~~~~~---~~~l~~~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~  221 (276)
                      .++ ++|++.+.....          +  .-+...   +.+..+.....+.+|++| ....+..........+.+..++.
T Consensus       115 d~I-ReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~  193 (598)
T PRK09111        115 DDI-REIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEA  193 (598)
T ss_pred             HHH-HHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCH
Confidence            443 345444321110          0  001111   112222445566776655 33434333233345788999999


Q ss_pred             HHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          222 EEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       222 ~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      ++....+.+.+...... --.+....|+..++|-+.-+...
T Consensus       194 ~el~~~L~~i~~kegi~-i~~eAl~lIa~~a~Gdlr~al~~  233 (598)
T PRK09111        194 DVLAAHLSRIAAKEGVE-VEDEALALIARAAEGSVRDGLSL  233 (598)
T ss_pred             HHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            99998888876411110 11245677888899887655443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.11  E-value=0.011  Score=55.01  Aligned_cols=157  Identities=18%  Similarity=0.225  Sum_probs=83.3

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .+.+.+..+. .+.+.++|+.|+||||+|+.+.....-.                    .|.+ .++++.+.......+ 
T Consensus        27 ~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~D-iieIdaas~igVd~I-  104 (605)
T PRK05896         27 ILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVD-IVELDAASNNGVDEI-  104 (605)
T ss_pred             HHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCc-eEEeccccccCHHHH-
Confidence            4444454443 4568899999999999999998775321                    1122 344443333333333 


Q ss_pred             HHHHHHhCCCcc----------c--ccchhhhhhccc---cCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKFH----------E--ESESGRANSLFT---HGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~~----------~--~~~~~~~~~l~~---~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +.+.+.+.....          +  .-.......+.+   ..+..+.+|++| ....+..........+++.++++++..
T Consensus       105 ReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~  184 (605)
T PRK05896        105 RNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQ  184 (605)
T ss_pred             HHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHH
Confidence            333332221100          0  001111122222   333455555554 333332222233457899999999999


Q ss_pred             HHHHHhhCC-C-CCChhHHHHHHHHHHHcCCCc-HHHHHHHH
Q 041612          226 SLFKKMAGD-Y-IEDSEFQSIARDVAKECAGLP-VSIVTIAR  264 (276)
Q Consensus       226 ~Lf~~~~~~-~-~~~~~~~~~~~~i~~~c~G~P-Lai~~i~~  264 (276)
                      ..+...+.. . ..+   .+.+..++..++|-| .|+..+-.
T Consensus       185 ~~L~~il~kegi~Is---~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        185 ELLKSIAKKEKIKIE---DNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             HHHHHHHHHcCCCCC---HHHHHHHHHHcCCcHHHHHHHHHH
Confidence            888887642 1 122   234667888898855 45555444

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.10  E-value=0.00084  Score=52.69  Aligned_cols=36  Identities=25%  Similarity=0.552  Sum_probs=29.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      ...+|.+.|++|+||||+|+.++......  +...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~--~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLK--YSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEE
Confidence            35689999999999999999999988654  5555555

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.08  E-value=0.00082  Score=51.09  Aligned_cols=29  Identities=34%  Similarity=0.432  Sum_probs=25.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      ...|.|.|++|+||||+++.+.+..+.++
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L~~~g   33 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKLREKG   33 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHHHhcC
Confidence            45799999999999999999998887663

>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=97.08  E-value=0.0005  Score=50.63  Aligned_cols=22  Identities=45%  Similarity=0.842  Sum_probs=20.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      |.|.|.+|+||||+|+.+....
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999998885

...

>PHA00729 NTP-binding motif containing protein

Probab=97.07  E-value=0.00074  Score=54.80  Aligned_cols=35  Identities=37%  Similarity=0.479  Sum_probs=28.3

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +++..+...+...|.|.|.+|+||||||..+.+..
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l   41 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDV   41 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHH
Confidence            34455556666789999999999999999998875

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.07  E-value=0.0031  Score=57.21  Aligned_cols=139  Identities=19%  Similarity=0.195  Sum_probs=71.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH--------HHHHhCCC----cccc---cc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE--------IGDKLGLK----FHEE---SE  177 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~--------i~~~l~~~----~~~~---~~  177 (276)
                      ..-+.|+|.+|+|||+|++.+.+....+..--.++|++...-  ...+...        +.+.+...    .++.   ..
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~--~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~  225 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKF--TNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAG  225 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHH--HHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcC
Confidence            356899999999999999999999865421123556554321  1111111        11111100    0000   00


Q ss_pred             -hhhhhhccc----cCCCCcEEEEEecccccc--------ccCCCCCCceeCCCCCHHHHHHHHHHhhCC--CCCChhHH
Q 041612          178 -SGRANSLFT----HGHKGCKVLLTARSQDVL--------SGKMDSRPNFSIGVLNEEEAWSLFKKMAGD--YIEDSEFQ  242 (276)
Q Consensus       178 -~~~~~~l~~----~~~~gs~IivTTR~~~va--------~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~  242 (276)
                       ......++.    ....|..||+||....-.        ...+.....+.+++.+.++-..++.+.+..  ...+   +
T Consensus       226 ~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~---~  302 (450)
T PRK00149        226 KERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLP---D  302 (450)
T ss_pred             CHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCC---H
Confidence             000111111    122355688887653210        012333457889999999999999888752  1122   2


Q ss_pred             HHHHHHHHHcCCCc
Q 041612          243 SIARDVAKECAGLP  256 (276)
Q Consensus       243 ~~~~~i~~~c~G~P  256 (276)
                      ++..-|+..+.|-.
T Consensus       303 e~l~~ia~~~~~~~  316 (450)
T PRK00149        303 EVLEFIAKNITSNV  316 (450)
T ss_pred             HHHHHHHcCcCCCH
Confidence            34555555555443

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.06  E-value=0.024  Score=49.75  Aligned_cols=60  Identities=17%  Similarity=0.294  Sum_probs=40.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-CCHHHHHHHHHHHhCCCcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-QDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~  173 (276)
                      ..+++.++|+.|+||||++..+......++  ..+.+++.... .....-++...+.++.+..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g--~~V~lItaDtyR~gAveQLk~yae~lgvpv~  265 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQN--RTVGFITTDTFRSGAVEQFQGYADKLDVELI  265 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCCccCccHHHHHHHHhhcCCCCEE
Confidence            477999999999999999999987765442  34566665432 2234455666676766543

>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=97.05  E-value=0.00057  Score=50.52  Aligned_cols=23  Identities=35%  Similarity=0.456  Sum_probs=21.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |.|+|++|+|||++|+.+.+...
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLG   23 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTT
T ss_pred             CEEECcCCCCeeHHHHHHHhhcc
Confidence            57899999999999999999985

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 ....

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.05  E-value=0.012  Score=55.00  Aligned_cols=162  Identities=18%  Similarity=0.206  Sum_probs=86.9

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC--------------------CCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK--------------------LFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .|.+.+..+. .+.+.++|+.|+||||+|+.+.+...-..                    |.+ ++++.......+..+ 
T Consensus        27 ~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpD-v~eId~a~~~~Id~i-  104 (624)
T PRK14959         27 ILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVD-VVEIDGASNRGIDDA-  104 (624)
T ss_pred             HHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCc-eEEEecccccCHHHH-
Confidence            3444444444 56788899999999999999988774321                    112 334433323333332 


Q ss_pred             HHHHHHhCCCc----------cc--ccchhhhhhccc---cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKF----------HE--ESESGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~----------~~--~~~~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +.+.+.+....          ++  .-.......+.+   .......+|++|.+ ..+..........+++++++.++..
T Consensus       105 R~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~  184 (624)
T PRK14959        105 KRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLE  184 (624)
T ss_pred             HHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHH
Confidence            23333322110          00  011111122222   23345556665544 3333222223347889999999999


Q ss_pred             HHHHHhhCCCCCChhHHHHHHHHHHHcCCC-cHHHHHHHHHHh
Q 041612          226 SLFKKMAGDYIEDSEFQSIARDVAKECAGL-PVSIVTIARALR  267 (276)
Q Consensus       226 ~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~-PLai~~i~~~L~  267 (276)
                      ..+...+..... .-..+....|++.++|- -.|+..+..++.
T Consensus       185 ~~L~~il~~egi-~id~eal~lIA~~s~GdlR~Al~lLeqll~  226 (624)
T PRK14959        185 AHLTKVLGREGV-DYDPAAVRLIARRAAGSVRDSMSLLGQVLA  226 (624)
T ss_pred             HHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            888876642111 01123567788888885 467777765543

>PRK06547 hypothetical protein; Provisional

Probab=97.05  E-value=0.00083  Score=52.56  Aligned_cols=33  Identities=30%  Similarity=0.310  Sum_probs=27.6

Q ss_pred             HhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          106 SALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       106 ~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+....+.+|+|.|.+|+||||+|+.+.....
T Consensus         8 ~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~~   40 (172)
T PRK06547          8 ARLCGGGMITVLIDGRSGSGKTTLAGALAARTG   40 (172)
T ss_pred             HHhhcCCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            334566788999999999999999999988754

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

Probab=97.04  E-value=0.0006  Score=54.46  Aligned_cols=26  Identities=38%  Similarity=0.639  Sum_probs=23.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +|+|.|.+|+||||+|+.+.......
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~~   26 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNKR   26 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCcc
Confidence            69999999999999999999988754

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 ....

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.04  E-value=0.011  Score=53.23  Aligned_cols=58  Identities=22%  Similarity=0.370  Sum_probs=37.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~  171 (276)
                      .+.+|.++|.+|+||||.+..+......++ + .+..++... .+...+.++.+.++++.+
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g-~-kV~lV~~D~~R~aa~eQL~~la~~~gvp  152 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKG-L-KVGLVAADTYRPAAYDQLKQLAEKIGVP  152 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcC-C-eEEEecCCCCCHHHHHHHHHHHHHcCCc
Confidence            477999999999999999999988776542 2 333333321 122234455556665554

>PRK14974 cell division protein FtsY; Provisional

Probab=97.03  E-value=0.012  Score=51.07  Aligned_cols=58  Identities=26%  Similarity=0.359  Sum_probs=37.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC--CHHHHHHHHHHHhCCCc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ--DIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~~~l~~~~  172 (276)
                      ++.+|.++|++|+||||++..+.......+ + .+..+.. ..+  ....-++.....++.+.
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~g-~-~V~li~~-Dt~R~~a~eqL~~~a~~lgv~v  198 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKNG-F-SVVIAAG-DTFRAGAIEQLEEHAERLGVKV  198 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcC-C-eEEEecC-CcCcHHHHHHHHHHHHHcCCce
Confidence            478999999999999998888887766542 3 2333332 222  22334556677777654

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.03  E-value=0.039  Score=50.16  Aligned_cols=60  Identities=17%  Similarity=0.239  Sum_probs=36.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~  172 (276)
                      ..+++++|+.|+||||++..+......+.....+..++... .....+-++...+.++.+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv  316 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPV  316 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCe
Confidence            47999999999999999999988764331112344444322 1123334455556665543

>PRK08233 hypothetical protein; Provisional

Probab=97.01  E-value=0.00065  Score=53.43  Aligned_cols=26  Identities=35%  Similarity=0.563  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|+|.|.+|+||||||..+.....
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            46899999999999999999998764

>PRK06762 hypothetical protein; Provisional

Probab=97.01  E-value=0.00065  Score=52.74  Aligned_cols=25  Identities=28%  Similarity=0.543  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.+|.|+|++|+||||+|+.+....
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999998776

>PRK05480 uridine/cytidine kinase; Provisional

Probab=97.00  E-value=0.00074  Score=54.61  Aligned_cols=27  Identities=33%  Similarity=0.476  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+..+|+|.|.+|+|||||++.+....
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            456799999999999999999999876

>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=97.00  E-value=0.0017  Score=48.71  Aligned_cols=41  Identities=27%  Similarity=0.356  Sum_probs=30.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHH
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      |.++|.+|+|||+||+.++.....     ...-+.+++..+..++.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~~-----~~~~i~~~~~~~~~dl~   42 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLGR-----PVIRINCSSDTTEEDLI   42 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHTC-----EEEEEE-TTTSTHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhc-----ceEEEEeccccccccce
Confidence            678999999999999999988832     24445666666666654

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.00  E-value=0.0052  Score=56.01  Aligned_cols=28  Identities=29%  Similarity=0.368  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++-|.++|++|+|||.+|+.+.+....
T Consensus       258 ~pkGILL~GPpGTGKTllAkaiA~e~~~  285 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIANDWQL  285 (489)
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHhCC
Confidence            3567899999999999999999988754

>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=96.99  E-value=0.00074  Score=50.85  Aligned_cols=24  Identities=29%  Similarity=0.567  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|.++|++|+||||+|+.+.....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            578999999999999999986654

...

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.98  E-value=0.031  Score=51.48  Aligned_cols=158  Identities=15%  Similarity=0.146  Sum_probs=84.6

Q ss_pred             HHHHhhcCCCcc-EEEEEcCCCCcHHHHHHHHHHhcccCCC------------------CC-eEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPDVN-MLGIYGMGGIGKTMLAEEIARKVKSDKL------------------FD-QVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~------------------f~-~~~wv~~~~~~~~~~l~~  162 (276)
                      .|...+..+... ...++|+.|+||||+|+.+....-....                  +. .++.+..........+. 
T Consensus        25 ~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas~~gId~IR-  103 (535)
T PRK08451         25 TLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIR-  103 (535)
T ss_pred             HHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEeccccccCHHHHH-
Confidence            555555555544 5689999999999999988877532110                  11 12333333222344443 


Q ss_pred             HHHHHhC-CCcc-----------cccchhhhhhcc---ccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLG-LKFH-----------EESESGRANSLF---THGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~-~~~~-----------~~~~~~~~~~l~---~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .++.... .+..           +.-.......+.   ...++.+++|++|.+. .+..........+++.+++.++...
T Consensus       104 elie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~  183 (535)
T PRK08451        104 ELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIIS  183 (535)
T ss_pred             HHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHH
Confidence            3333321 1100           011111112222   2445667777777553 2222222334578999999999988


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      .+.+.+...... --.+....|+..++|-+--+..+
T Consensus       184 ~L~~Il~~EGi~-i~~~Al~~Ia~~s~GdlR~alnl  218 (535)
T PRK08451        184 HLKTILEKEGVS-YEPEALEILARSGNGSLRDTLTL  218 (535)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCCcHHHHHHH
Confidence            888776421111 11245677888888887444433

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.97  E-value=0.0078  Score=58.03  Aligned_cols=29  Identities=28%  Similarity=0.415  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..++-+.++|++|+|||+||+.+.+....
T Consensus       485 ~~~~giLL~GppGtGKT~lakalA~e~~~  513 (733)
T TIGR01243       485 RPPKGVLLFGPPGTGKTLLAKAVATESGA  513 (733)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHhcCC
Confidence            34566899999999999999999988754

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.96  E-value=0.093  Score=46.91  Aligned_cols=62  Identities=18%  Similarity=0.251  Sum_probs=36.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~  173 (276)
                      ...+++++|+.|+||||+...+............+..+.... .....+-+....+.++.+..
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~  252 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVR  252 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCcee
Confidence            357999999999999999998877543221123333333222 12233334455556665543

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

Probab=96.95  E-value=0.0042  Score=54.87  Aligned_cols=120  Identities=19%  Similarity=0.249  Sum_probs=66.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHH----------HhCCCcccc-----c
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGD----------KLGLKFHEE-----S  176 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~----------~l~~~~~~~-----~  176 (276)
                      ....+-|+|..|.|||+|++.+.+.....  ......++++...-...+...+.+          ++..-..++     .
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~--~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y~~dlllIDDiq~l~g  189 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALAN--GPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKYSLDLLLIDDIQFLAG  189 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhh--CCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhhccCeeeechHhHhcC
Confidence            36789999999999999999999998765  332333333333222222222222          111100000     0


Q ss_pred             chhhhhhccc----cCCCCcEEEEEecccccccc--------CCCCCCceeCCCCCHHHHHHHHHHhhC
Q 041612          177 ESGRANSLFT----HGHKGCKVLLTARSQDVLSG--------KMDSRPNFSIGVLNEEEAWSLFKKMAG  233 (276)
Q Consensus       177 ~~~~~~~l~~----~~~~gs~IivTTR~~~va~~--------~~~~~~~~~l~~L~~~ea~~Lf~~~~~  233 (276)
                      .......++.    ....|..||+|++...-.-.        .+...-.+.+++++.+....++.+.+.
T Consensus       190 k~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~  258 (408)
T COG0593         190 KERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAE  258 (408)
T ss_pred             ChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHH
Confidence            0000111222    23344489999865432111        123345789999999999999988664

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.95  E-value=0.0012  Score=48.89  Aligned_cols=37  Identities=30%  Similarity=0.483  Sum_probs=28.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      ..+.|+|++|+||||+++.+........  ...++++.+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~~~~   39 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGE   39 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC--CCEEEECCE
Confidence            5789999999999999999998887652  235555444

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.

>PTZ00301 uridine kinase; Provisional

Probab=96.94  E-value=0.00081  Score=54.35  Aligned_cols=26  Identities=31%  Similarity=0.590  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|+|.|.+|+||||||+.+.....
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~   28 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELM   28 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHH
Confidence            46899999999999999998877653

>PRK06696 uridine kinase; Validated

Probab=96.94  E-value=0.0012  Score=54.01  Aligned_cols=30  Identities=30%  Similarity=0.391  Sum_probs=26.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+.+.+|+|.|.+|+||||||+.+......
T Consensus        19 ~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696         19 LTRPLRVAIDGITASGKTTFADELAEEIKK   48 (223)
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            345789999999999999999999988753

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.94  E-value=0.0076  Score=51.93  Aligned_cols=36  Identities=28%  Similarity=0.278  Sum_probs=27.0

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+..++.... +..+.++|++|+|||++|+.+++...
T Consensus        32 ~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~   68 (316)
T PHA02544         32 TFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVG   68 (316)
T ss_pred             HHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhC
Confidence            4555555544 45666699999999999999988763

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.93  E-value=0.018  Score=53.62  Aligned_cols=159  Identities=17%  Similarity=0.188  Sum_probs=83.9

Q ss_pred             HHHHhhcCCCcc-EEEEEcCCCCcHHHHHHHHHHhcccC----------------------CCCCeEEEEEecCcCCHHH
Q 041612          103 NILSALEDPDVN-MLGIYGMGGIGKTMLAEEIARKVKSD----------------------KLFDQVVFVEVSQNQDIRK  159 (276)
Q Consensus       103 ~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~----------------------~~f~~~~wv~~~~~~~~~~  159 (276)
                      .|.+.+..+... ...++|+.|+||||+|+.+.....-.                      .+++ ++.+..++...+..
T Consensus        24 ~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~d-vieidaas~~gvd~  102 (584)
T PRK14952         24 PLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSID-VVELDAASHGGVDD  102 (584)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCce-EEEeccccccCHHH
Confidence            556666665544 46899999999999999998775421                      1112 33444433334444


Q ss_pred             HHHHHHHHhCCCc----c------c--ccchhhhhhc---cccCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHH
Q 041612          160 IQEEIGDKLGLKF----H------E--ESESGRANSL---FTHGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEE  223 (276)
Q Consensus       160 l~~~i~~~l~~~~----~------~--~~~~~~~~~l---~~~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~e  223 (276)
                      + ++|.+.+....    .      +  .-.....+.+   .+.......+|++| ....+..........+++..++.++
T Consensus       103 i-Rel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~  181 (584)
T PRK14952        103 T-RELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRT  181 (584)
T ss_pred             H-HHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHH
Confidence            3 33433321110    0      0  0011111222   22444455555544 4444433222334578999999999


Q ss_pred             HHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcH-HHHHHHH
Q 041612          224 AWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPV-SIVTIAR  264 (276)
Q Consensus       224 a~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PL-ai~~i~~  264 (276)
                      ..+.+.+.+...... --.+....|+..++|-+- |+..+-.
T Consensus       182 i~~~L~~i~~~egi~-i~~~al~~Ia~~s~GdlR~aln~Ldq  222 (584)
T PRK14952        182 MRALIARICEQEGVV-VDDAVYPLVIRAGGGSPRDTLSVLDQ  222 (584)
T ss_pred             HHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            988887766421111 112345667888888663 4444433

>TIGR00235 udk uridine kinase

Probab=96.93  E-value=0.00093  Score=53.95  Aligned_cols=28  Identities=36%  Similarity=0.526  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +...+|+|+|++|+|||||++.+.....
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3457999999999999999999988764

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

>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=96.92  E-value=0.0009  Score=43.82  Aligned_cols=23  Identities=30%  Similarity=0.615  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|.|.|.+|+||||+++.+....
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999885

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.92  E-value=0.017  Score=52.29  Aligned_cols=112  Identities=15%  Similarity=0.275  Sum_probs=61.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC-----------C----c-ccc--
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL-----------K----F-HEE--  175 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~-----------~----~-~~~--  175 (276)
                      .-+.|+|++|+|||+|++.+.+.....  .-.+++++..      .+...+...+..           .    . ++.  
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~--~~~v~yi~~~------~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~  213 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRES--GGKILYVRSE------LFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEV  213 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHc--CCCEEEeeHH------HHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhh
Confidence            568899999999999999999987643  2334555432      111111111110           0    0 000  


Q ss_pred             -cc-hhhhhhccc----cCCCCcEEEEEecccc-----cccc---CCCCCCceeCCCCCHHHHHHHHHHhhC
Q 041612          176 -SE-SGRANSLFT----HGHKGCKVLLTARSQD-----VLSG---KMDSRPNFSIGVLNEEEAWSLFKKMAG  233 (276)
Q Consensus       176 -~~-~~~~~~l~~----~~~~gs~IivTTR~~~-----va~~---~~~~~~~~~l~~L~~~ea~~Lf~~~~~  233 (276)
                       .. ......++.    ....|..||+||....     +...   .+.....+.+++++.++-..++.+.+.
T Consensus       214 l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~  285 (445)
T PRK12422        214 FSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAE  285 (445)
T ss_pred             hcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHH
Confidence             00 000111111    1124567888885421     1111   123345788999999999999988764

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.91  E-value=0.0095  Score=55.39  Aligned_cols=118  Identities=15%  Similarity=0.207  Sum_probs=63.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH--------HH---HHhCCCc-cc---ccc-
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE--------IG---DKLGLKF-HE---ESE-  177 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~--------i~---~~l~~~~-~~---~~~-  177 (276)
                      ..+.|+|..|+|||+|+..+.+.......--.++|++...-.  ..+...        +.   .....-. ++   ... 
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~--~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gk  392 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFT--NEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDK  392 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHH--HHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCC
Confidence            458999999999999999999987543111245566543211  011111        11   1110000 00   000 


Q ss_pred             hhhhhhccc----cCCCCcEEEEEecccc-----ccc---cCCCCCCceeCCCCCHHHHHHHHHHhhC
Q 041612          178 SGRANSLFT----HGHKGCKVLLTARSQD-----VLS---GKMDSRPNFSIGVLNEEEAWSLFKKMAG  233 (276)
Q Consensus       178 ~~~~~~l~~----~~~~gs~IivTTR~~~-----va~---~~~~~~~~~~l~~L~~~ea~~Lf~~~~~  233 (276)
                      ......++.    ....|..|||||....     +..   ..+...-.+.++..+.+.-..++.+.+.
T Consensus       393 e~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~  460 (617)
T PRK14086        393 ESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAV  460 (617)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHH
Confidence            000111111    2234567888887531     101   1233445789999999999999988774

>PRK03839 putative kinase; Provisional

Probab=96.89  E-value=0.00091  Score=52.70  Aligned_cols=25  Identities=32%  Similarity=0.569  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|.|.|++|+||||+++.+.+....
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~   26 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGY   26 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            5899999999999999999988754

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.88  E-value=0.015  Score=50.07  Aligned_cols=29  Identities=28%  Similarity=0.449  Sum_probs=25.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+++++|++|+||||++..+......+
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~  141 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQ  141 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            46799999999999999999998887654

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.86  E-value=0.039  Score=52.74  Aligned_cols=61  Identities=21%  Similarity=0.312  Sum_probs=38.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~  173 (276)
                      ..+++++|+.|+||||.+..+............+..++... .....+-++...+.++.+..
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~  246 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVH  246 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCcc
Confidence            46999999999999999999887764321112444444322 11234555666677776544

>PRK08116 hypothetical protein; Validated

Probab=96.86  E-value=0.0014  Score=55.05  Aligned_cols=36  Identities=36%  Similarity=0.391  Sum_probs=28.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      .-+.++|.+|+|||+||..+++....+  -..++++++
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~--~~~v~~~~~  150 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEK--GVPVIFVNF  150 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEH
Confidence            358899999999999999999998654  334566654

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.84  E-value=0.0011  Score=52.39  Aligned_cols=26  Identities=31%  Similarity=0.373  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.++|.|.|++|+||||+++.+....
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            35789999999999999999998765

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.82  E-value=0.047  Score=48.36  Aligned_cols=62  Identities=16%  Similarity=0.251  Sum_probs=38.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCC--CCCeEEEEEecCc-CCHHHHHHHHHHHhCCCcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDK--LFDQVVFVEVSQN-QDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~  173 (276)
                      .++++.++|+.|+||||.+..+........  .-..+..++.... .....-++..++.++.+..
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~  237 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVK  237 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceE
Confidence            467999999999999999998887765321  1124444544321 1223335666666666543

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

Probab=96.81  E-value=0.0084  Score=55.91  Aligned_cols=29  Identities=34%  Similarity=0.532  Sum_probs=25.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .-++++.+|++|+|||++|+.|......+
T Consensus       437 qGkIlCf~GPPGVGKTSI~kSIA~ALnRk  465 (906)
T KOG2004|consen  437 QGKILCFVGPPGVGKTSIAKSIARALNRK  465 (906)
T ss_pred             CCcEEEEeCCCCCCcccHHHHHHHHhCCc
Confidence            46799999999999999999999888654

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.79  E-value=0.044  Score=50.12  Aligned_cols=158  Identities=14%  Similarity=0.172  Sum_probs=80.2

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhccc---C----------------CCCCeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKS---D----------------KLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~---~----------------~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      .|.+.+..+. .+...++|+.|+||||+|+.+......   .                ..|...+.+..++......+ +
T Consensus        27 ~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eidaas~~gvd~i-r  105 (486)
T PRK14953         27 ILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEIDAASNRGIDDI-R  105 (486)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEeCccCCCHHHH-H
Confidence            5555555544 345678999999999999998876531   0                01222344444333333322 2


Q ss_pred             HHHHHhCCC-cc---------c--ccchhhhhhc---cccCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLK-FH---------E--ESESGRANSL---FTHGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~-~~---------~--~~~~~~~~~l---~~~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .+.+.+... ..         +  .-.......+   ....++...+|++| +...+..........+.+.+++.++...
T Consensus       106 ~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~  185 (486)
T PRK14953        106 ALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKE  185 (486)
T ss_pred             HHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHH
Confidence            333332211 00         0  0011111112   22334455555555 3333322212223468899999999888


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      .+.+.+...... --.+....|+..++|.+..+...
T Consensus       186 ~L~~i~k~egi~-id~~al~~La~~s~G~lr~al~~  220 (486)
T PRK14953        186 YLKRICNEEKIE-YEEKALDLLAQASEGGMRDAASL  220 (486)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            888766421111 11234667888888876544433

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.79  E-value=0.037  Score=48.07  Aligned_cols=128  Identities=14%  Similarity=0.126  Sum_probs=70.8

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .|.+.+..++ .+...++|+.|+|||++|..+....--.                    .|.|..+...-+.....+++.
T Consensus        17 ~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir   96 (329)
T PRK08058         17 MLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPDGQSIKKDQIR   96 (329)
T ss_pred             HHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccccccCCHHHHH
Confidence            4444444444 4566899999999999999987765321                    144443332223333444443


Q ss_pred             HHHHHHhCCCcc------------cccchhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKFH------------EESESGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~~------------~~~~~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                       .+.+.+.....            +.-+....+.+   .+..+.++.+|++|.+.. +..........+++.++++++..
T Consensus        97 -~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~  175 (329)
T PRK08058         97 -YLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLI  175 (329)
T ss_pred             -HHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHH
Confidence             33343332111            11111112222   225566777787776543 33333344557899999999988


Q ss_pred             HHHHHh
Q 041612          226 SLFKKM  231 (276)
Q Consensus       226 ~Lf~~~  231 (276)
                      +.+...
T Consensus       176 ~~L~~~  181 (329)
T PRK08058        176 QRLQEE  181 (329)
T ss_pred             HHHHHc
Confidence            777654

>PRK04040 adenylate kinase; Provisional

Probab=96.78  E-value=0.0013  Score=52.30  Aligned_cols=26  Identities=27%  Similarity=0.526  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +++|+|+|++|+||||+++.+.....
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            46899999999999999999988874

>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=96.78  E-value=0.0025  Score=48.80  Aligned_cols=36  Identities=25%  Similarity=0.361  Sum_probs=28.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVE  150 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~  150 (276)
                      ..+|-|.|.+|+||||||+.+.......  -..+.+++
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~--g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFAR--GIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHT--TS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEec
Confidence            3589999999999999999999999876  34455553

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 ....

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.77  E-value=0.0036  Score=50.53  Aligned_cols=47  Identities=21%  Similarity=0.335  Sum_probs=36.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~  162 (276)
                      -.++.|+|.+|+|||+++.++.......  -..++|++... .+...+.+
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQ--GKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC-CCHHHHHH
Confidence            5689999999999999999988776543  46788998865 55555443

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

>CHL00176 ftsH cell division protein; Validated

Probab=96.77  E-value=0.044  Score=51.73  Aligned_cols=27  Identities=33%  Similarity=0.372  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++-+.++|++|+|||+||+.+.+...
T Consensus       215 ~p~gVLL~GPpGTGKT~LAralA~e~~  241 (638)
T CHL00176        215 IPKGVLLVGPPGTGKTLLAKAIAGEAE  241 (638)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            356799999999999999999988764

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.75  E-value=0.055  Score=50.82  Aligned_cols=156  Identities=14%  Similarity=0.170  Sum_probs=82.4

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC---------------------CCCeEEEEEecCcCCHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK---------------------LFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---------------------~f~~~~wv~~~~~~~~~~l  160 (276)
                      .|...+..+. .+.+.++|+.|+||||+|+.+........                     |++ .+.+..+.......+
T Consensus        27 ~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~~~d-~~~i~~~~~~~vd~i  105 (585)
T PRK14950         27 TLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVD-VIEMDAASHTSVDDA  105 (585)
T ss_pred             HHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCCCCe-EEEEeccccCCHHHH
Confidence            4444444444 34568999999999999999987753211                     111 233333233333333


Q ss_pred             HHHHHHHhCCCcc------------cccchhhhhhccc---cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHH
Q 041612          161 QEEIGDKLGLKFH------------EESESGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       161 ~~~i~~~l~~~~~------------~~~~~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                       ++|.+.+.....            +.-.....+.+.+   .....+.+|++|.+ ..+..........+.+..++.++.
T Consensus       106 -r~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el  184 (585)
T PRK14950        106 -REIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADM  184 (585)
T ss_pred             -HHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHH
Confidence             444444322110            0001111122222   33455666666643 333222222234678889999998


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      ...+.+.+...... --.+....|+..++|.+..+..
T Consensus       185 ~~~L~~~a~~egl~-i~~eal~~La~~s~Gdlr~al~  220 (585)
T PRK14950        185 AAHLRKIAAAEGIN-LEPGALEAIARAATGSMRDAEN  220 (585)
T ss_pred             HHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            88888776521111 1124577888999998864443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.75  E-value=0.043  Score=49.79  Aligned_cols=157  Identities=14%  Similarity=0.129  Sum_probs=80.3

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccC---------------------CCCCeEEEEEecCcCCHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSD---------------------KLFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~---------------------~~f~~~~wv~~~~~~~~~~l  160 (276)
                      .|.+.+..+.. +...++|++|+||||+|+.+.......                     .+++. +++..........+
T Consensus        28 ~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d~-~~i~g~~~~gid~i  106 (451)
T PRK06305         28 VLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDV-LEIDGASHRGIEDI  106 (451)
T ss_pred             HHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCce-EEeeccccCCHHHH
Confidence            44455555543 567889999999999999988765321                     12232 22222222223332


Q ss_pred             HHHHHHHhCCC---c-------cc--ccchhh---hhhccccCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHH
Q 041612          161 QEEIGDKLGLK---F-------HE--ESESGR---ANSLFTHGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       161 ~~~i~~~l~~~---~-------~~--~~~~~~---~~~l~~~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                       +.+.+.+...   .       ++  .-....   +.+..........+|++|.+ ..+..........++++++++++.
T Consensus       107 -r~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el  185 (451)
T PRK06305        107 -RQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETI  185 (451)
T ss_pred             -HHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHH
Confidence             2333332211   0       00  001111   11222244446667666633 333222222345789999999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCc-HHHHHH
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLP-VSIVTI  262 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~P-Lai~~i  262 (276)
                      ...+...+..... .--.+.+..|+..++|-+ .|+..+
T Consensus       186 ~~~L~~~~~~eg~-~i~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        186 IDKLALIAKQEGI-ETSREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             HHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            8888776541111 011234667888888855 444443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.75  E-value=0.057  Score=46.63  Aligned_cols=150  Identities=14%  Similarity=0.137  Sum_probs=83.9

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEE-ecCcCCHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVE-VSQNQDIRKI  160 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~-~~~~~~~~~l  160 (276)
                      .+.+.+..+. .+-..+.|+.|+||+++|+.+....--.                    .|.|....-. -+....++++
T Consensus        13 ~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~id~i   92 (325)
T PRK06871         13 QITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIGVDQV   92 (325)
T ss_pred             HHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCCHHHH
Confidence            4555555544 4677789999999999999987665321                    2333222211 1122234443


Q ss_pred             HHHHHHHhCCCccc------------ccchhh---hhhccccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHH
Q 041612          161 QEEIGDKLGLKFHE------------ESESGR---ANSLFTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       161 ~~~i~~~l~~~~~~------------~~~~~~---~~~l~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                       +.+.+.+......            .-+...   +.+..+..++++.+|++|.+. .+......-...+.+.++++++.
T Consensus        93 -R~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~  171 (325)
T PRK06871         93 -REINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQA  171 (325)
T ss_pred             -HHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHH
Confidence             3444444322111            011111   222222566677777777765 34333333455789999999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      .+.+......   ..   ..+...+..++|.|+.+
T Consensus       172 ~~~L~~~~~~---~~---~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        172 LDWLQAQSSA---EI---SEILTALRINYGRPLLA  200 (325)
T ss_pred             HHHHHHHhcc---Ch---HHHHHHHHHcCCCHHHH
Confidence            9888776421   11   12456678889988643

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.74  E-value=0.059  Score=52.15  Aligned_cols=55  Identities=22%  Similarity=0.236  Sum_probs=38.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC---CCCC--eEEEEEecCcCCHHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD---KLFD--QVVFVEVSQNQDIRKIQEEIGDKL  168 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~f~--~~~wv~~~~~~~~~~l~~~i~~~l  168 (276)
                      .++-|+|++|+|||+.++.+.......   ....  ..+++......+...+...|.+++
T Consensus       782 nvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL  841 (1164)
T PTZ00112        782 QILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQL  841 (1164)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHH
Confidence            466799999999999999998876432   1122  245666555556677777777666

>PRK10867 signal recognition particle protein; Provisional

Probab=96.73  E-value=0.018  Score=51.61  Aligned_cols=29  Identities=28%  Similarity=0.450  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+.+|.++|.+|+||||.+..+......+
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~  127 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKK  127 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            47899999999999999888877665443

>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=96.73  E-value=0.0042  Score=49.68  Aligned_cols=59  Identities=19%  Similarity=0.327  Sum_probs=43.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~  173 (276)
                      ++++.++|+.|+||||.+-++......+  -..+..++... .....+-++..++.++.+..
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~   60 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVPFY   60 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEE
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccccc
Confidence            4789999999999999888888877655  34566666543 23456667788888887754

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 ....

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.73  E-value=0.04  Score=52.38  Aligned_cols=157  Identities=15%  Similarity=0.151  Sum_probs=80.4

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC-----------------CCCeEEEEEecCcCCHHHHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK-----------------LFDQVVFVEVSQNQDIRKIQEEI  164 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-----------------~f~~~~wv~~~~~~~~~~l~~~i  164 (276)
                      .|...+..+. .+...++|+.|+||||+|+.+....-...                 +++ ++++...+...... .+.+
T Consensus        29 ~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~D-vieidaasn~~vd~-IReL  106 (725)
T PRK07133         29 TLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLD-IIEMDAASNNGVDE-IREL  106 (725)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCc-EEEEeccccCCHHH-HHHH
Confidence            4555555544 45678999999999999999877653211                 111 22333222223333 2344


Q ss_pred             HHHhCCCcc----------c--ccchhhhhhccc---cCCCCcEEEE-EeccccccccCCCCCCceeCCCCCHHHHHHHH
Q 041612          165 GDKLGLKFH----------E--ESESGRANSLFT---HGHKGCKVLL-TARSQDVLSGKMDSRPNFSIGVLNEEEAWSLF  228 (276)
Q Consensus       165 ~~~l~~~~~----------~--~~~~~~~~~l~~---~~~~gs~Iiv-TTR~~~va~~~~~~~~~~~l~~L~~~ea~~Lf  228 (276)
                      .+.+.....          +  .-.......+.+   ..+....+|+ ||....+..........+++.+++.++....+
T Consensus       107 ie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L  186 (725)
T PRK07133        107 IENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRL  186 (725)
T ss_pred             HHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHH
Confidence            433321110          0  000111122222   3334455454 44444443332333457899999999998888


Q ss_pred             HHhhCCCCCChhHHHHHHHHHHHcCCCcH-HHHHH
Q 041612          229 KKMAGDYIEDSEFQSIARDVAKECAGLPV-SIVTI  262 (276)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~i~~~c~G~PL-ai~~i  262 (276)
                      ...+...... --.+.+..|+..++|-+- |+..+
T Consensus       187 ~~il~kegI~-id~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        187 EFILEKENIS-YEKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             HHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            7765311111 112346678888888654 44433

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

Probab=96.72  E-value=0.058  Score=49.71  Aligned_cols=38  Identities=26%  Similarity=0.381  Sum_probs=31.8

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++...+.-+-+.=|.++|++|+|||-||+++.|....+
T Consensus       535 d~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~N  572 (802)
T KOG0733|consen  535 DLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGAN  572 (802)
T ss_pred             HHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCc
Confidence            55566666667779999999999999999999998766

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.71  E-value=0.0017  Score=50.53  Aligned_cols=27  Identities=19%  Similarity=0.361  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....|.++|++|+||||+|+.+.....
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            346899999999999999999998874

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

Probab=96.71  E-value=0.0093  Score=50.19  Aligned_cols=152  Identities=22%  Similarity=0.220  Sum_probs=80.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeE-EEEEecCcCCHHHHHHHH--HHHh--------CCC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQV-VFVEVSQNQDIRKIQEEI--GDKL--------GLK  171 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~-~wv~~~~~~~~~~l~~~i--~~~l--------~~~  171 (276)
                      -|.+.+.....+....+|++|.|||+-|+.+....-..+.|.+. .=.++|......-+-..+  ..++        +.+
T Consensus        47 ~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~  126 (346)
T KOG0989|consen   47 VLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYP  126 (346)
T ss_pred             HHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhhccccccCCC
Confidence            44455555667889999999999999999988887665556543 334444332221111111  0111        111


Q ss_pred             ccc-------c---cchhhhhhccc---cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCC
Q 041612          172 FHE-------E---SESGRANSLFT---HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIE  237 (276)
Q Consensus       172 ~~~-------~---~~~~~~~~l~~---~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~  237 (276)
                      .+.       +   -..+.+..+++   .....++.|+.|-.-+ +.........-++.++|.+++..+-+..++.....
T Consensus       127 ~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v  206 (346)
T KOG0989|consen  127 CPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGV  206 (346)
T ss_pred             CCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhCC
Confidence            000       0   00111222222   4445555554443322 21111222335788999999999999888862221


Q ss_pred             ChhHHHHHHHHHHHcCCC
Q 041612          238 DSEFQSIARDVAKECAGL  255 (276)
Q Consensus       238 ~~~~~~~~~~i~~~c~G~  255 (276)
                      +- -.+..+.|++.++|-
T Consensus       207 ~~-d~~al~~I~~~S~Gd  223 (346)
T KOG0989|consen  207 DI-DDDALKLIAKISDGD  223 (346)
T ss_pred             CC-CHHHHHHHHHHcCCc
Confidence            11 124567888888774

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

Probab=96.70  E-value=0.0023  Score=59.45  Aligned_cols=56  Identities=25%  Similarity=0.356  Sum_probs=36.7

Q ss_pred             HHhhhhhhhhhhccccchHHHHHhh------cCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612           84 AADNFTKDEATTNKRCFKGNILSAL------EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus        84 ~~ed~ld~~~~~~~~~~~~~l~~~L------~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .|+.++|...|.... ...+++++|      ..-+-++++++|+||+|||+|++.|.......
T Consensus       316 ~a~~iLd~dHYGLek-VKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rk  377 (782)
T COG0466         316 KAEKILDKDHYGLEK-VKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRK  377 (782)
T ss_pred             HHHHHhcccccCchh-HHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCC
Confidence            344555554443211 111444444      23345799999999999999999999988655

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.70  E-value=0.028  Score=53.26  Aligned_cols=149  Identities=19%  Similarity=0.243  Sum_probs=81.7

Q ss_pred             HHHHhhcCCC---------ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-----------CCHHHHHH
Q 041612          103 NILSALEDPD---------VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-----------QDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~~---------~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-----------~~~~~l~~  162 (276)
                      +++.+|.+++         ++=+.++|++|+|||-||++++....+-  |     ++++..           ....+++.
T Consensus       325 E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVP--F-----~svSGSEFvE~~~g~~asrvr~lf~  397 (774)
T KOG0731|consen  325 EFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVP--F-----FSVSGSEFVEMFVGVGASRVRDLFP  397 (774)
T ss_pred             HHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCc--e-----eeechHHHHHHhcccchHHHHHHHH
Confidence            7777777642         6778999999999999999999887654  3     222221           11122221


Q ss_pred             HHH------------HHhCCCc-------ccccchhhhhhccc----cCCCCcEEE-EEecccccccc-CC---CCCCce
Q 041612          163 EIG------------DKLGLKF-------HEESESGRANSLFT----HGHKGCKVL-LTARSQDVLSG-KM---DSRPNF  214 (276)
Q Consensus       163 ~i~------------~~l~~~~-------~~~~~~~~~~~l~~----~~~~gs~Ii-vTTR~~~va~~-~~---~~~~~~  214 (276)
                      .--            +.++...       .+......++++..    ....+.-|+ -+|...++.+. .+   ..+..+
T Consensus       398 ~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i  477 (774)
T KOG0731|consen  398 LARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQI  477 (774)
T ss_pred             HhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccce
Confidence            110            1111111       00111112222222    222222233 34555555443 12   233467


Q ss_pred             eCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          215 SIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       215 ~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      .++.-+.....++|.-++.......+..++.+ |+....|+|=|.
T Consensus       478 ~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~-~a~~t~gf~gad  521 (774)
T KOG0731|consen  478 QIDLPDVKGRASILKVHLRKKKLDDEDVDLSK-LASLTPGFSGAD  521 (774)
T ss_pred             eccCCchhhhHHHHHHHhhccCCCcchhhHHH-HHhcCCCCcHHH
Confidence            78888888889999988874444445556666 887777776543

>PRK09183 transposase/IS protein; Provisional

Probab=96.69  E-value=0.0085  Score=50.14  Aligned_cols=28  Identities=25%  Similarity=0.339  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+.|+|++|+|||+||..+.+....+
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~~  129 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVRA  129 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHc
Confidence            3568899999999999999998775443

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.68  E-value=0.0019  Score=51.99  Aligned_cols=29  Identities=34%  Similarity=0.598  Sum_probs=25.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+.+|+|.|.+|+||||+|+.++......
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~~~~   35 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHhCcC
Confidence            45799999999999999999999988754

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=96.67  E-value=0.0025  Score=53.36  Aligned_cols=58  Identities=28%  Similarity=0.371  Sum_probs=44.3

Q ss_pred             HHHHhhcC--CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHH
Q 041612          103 NILSALED--PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       103 ~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l  160 (276)
                      +|+..+..  .+..+|+|.|.||+|||||.-.+......++|--.++-|+-|++++-..+
T Consensus        39 ~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsi   98 (323)
T COG1703          39 ELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSI   98 (323)
T ss_pred             HHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCccc
Confidence            56666654  45779999999999999999999998877765556677777777654444

>PRK07667 uridine kinase; Provisional

Probab=96.65  E-value=0.0025  Score=50.92  Aligned_cols=28  Identities=29%  Similarity=0.497  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...+|+|.|.+|+||||+|..+......
T Consensus        16 ~~~iIgI~G~~gsGKStla~~L~~~l~~   43 (193)
T PRK07667         16 NRFILGIDGLSRSGKTTFVANLKENMKQ   43 (193)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3479999999999999999999887654

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

Probab=96.65  E-value=0.0015  Score=46.86  Aligned_cols=23  Identities=48%  Similarity=0.779  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |-|+|.+|+|||+||..+.....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999776554

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PRK00625 shikimate kinase; Provisional

Probab=96.65  E-value=0.0019  Score=50.53  Aligned_cols=25  Identities=20%  Similarity=0.371  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|.++|++|+||||+++.+.+....
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~   26 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSL   26 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            5889999999999999999887653

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=96.64  E-value=0.0036  Score=47.21  Aligned_cols=39  Identities=18%  Similarity=0.316  Sum_probs=28.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ  153 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~  153 (276)
                      ++|.|+|..|+|||||++.+.+....++ +...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g-~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRRG-YRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT---EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHcC-CceEEEEEccC
Confidence            4799999999999999999999988653 55555555544

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.61  E-value=0.0016  Score=52.13  Aligned_cols=23  Identities=48%  Similarity=0.754  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|+|.|.+|+|||||++.+....
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998875

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.

>TIGR00959 ffh signal recognition particle protein

Probab=96.61  E-value=0.038  Score=49.55  Aligned_cols=27  Identities=26%  Similarity=0.374  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.++.++|.+|+||||.+..+.....
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            367999999999999999888877754

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.60  E-value=0.035  Score=51.92  Aligned_cols=160  Identities=16%  Similarity=0.183  Sum_probs=82.1

Q ss_pred             HHHHhhcCCCc-cEEEEEcCCCCcHHHHHHHHHHhcccCC--------------------CCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPDV-NMLGIYGMGGIGKTMLAEEIARKVKSDK--------------------LFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .|.+.+..+.. +.+.++|+.|+||||+|+.+.+...-.+                    +++. +.+...+.....++ 
T Consensus        27 ~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~-~eid~~s~~~v~~i-  104 (576)
T PRK14965         27 TLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDV-FEIDGASNTGVDDI-  104 (576)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCe-eeeeccCccCHHHH-
Confidence            55555555554 4668999999999999999887754211                    2222 22232333333333 


Q ss_pred             HHHHHHhCCCcc----------c--ccchhhhhhcc---ccCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKFH----------E--ESESGRANSLF---THGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~~----------~--~~~~~~~~~l~---~~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +++.+.+.....          +  .-+....+.+.   +.....+.+|++| ....+..........++++.++.++..
T Consensus       105 r~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~  184 (576)
T PRK14965        105 RELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIV  184 (576)
T ss_pred             HHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHH
Confidence            344433321110          0  00111111222   2444556666555 444443332333456788899999888


Q ss_pred             HHHHHhhCCCCCChhHHHHHHHHHHHcCCCc-HHHHHHHHH
Q 041612          226 SLFKKMAGDYIEDSEFQSIARDVAKECAGLP-VSIVTIARA  265 (276)
Q Consensus       226 ~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~P-Lai~~i~~~  265 (276)
                      ..+...+...... --.+....|+..++|-. .|+..+-.+
T Consensus       185 ~~L~~i~~~egi~-i~~~al~~la~~a~G~lr~al~~Ldql  224 (576)
T PRK14965        185 DRLRYIADQEGIS-ISDAALALVARKGDGSMRDSLSTLDQV  224 (576)
T ss_pred             HHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            8777765411111 11234566777777754 455444333

>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=96.60  E-value=0.14  Score=45.50  Aligned_cols=85  Identities=8%  Similarity=0.028  Sum_probs=58.6

Q ss_pred             CCCCcEEEEEecccccccc---CC--CCCCceeCCCCCHHHHHHHHHHhhCCC-CC-------------C-----hhHHH
Q 041612          188 GHKGCKVLLTARSQDVLSG---KM--DSRPNFSIGVLNEEEAWSLFKKMAGDY-IE-------------D-----SEFQS  243 (276)
Q Consensus       188 ~~~gs~IivTTR~~~va~~---~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~-~~-------------~-----~~~~~  243 (276)
                      .++--+||++|-+......   .+  ...+.+.|...+++.|.++...+.... ..             +     .....
T Consensus       180 ~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (431)
T PF10443_consen  180 QNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLA  259 (431)
T ss_pred             hcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHHhcccccccccccccccccccccccccccchH
Confidence            3455678888876554321   12  234578899999999999998887521 00             0     12334


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHh-CCCcc
Q 041612          244 IARDVAKECAGLPVSIVTIARALR-NKRLF  272 (276)
Q Consensus       244 ~~~~i~~~c~G~PLai~~i~~~L~-~~~~~  272 (276)
                      -....+..+||-=.-+..+++.++ +.+++
T Consensus       260 eld~~i~~LGGRltDLe~lvrRiksGe~p~  289 (431)
T PF10443_consen  260 ELDECIEPLGGRLTDLEFLVRRIKSGESPE  289 (431)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHcCCCHH
Confidence            466788889999999999999998 66654

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 [].

>PRK06217 hypothetical protein; Validated

Probab=96.59  E-value=0.0021  Score=50.78  Aligned_cols=36  Identities=22%  Similarity=0.386  Sum_probs=27.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCC--CeEEEEE
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLF--DQVVFVE  150 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f--~~~~wv~  150 (276)
                      ..|.|.|.+|+||||+|+.+....... +|  |..+|-.
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~l~~~-~~~~D~~~~~~   39 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAERLDIP-HLDTDDYFWLP   39 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCc-EEEcCceeecc
Confidence            469999999999999999999887543 33  4456643

>PF14516 AAA_35: AAA-like domain

Probab=96.59  E-value=0.092  Score=45.66  Aligned_cols=54  Identities=11%  Similarity=0.071  Sum_probs=42.7

Q ss_pred             CCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          209 DSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       209 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      +....+.|++++.+|...|+..+-..  ..+   ...+.|...++|+|.-+..++..+.
T Consensus       191 NIg~~i~L~~Ft~~ev~~L~~~~~~~--~~~---~~~~~l~~~tgGhP~Lv~~~~~~l~  244 (331)
T PF14516_consen  191 NIGQPIELPDFTPEEVQELAQRYGLE--FSQ---EQLEQLMDWTGGHPYLVQKACYLLV  244 (331)
T ss_pred             ccccceeCCCCCHHHHHHHHHhhhcc--CCH---HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            33457889999999999999877432  111   2278899999999999999999997

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.59  E-value=0.0018  Score=51.09  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|.|+|++|+||||+|+.+.....
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~~   24 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENFG   24 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcC
Confidence            578999999999999999987764

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.58  E-value=0.036  Score=49.60  Aligned_cols=29  Identities=24%  Similarity=0.355  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+.+|.++|.+|+||||++..+......+
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~  127 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRK  127 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            36799999999999999999988766543

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.58  E-value=0.097  Score=45.11  Aligned_cols=149  Identities=15%  Similarity=0.185  Sum_probs=85.4

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhccc-------------------CCCCCeEEEEEe---cCcCCHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKS-------------------DKLFDQVVFVEV---SQNQDIRK  159 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~-------------------~~~f~~~~wv~~---~~~~~~~~  159 (276)
                      .+...+..+. .+.+.+.|+.|+||+++|..+....--                   ..|.|.. |+.-   ++.-.+++
T Consensus        14 ~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~-~i~p~~~~~~I~vdq   92 (319)
T PRK06090         14 NWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLH-VIKPEKEGKSITVEQ   92 (319)
T ss_pred             HHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEE-EEecCcCCCcCCHHH
Confidence            4444454444 557889999999999999988665421                   1234433 3322   12234444


Q ss_pred             HHHHHHHHhCCCcc------------cccchhhhhhc---cccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHH
Q 041612          160 IQEEIGDKLGLKFH------------EESESGRANSL---FTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEE  223 (276)
Q Consensus       160 l~~~i~~~l~~~~~------------~~~~~~~~~~l---~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~e  223 (276)
                      + +.+.+.+.....            +.-+....+.+   .+..++++.+|++|.+. .+......-...+.+.++++++
T Consensus        93 i-R~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~  171 (319)
T PRK06090         93 I-RQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQ  171 (319)
T ss_pred             H-HHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHH
Confidence            4 344444432211            01111122222   22555667777776654 4544444445678999999999


Q ss_pred             HHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          224 AWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       224 a~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      +.+.+.....+         ....++..++|.|+.+..+
T Consensus       172 ~~~~L~~~~~~---------~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        172 AMQWLKGQGIT---------VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             HHHHHHHcCCc---------hHHHHHHHcCCCHHHHHHH
Confidence            99888654211         1346788899999876554

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.58  E-value=0.0069  Score=49.75  Aligned_cols=48  Identities=21%  Similarity=0.293  Sum_probs=35.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCC----CCeEEEEEecCcCCHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKL----FDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----f~~~~wv~~~~~~~~~~l  160 (276)
                      -.++.|+|.+|+|||+|+.++.........    ...++|++....++...+
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl   70 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL   70 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH
Confidence            468999999999999999999765432211    257889988776665544

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 .

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.57  E-value=0.0018  Score=49.81  Aligned_cols=21  Identities=29%  Similarity=0.551  Sum_probs=19.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      +.|+|.|.||+||||+++.+.
T Consensus         1 m~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           1 MLIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             CeEEEeCCCCCchHHHHHHHH
Confidence            468999999999999999987

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.57  E-value=0.019  Score=48.73  Aligned_cols=28  Identities=18%  Similarity=0.201  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.+|+|.|.+|+||||+|+.+..-..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALLS   87 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4577999999999999999988765553

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.56  E-value=0.0023  Score=50.35  Aligned_cols=26  Identities=19%  Similarity=0.370  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++.|.|++|+|||||++.+......
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCc
Confidence            47899999999999999999887643

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.

>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=96.55  E-value=0.0018  Score=52.86  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|+|.|.+|+||||+|+.+.....
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            589999999999999999998875

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

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.54  E-value=0.0034  Score=47.96  Aligned_cols=39  Identities=28%  Similarity=0.524  Sum_probs=29.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      ++.|+|.+|+|||+++..+......+  -..++|++.....
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~e~~~   39 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATK--GGKVVYVDIEEEI   39 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhc--CCEEEEEECCcch
Confidence            36899999999999999998887553  3456676665443

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.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.53  E-value=0.0031  Score=51.79  Aligned_cols=30  Identities=33%  Similarity=0.492  Sum_probs=26.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ....+++|.|++|.|||||++.+.......
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            457799999999999999999999887654

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=96.53  E-value=0.0045  Score=48.91  Aligned_cols=37  Identities=24%  Similarity=0.370  Sum_probs=29.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      .+++.|+|++|+|||||+..+......+  |...+..+-
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~--~~~~v~~TT   38 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPDK--FGRVVSHTT   38 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTTT--EEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcccc--cccceeecc
Confidence            4789999999999999999999987655  755555443

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 ....

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=96.53  E-value=0.0033  Score=51.13  Aligned_cols=28  Identities=39%  Similarity=0.469  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      --+++|+|.+|+|||||++.+..-.+..
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~Gl~~p~   60 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAGLEKPS   60 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhcccCCC
Confidence            3489999999999999999998766543

>PRK06526 transposase; Provisional

Probab=96.52  E-value=0.0079  Score=50.15  Aligned_cols=29  Identities=24%  Similarity=0.230  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ....+.++|++|+|||+||..+.+....+
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~  125 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQA  125 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHC
Confidence            45578999999999999999998876544

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.52  E-value=0.0024  Score=50.17  Aligned_cols=25  Identities=36%  Similarity=0.511  Sum_probs=22.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|.|.|.+|.||||+|+.+.+....
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i   26 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGL   26 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC
Confidence            5889999999999999999999543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.51  E-value=0.1  Score=45.00  Aligned_cols=152  Identities=18%  Similarity=0.193  Sum_probs=84.5

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC-----------------CCCCeEEEEEe-cCc-------CC
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD-----------------KLFDQVVFVEV-SQN-------QD  156 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~-----------------~~f~~~~wv~~-~~~-------~~  156 (276)
                      .+...+..+. .+.+.++|+.|+||+++|..+....--.                 .|.| ..|+.. ...       .-
T Consensus        15 ~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD-~~~i~~~p~~~~~k~~~~I   93 (319)
T PRK08769         15 QTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPD-LQLVSFIPNRTGDKLRTEI   93 (319)
T ss_pred             HHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCC-EEEEecCCCcccccccccc
Confidence            4555555554 4468899999999999998877654211                 2333 333421 110       01


Q ss_pred             HHHHHHHHHHHhCCCccc------------ccchhhhh---hccccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCC
Q 041612          157 IRKIQEEIGDKLGLKFHE------------ESESGRAN---SLFTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLN  220 (276)
Q Consensus       157 ~~~l~~~i~~~l~~~~~~------------~~~~~~~~---~l~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~  220 (276)
                      ..+-.+++.+.+......            .-+....+   +..+....++.+|++|.+. .+......-...+.+.+++
T Consensus        94 ~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~  173 (319)
T PRK08769         94 VIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPP  173 (319)
T ss_pred             cHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcC
Confidence            122334555544432211            01111122   2222555677777777654 3443333344578899999


Q ss_pred             HHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          221 EEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       221 ~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      .+++.+.+... +  ..    ..-+..++..++|.|+.+...
T Consensus       174 ~~~~~~~L~~~-~--~~----~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        174 AHEALAWLLAQ-G--VS----ERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             HHHHHHHHHHc-C--CC----hHHHHHHHHHcCCCHHHHHHH
Confidence            99998888654 1  11    112557789999999866543

>PRK06851 hypothetical protein; Provisional

Probab=96.51  E-value=0.049  Score=47.72  Aligned_cols=55  Identities=20%  Similarity=0.286  Sum_probs=40.6

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHH
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIR  158 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~  158 (276)
                      .....+..+-.+++.|.|.+|+|||||++.++.....++ ++..++.|-..+.+++
T Consensus       204 s~~~~l~~~~~~~~~i~G~pG~GKstl~~~i~~~a~~~G-~~v~~~hC~~dPdslD  258 (367)
T PRK06851        204 DFVPSLTEGVKNRYFLKGRPGTGKSTMLKKIAKAAEERG-FDVEVYHCGFDPDSLD  258 (367)
T ss_pred             hhHHhHhcccceEEEEeCCCCCcHHHHHHHHHHHHHhCC-CeEEEEeCCCCCCCcc
Confidence            444555555678899999999999999999999987664 6666666655544433

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.51  E-value=0.0025  Score=49.95  Aligned_cols=25  Identities=16%  Similarity=0.311  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.+.|++|+||||+|+.+.....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            5899999999999999999987753

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.50  E-value=0.13  Score=43.05  Aligned_cols=163  Identities=17%  Similarity=0.187  Sum_probs=89.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEEEec----------CcC-----------CH
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFVEVS----------QNQ-----------DI  157 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv~~~----------~~~-----------~~  157 (276)
                      .+.+.....+.+-..++|++|.||-|.+..+.++...-+    .-+...|.+-+          +++           .-
T Consensus        24 ~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEitPSDaG~~D  103 (351)
T KOG2035|consen   24 LLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEITPSDAGNYD  103 (351)
T ss_pred             HHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeChhhcCccc
Confidence            555555567788999999999999998888777764311    12334444322          211           11


Q ss_pred             HHHHHHHHHHhCCCcccccc---------hhhhhhccc-----------cCCCCcEEEEEeccc-cccccCCCCCCceeC
Q 041612          158 RKIQEEIGDKLGLKFHEESE---------SGRANSLFT-----------HGHKGCKVLLTARSQ-DVLSGKMDSRPNFSI  216 (276)
Q Consensus       158 ~~l~~~i~~~l~~~~~~~~~---------~~~~~~l~~-----------~~~~gs~IivTTR~~-~va~~~~~~~~~~~l  216 (276)
                      .-+.+++++.++....-+..         ....+.+..           .-...+|+|+..-+- .+....-...-.+++
T Consensus       104 RvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIrSRCl~iRv  183 (351)
T KOG2035|consen  104 RVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRV  183 (351)
T ss_pred             HHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHhhheeEEeC
Confidence            23445555544332111000         001111111           334456666643221 111211222336789


Q ss_pred             CCCCHHHHHHHHHHhhC-CCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          217 GVLNEEEAWSLFKKMAG-DYIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       217 ~~L~~~ea~~Lf~~~~~-~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ...+++|....+.+... +...-|  .+++.+|+++++|.---...+-...+
T Consensus       184 paps~eeI~~vl~~v~~kE~l~lp--~~~l~rIa~kS~~nLRrAllmlE~~~  233 (351)
T KOG2035|consen  184 PAPSDEEITSVLSKVLKKEGLQLP--KELLKRIAEKSNRNLRRALLMLEAVR  233 (351)
T ss_pred             CCCCHHHHHHHHHHHHHHhcccCc--HHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            99999999999988875 222223  56899999999886544444444444

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=96.49  E-value=0.0052  Score=50.65  Aligned_cols=48  Identities=23%  Similarity=0.294  Sum_probs=31.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRK  159 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~  159 (276)
                      +..+|+|.|+||.|||||.-.+...+..+++--.++-|+-+++++-..
T Consensus        28 ~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGGA   75 (266)
T PF03308_consen   28 RAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGGA   75 (266)
T ss_dssp             -SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC---
T ss_pred             CceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCCc
Confidence            467999999999999999999988887654334555555555554433

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.

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

Probab=96.49  E-value=0.058  Score=48.14  Aligned_cols=117  Identities=15%  Similarity=0.181  Sum_probs=65.0

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-CH---HHHHHHHHHHhCCC-----cc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-DI---RKIQEEIGDKLGLK-----FH  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-~~---~~l~~~i~~~l~~~-----~~  173 (276)
                      +++..+..... ++.|.|+-++||||+.+.+.......     .++++..... +.   .+.+......-..+     .+
T Consensus        28 ~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~-----~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLD  101 (398)
T COG1373          28 RLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLEE-----IIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLD  101 (398)
T ss_pred             HHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCcc-----eEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEe
Confidence            44444444433 99999999999999996666555432     4444433322 22   22233322222210     11


Q ss_pred             cccchhhhhhccc---cCCCCcEEEEEeccccccc-----cCCCCCCceeCCCCCHHHHHH
Q 041612          174 EESESGRANSLFT---HGHKGCKVLLTARSQDVLS-----GKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       174 ~~~~~~~~~~l~~---~~~~gs~IivTTR~~~va~-----~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      +......|....+   +..+. +|++|+-+.....     ...+-...+.+.||+-.|...
T Consensus       102 EIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~  161 (398)
T COG1373         102 EIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLK  161 (398)
T ss_pred             cccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHh
Confidence            2222223333332   33333 8999987766532     234555688999999999865

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=96.48  E-value=0.0033  Score=49.05  Aligned_cols=29  Identities=24%  Similarity=0.365  Sum_probs=25.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..++++|+|..|+|||||++.+......+
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~~   33 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCAR   33 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhhc
Confidence            46799999999999999999999887654

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=96.47  E-value=0.0031  Score=50.91  Aligned_cols=32  Identities=28%  Similarity=0.432  Sum_probs=27.3

Q ss_pred             hhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          107 ALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       107 ~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.+.++++|+++|..|+|||||...+.....
T Consensus        16 ~~~~~~~~~i~~~G~~gsGKTTli~~l~~~~~   47 (207)
T TIGR00073        16 RLDKHGLVVLNFMSSPGSGKTTLIEKLIDNLK   47 (207)
T ss_pred             HhhhcCcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34556799999999999999999999987753

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.47  E-value=0.0023  Score=50.66  Aligned_cols=23  Identities=39%  Similarity=0.612  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|+|.|.+|+||||||+.+....
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999886

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.47  E-value=0.045  Score=53.59  Aligned_cols=37  Identities=24%  Similarity=0.364  Sum_probs=30.2

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +++..|......-+.++|.+|+|||++|..+......
T Consensus       198 ~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~  234 (852)
T TIGR03345       198 QMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAA  234 (852)
T ss_pred             HHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhh
Confidence            6666666666667789999999999999999988753

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.

>PRK05439 pantothenate kinase; Provisional

Probab=96.47  E-value=0.014  Score=50.02  Aligned_cols=28  Identities=21%  Similarity=0.264  Sum_probs=24.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.+|+|.|.+|+||||+|+.+.....
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLS  111 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4577999999999999999999887654

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.47  E-value=0.078  Score=49.44  Aligned_cols=154  Identities=18%  Similarity=0.213  Sum_probs=78.7

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .|.+.+..+. .+...++|+.|+|||++|+.+.......                    .+++ ++.++.........+ 
T Consensus        27 ~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~d-v~eidaas~~~vd~i-  104 (559)
T PRK05563         27 TLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMD-VIEIDAASNNGVDEI-  104 (559)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCC-eEEeeccccCCHHHH-
Confidence            4555555443 4557789999999999999987765321                    1233 233444333333322 


Q ss_pred             HHHHHHhCCCcc----------c--ccchhhhhhccc---cCCCCcEEEEEe-ccccccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKFH----------E--ESESGRANSLFT---HGHKGCKVLLTA-RSQDVLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~~----------~--~~~~~~~~~l~~---~~~~gs~IivTT-R~~~va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +.+.+.+.....          +  .-.......+.+   ..+....+|++| ....+..........+...+++.++..
T Consensus       105 r~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~  184 (559)
T PRK05563        105 RDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIV  184 (559)
T ss_pred             HHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHH
Confidence            334343321110          0  001111112222   333444555444 444343222223346788899999988


Q ss_pred             HHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          226 SLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       226 ~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      ..+...+......- -.+....|+..++|-+.-+
T Consensus       185 ~~L~~i~~~egi~i-~~~al~~ia~~s~G~~R~a  217 (559)
T PRK05563        185 ERLKYILDKEGIEY-EDEALRLIARAAEGGMRDA  217 (559)
T ss_pred             HHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            88887764211111 1234667788888766543

>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=96.47  E-value=0.0088  Score=47.54  Aligned_cols=27  Identities=30%  Similarity=0.495  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|.|+.|+||||+++.+.+.....
T Consensus         1 ~~I~ieG~~GsGKtT~~~~L~~~l~~~   27 (200)
T cd01672           1 MFIVFEGIDGAGKTTLIELLAERLEAR   27 (200)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            368999999999999999999888643

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK13949 shikimate kinase; Provisional

Probab=96.47  E-value=0.003  Score=49.27  Aligned_cols=26  Identities=31%  Similarity=0.425  Sum_probs=23.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.|.|+|++|+||||+++.+......
T Consensus         2 ~~I~liG~~GsGKstl~~~La~~l~~   27 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALARELGL   27 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            46899999999999999999988753

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.07  Score=49.07  Aligned_cols=30  Identities=33%  Similarity=0.460  Sum_probs=25.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..++.+.++|++|+|||.||+.+.+.....
T Consensus       274 ~~~~giLl~GpPGtGKT~lAkava~~~~~~  303 (494)
T COG0464         274 RPPKGVLLYGPPGTGKTLLAKAVALESRSR  303 (494)
T ss_pred             CCCCeeEEECCCCCCHHHHHHHHHhhCCCe
Confidence            456689999999999999999999966544

>PRK13947 shikimate kinase; Provisional

Probab=96.46  E-value=0.003  Score=49.23  Aligned_cols=26  Identities=23%  Similarity=0.390  Sum_probs=22.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .|.|+|++|+||||+|+.+.+.....
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~   28 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFG   28 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCC
Confidence            58999999999999999999887543

>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=96.43  E-value=0.0026  Score=47.99  Aligned_cols=25  Identities=32%  Similarity=0.527  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +|.|.|.+|+||||+|+.+......
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~~   25 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLGL   25 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCC
Confidence            5899999999999999999987643

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.43  E-value=0.0026  Score=48.44  Aligned_cols=23  Identities=22%  Similarity=0.618  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++.+.|++|+||||+|+.+....
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999998764

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=96.43  E-value=0.0029  Score=50.40  Aligned_cols=28  Identities=32%  Similarity=0.429  Sum_probs=25.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++|+|-||=|+||||||+.+.++....
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~~~   31 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLGFK   31 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhCCc
Confidence            4689999999999999999999998744

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.43  E-value=0.096  Score=49.43  Aligned_cols=156  Identities=15%  Similarity=0.090  Sum_probs=79.6

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCCCC---------------------CeEEEEEecCcCCHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDKLF---------------------DQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f---------------------~~~~wv~~~~~~~~~~l  160 (276)
                      .|...+..+. .+.+.++|+.|+||||+|+.+.....-....                     ...+.+.......... 
T Consensus        27 ~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~vd~-  105 (620)
T PRK14948         27 TLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDN-  105 (620)
T ss_pred             HHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEeccccCCHHH-
Confidence            4444444443 3577899999999999999998886432100                     0122233222223333 


Q ss_pred             HHHHHHHhCCCcc------------cccchhhhhhccc---cCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHH
Q 041612          161 QEEIGDKLGLKFH------------EESESGRANSLFT---HGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       161 ~~~i~~~l~~~~~------------~~~~~~~~~~l~~---~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                      .+++++.+.....            +.-.......+.+   .......+|++|.+. .+..........+.+..++.++.
T Consensus       106 IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei  185 (620)
T PRK14948        106 IRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAM  185 (620)
T ss_pred             HHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHH
Confidence            3444444322110            0001111222222   333445555555433 33222222344677888999888


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      ...+.+.+...... --.+....|++.++|.+..+.
T Consensus       186 ~~~L~~ia~kegi~-is~~al~~La~~s~G~lr~A~  220 (620)
T PRK14948        186 VQHLSEIAEKESIE-IEPEALTLVAQRSQGGLRDAE  220 (620)
T ss_pred             HHHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHHHH
Confidence            88777766421111 012346788888988775443

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.43  E-value=0.035  Score=46.78  Aligned_cols=40  Identities=25%  Similarity=0.379  Sum_probs=29.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      .+.+++.++|++|+||||.+..+.......  -..+..++..
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~--g~~V~li~~D  109 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQ--GKSVLLAAGD  109 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhc--CCEEEEEeCC
Confidence            457899999999999999999988777544  1345555543

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.

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

Probab=96.43  E-value=0.0025  Score=53.93  Aligned_cols=28  Identities=29%  Similarity=0.415  Sum_probs=25.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -|+|.++|+||.|||+|.+.+++....+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR  204 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIR  204 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheee
Confidence            6799999999999999999999997654

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.42  E-value=0.0059  Score=49.42  Aligned_cols=27  Identities=33%  Similarity=0.592  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      .|+|+|-||+||||+|..+......++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~   28 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKG   28 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcC
Confidence            689999999999999999666665553

>PRK14530 adenylate kinase; Provisional

Probab=96.42  E-value=0.003  Score=51.34  Aligned_cols=25  Identities=20%  Similarity=0.311  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|.|+|++|+||||+++.+.....
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~   28 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFG   28 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3689999999999999999987764

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.41  E-value=0.014  Score=48.26  Aligned_cols=36  Identities=22%  Similarity=0.289  Sum_probs=28.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVE  150 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~  150 (276)
                      ...+.++|.+|+|||+|+..+.+....+  -..+++++
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~--g~~v~~it  134 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLR--GKSVLIIT  134 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEE
Confidence            3578899999999999999999987654  23455554

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

Probab=96.41  E-value=0.032  Score=52.22  Aligned_cols=53  Identities=25%  Similarity=0.285  Sum_probs=36.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc--CCHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN--QDIRKIQEEIGD  166 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i~~  166 (276)
                      ..-|.|.|..|+|||+|++.+++... +++.-.+.+++.+.-  ...+.+++.+.+
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~  485 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNN  485 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHH
Confidence            45788999999999999999999887 334445666665532  245555554433

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.41  E-value=0.0047  Score=51.73  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=39.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHH
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEI  164 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  164 (276)
                      +.-+++.|+|.+|+|||+++.++.......  ...++|++....  ...+.+..
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e~--~~~l~~~~   70 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGARE--GEPVLYVSTEES--PEELLENA   70 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhc--CCcEEEEEecCC--HHHHHHHH
Confidence            345799999999999999999999888766  788999988654  34444443

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.41  E-value=0.1  Score=45.37  Aligned_cols=150  Identities=13%  Similarity=0.116  Sum_probs=85.0

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhccc--------------------CCCCCeEEEEEec--CcCCHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKS--------------------DKLFDQVVFVEVS--QNQDIRK  159 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~--------------------~~~f~~~~wv~~~--~~~~~~~  159 (276)
                      ++++.+..+. .+-..+.|+.|+||+++|..+....--                    ..|.|..+.....  ....+++
T Consensus        13 ~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~idq   92 (334)
T PRK07993         13 QLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSLGVDA   92 (334)
T ss_pred             HHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccCCHHH
Confidence            5555665544 567789999999999999987666521                    1244443222221  1233444


Q ss_pred             HHHHHHHHhCCCccc------------ccchhhhh---hccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHH
Q 041612          160 IQEEIGDKLGLKFHE------------ESESGRAN---SLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEE  223 (276)
Q Consensus       160 l~~~i~~~l~~~~~~------------~~~~~~~~---~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~e  223 (276)
                      + +.+.+.+......            .-+....+   +..+..+.++.+|++|.+.+ +......-...+.+.++++++
T Consensus        93 i-R~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~  171 (334)
T PRK07993         93 V-REVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQY  171 (334)
T ss_pred             H-HHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHH
Confidence            3 3444444322111            11111222   22335566777777777644 443333334578899999999


Q ss_pred             HHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          224 AWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       224 a~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      +.+.+....+   .++   +.+..++..++|.|..+
T Consensus       172 ~~~~L~~~~~---~~~---~~a~~~~~la~G~~~~A  201 (334)
T PRK07993        172 ALTWLSREVT---MSQ---DALLAALRLSAGAPGAA  201 (334)
T ss_pred             HHHHHHHccC---CCH---HHHHHHHHHcCCCHHHH
Confidence            9888765422   111   22567888999999643

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

Probab=96.40  E-value=0.0088  Score=48.81  Aligned_cols=48  Identities=23%  Similarity=0.322  Sum_probs=35.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEEEecCcCCHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv~~~~~~~~~~l  160 (276)
                      -.++.|+|.+|+|||+|+..+........    .-..++|++....++...+
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl   70 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERL   70 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHH
Confidence            46999999999999999999877654321    0156788887776665544

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.

>TIGR03263 guanyl_kin guanylate kinase

Probab=96.39  E-value=0.0029  Score=49.76  Aligned_cols=24  Identities=25%  Similarity=0.445  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++++|+|++|+|||||++.+....
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            479999999999999999998854

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.

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

Probab=96.38  E-value=0.093  Score=47.66  Aligned_cols=147  Identities=20%  Similarity=0.210  Sum_probs=74.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH-----HHHHHHHHHHhCCCccc------------
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI-----RKIQEEIGDKLGLKFHE------------  174 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~-----~~l~~~i~~~l~~~~~~------------  174 (276)
                      .+..+.+.|++|+|||+||..+.....    |..+--++.......     -.-.+.+.+......-.            
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~S~----FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD  612 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALSSD----FPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLD  612 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhhcC----CCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhc
Confidence            456778899999999999999886653    665554443222111     11112222222111100            


Q ss_pred             ------c-cc--hhhh-hhccccCCCCcEEEE--EeccccccccCCC----CCCceeCCCCCH-HHHHHHHHHhhCCCCC
Q 041612          175 ------E-SE--SGRA-NSLFTHGHKGCKVLL--TARSQDVLSGKMD----SRPNFSIGVLNE-EEAWSLFKKMAGDYIE  237 (276)
Q Consensus       175 ------~-~~--~~~~-~~l~~~~~~gs~Iiv--TTR~~~va~~~~~----~~~~~~l~~L~~-~ea~~Lf~~~~~~~~~  237 (276)
                            . ++  .+.+ ..+.+..+.|-|.+|  ||....|... ++    ....|+++.++. ++..+.+...-  ...
T Consensus       613 ~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~-m~i~~~F~~~i~Vpnl~~~~~~~~vl~~~n--~fs  689 (744)
T KOG0741|consen  613 YVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQE-MGILDCFSSTIHVPNLTTGEQLLEVLEELN--IFS  689 (744)
T ss_pred             ccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHH-cCHHHhhhheeecCccCchHHHHHHHHHcc--CCC
Confidence                  0 00  0111 111124555666554  5555666543 22    223688888876 66777776553  123


Q ss_pred             ChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          238 DSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       238 ~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      +.+...++.+...+|  +-..|+.+-.++-
T Consensus       690 d~~~~~~~~~~~~~~--~~vgIKklL~lie  717 (744)
T KOG0741|consen  690 DDEVRAIAEQLLSKK--VNVGIKKLLMLIE  717 (744)
T ss_pred             cchhHHHHHHHhccc--cchhHHHHHHHHH
Confidence            344455566666666  3344555544443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.37  E-value=0.099  Score=50.56  Aligned_cols=36  Identities=28%  Similarity=0.409  Sum_probs=27.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++...+.-...+-+.++|++|+|||+||+.+.+...
T Consensus       202 ~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~  237 (733)
T TIGR01243       202 ELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG  237 (733)
T ss_pred             HHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhC
Confidence            334444444566789999999999999999998764

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.

>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=96.37  E-value=0.0029  Score=49.84  Aligned_cols=24  Identities=33%  Similarity=0.693  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|+|.|.+|+||||||..+.....
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~   24 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLR   24 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999998865

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=96.36  E-value=0.0025  Score=46.82  Aligned_cols=28  Identities=36%  Similarity=0.610  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcccCCCCCe
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVKSDKLFDQ  145 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~~~~~f~~  145 (276)
                      |.|.|.+|+|||++|+.+.......  |..
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~--f~R   29 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLS--FKR   29 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT----EEE
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCc--eeE
Confidence            6789999999999999999887655  543

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.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.36  E-value=0.069  Score=49.74  Aligned_cols=154  Identities=14%  Similarity=0.181  Sum_probs=80.6

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------------CCCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------------KLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .|...+..+. .+...++|+.|+||||+|+.+.+.....                    .+++. +++..........+.
T Consensus        27 ~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv-~~idgas~~~vddIr  105 (563)
T PRK06647         27 TLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDV-IEIDGASNTSVQDVR  105 (563)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCe-EEecCcccCCHHHHH
Confidence            5555555544 4468899999999999999998876421                    12332 233333333444443


Q ss_pred             HHHHHHhCC-Ccc-----------cccchhhhhhc---cccCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGL-KFH-----------EESESGRANSL---FTHGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~-~~~-----------~~~~~~~~~~l---~~~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                       ++.+.+.. +..           +.-.....+.+   .+..++.+.+|++|.+ ..+..........+++.+++.++..
T Consensus       106 -~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~  184 (563)
T PRK06647        106 -QIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIY  184 (563)
T ss_pred             -HHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHH
Confidence             33322211 100           00111111122   2244455666665533 3332222222346889999999988


Q ss_pred             HHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHH
Q 041612          226 SLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI  259 (276)
Q Consensus       226 ~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai  259 (276)
                      ..+.+.+...... --.+....|+..++|-+-.+
T Consensus       185 ~~L~~i~~~egi~-id~eAl~lLa~~s~GdlR~a  217 (563)
T PRK06647        185 NMLKKVCLEDQIK-YEDEALKWIAYKSTGSVRDA  217 (563)
T ss_pred             HHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHH
Confidence            8888776421111 11234667888888876433

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.36  E-value=0.0041  Score=48.70  Aligned_cols=28  Identities=29%  Similarity=0.440  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...+|.+.|++|+||||+|+.+......
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3458999999999999999999988754

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

Probab=96.35  E-value=0.057  Score=52.32  Aligned_cols=28  Identities=32%  Similarity=0.471  Sum_probs=24.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...++.++|++|+||||+++.+......
T Consensus       348 ~g~~i~l~GppG~GKTtl~~~ia~~l~~  375 (784)
T PRK10787        348 KGPILCLVGPPGVGKTSLGQSIAKATGR  375 (784)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4568999999999999999999987653

>PRK04182 cytidylate kinase; Provisional

Probab=96.35  E-value=0.0089  Score=46.78  Aligned_cols=24  Identities=38%  Similarity=0.510  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg   25 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            799999999999999999988764

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=96.35  E-value=0.0035  Score=47.09  Aligned_cols=24  Identities=21%  Similarity=0.506  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++|+|++|+|||||++.+.....
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~~   24 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFD   24 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcCC
Confidence            378999999999999999997753

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.

>cd01394 radB RadB

Probab=96.35  E-value=0.01  Score=48.25  Aligned_cols=41  Identities=22%  Similarity=0.353  Sum_probs=31.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      -.++.|.|.+|+|||+++.++......+  -..++|++....+
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~--g~~v~yi~~e~~~   59 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQ--GKKVAYIDTEGLS   59 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCCCC
Confidence            5689999999999999999998776543  2456777654443

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

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.35  E-value=0.0095  Score=48.67  Aligned_cols=45  Identities=20%  Similarity=0.375  Sum_probs=34.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l  160 (276)
                      -.++.|+|.+|+|||+++.++.......  -..++|++.. ..+...+
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~--~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKN--GKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEECC-CCCHHHH
Confidence            4689999999999999999998876544  4678888876 4444443

>PRK13975 thymidylate kinase; Provisional

Probab=96.33  E-value=0.0037  Score=49.85  Aligned_cols=26  Identities=31%  Similarity=0.483  Sum_probs=23.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.|.|.|+.|+||||+++.+......
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999988864

>PRK00300 gmk guanylate kinase; Provisional

Probab=96.32  E-value=0.0036  Score=50.33  Aligned_cols=26  Identities=19%  Similarity=0.316  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+|+|+|++|+|||||++.+.....
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            46899999999999999999988753

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.32  E-value=0.0061  Score=47.64  Aligned_cols=25  Identities=20%  Similarity=0.359  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.++.|.|++|+|||||++.++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3578999999999999999999877

>PRK14527 adenylate kinase; Provisional

Probab=96.30  E-value=0.0049  Score=49.06  Aligned_cols=28  Identities=25%  Similarity=0.320  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...+|.|+|++|+||||+|+.+......
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~~~   32 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQELGL   32 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4578999999999999999999877654

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.29  E-value=0.0043  Score=49.63  Aligned_cols=25  Identities=36%  Similarity=0.442  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+|.|.|.+|+||||+|+.+....
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998875

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.29  E-value=0.0055  Score=49.05  Aligned_cols=37  Identities=22%  Similarity=0.252  Sum_probs=28.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      .--+++|+|++|+|||||.+.+..-...+   +..+|+.-
T Consensus        27 ~Gevv~iiGpSGSGKSTlLRclN~LE~~~---~G~I~i~g   63 (240)
T COG1126          27 KGEVVVIIGPSGSGKSTLLRCLNGLEEPD---SGSITVDG   63 (240)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCcCCC---CceEEECC
Confidence            34589999999999999999987666544   56677653

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

Probab=96.28  E-value=0.016  Score=54.26  Aligned_cols=52  Identities=31%  Similarity=0.456  Sum_probs=37.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK  167 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  167 (276)
                      +.-++..++|++|.||||||..+.++....     ++=+++|..-+...+-..|...
T Consensus       324 P~kKilLL~GppGlGKTTLAHViAkqaGYs-----VvEINASDeRt~~~v~~kI~~a  375 (877)
T KOG1969|consen  324 PPKKILLLCGPPGLGKTTLAHVIAKQAGYS-----VVEINASDERTAPMVKEKIENA  375 (877)
T ss_pred             CccceEEeecCCCCChhHHHHHHHHhcCce-----EEEecccccccHHHHHHHHHHH
Confidence            357799999999999999999999887533     5556666665555555555443

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.27  E-value=0.041  Score=45.44  Aligned_cols=38  Identities=37%  Similarity=0.543  Sum_probs=31.5

Q ss_pred             HHHHhhcCC------CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDP------DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -|...|.++      -++.|..+|++|.|||.+|+.+.+..++-
T Consensus       135 li~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp  178 (368)
T COG1223         135 LIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVP  178 (368)
T ss_pred             HHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCc
Confidence            566667664      38899999999999999999999887653

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=96.27  E-value=0.0033  Score=48.61  Aligned_cols=23  Identities=26%  Similarity=0.582  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |.|+|++|+||||+|+.+.....
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~   23 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLG   23 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcC
Confidence            46899999999999999987763

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.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.27  E-value=0.01  Score=45.98  Aligned_cols=24  Identities=38%  Similarity=0.540  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|.|.|.+|+||||+|+.+.+...
T Consensus         2 iI~i~G~~GSGKstia~~la~~lg   25 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLS   25 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            799999999999999999987653

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.

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

Probab=96.24  E-value=0.0088  Score=49.14  Aligned_cols=37  Identities=24%  Similarity=0.404  Sum_probs=30.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      +-.++|+|.+|+|||+|...+.......  |.++++++-
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~~~~~~--f~~I~l~t~   49 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLYYLRHK--FDHIFLITP   49 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhccc--CCEEEEEec
Confidence            3478899999999999999999887665  877776643

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

>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=96.23  E-value=0.0042  Score=47.33  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=21.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhccc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      |.++|++|+||||+|+.+......
T Consensus         2 i~l~G~~GsGKstla~~la~~l~~   25 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALGL   25 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCC
Confidence            789999999999999999877643

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.

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.20  E-value=0.019  Score=50.18  Aligned_cols=70  Identities=11%  Similarity=0.157  Sum_probs=50.5

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCe-EEEEEecCcC-CHHHHHHHHHHHhCCCcc
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQ-VVFVEVSQNQ-DIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~-~~wv~~~~~~-~~~~l~~~i~~~l~~~~~  173 (276)
                      ++++.+.. ..-..+.|+|.+|+|||||++.+.+....+ +.+. .+|+.+.+.. .+.++.+.+...+.....
T Consensus       122 RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~-~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~  194 (380)
T PRK12608        122 RVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAAN-HPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTF  194 (380)
T ss_pred             hhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEEecCCCCCHHHHHHHHhhhEEeecC
Confidence            56666654 234577999999999999999999887654 3454 4677777654 678888888776665443

>PRK14737 gmk guanylate kinase; Provisional

Probab=96.20  E-value=0.0049  Score=48.88  Aligned_cols=26  Identities=15%  Similarity=0.285  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.++|.|+|++|+|||||++.+....
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45789999999999999999998764

>PRK03846 adenylylsulfate kinase; Provisional

Probab=96.19  E-value=0.008  Score=48.15  Aligned_cols=29  Identities=21%  Similarity=0.331  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +...+|.|+|.+|+||||||+.+......
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l~~   50 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHE   50 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            45679999999999999999999887643

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=96.19  E-value=0.015  Score=46.22  Aligned_cols=27  Identities=26%  Similarity=0.427  Sum_probs=24.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..|+|.|..|+||||+++.+.+.....
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l~~~   30 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLLQEN   30 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            579999999999999999999887654

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.

>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE

Probab=96.18  E-value=0.017  Score=52.13  Aligned_cols=52  Identities=15%  Similarity=0.155  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhhccccchHHHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612           73 NWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus        73 ~wl~~l~~~~~~~ed~ld~~~~~~~~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+...+..+..+.+++++.+ ..       +    ...++ ..|+|+|.+|+|||||...+.+..
T Consensus       176 ~~~~~l~~~~~~l~~ll~~~-~~-------~----~~~~g-~kVvIvG~~nvGKSSLiN~L~~~~  227 (442)
T TIGR00450       176 SLNQLLLSIIAELKDILNSY-KL-------E----KLDDG-FKLAIVGSPNVGKSSLLNALLKQD  227 (442)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HH-------H----HhhcC-CEEEEECCCCCcHHHHHHHHhCCC
Confidence            66777777777777777766 21       1    11222 468999999999999999998763

TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer.

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

Probab=96.18  E-value=0.016  Score=50.26  Aligned_cols=62  Identities=26%  Similarity=0.382  Sum_probs=51.4

Q ss_pred             HHHHhhcCCC---ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          103 NILSALEDPD---VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       103 ~l~~~L~~~~---~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      .+...+.+++   +..+-|+|..|.|||.+.+++++....     ..+|+++-.+++...++..|+.+++
T Consensus        17 ~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~~~   81 (438)
T KOG2543|consen   17 RLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNKSQ   81 (438)
T ss_pred             HHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHHhc
Confidence            5666666543   445688999999999999999988843     3589999999999999999999885

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=96.17  E-value=0.0059  Score=47.77  Aligned_cols=26  Identities=19%  Similarity=0.374  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.|.|+|+.|+||||+++.+.....
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~   29 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcC
Confidence            35799999999999999999998764

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.16  E-value=0.021  Score=46.88  Aligned_cols=53  Identities=19%  Similarity=0.288  Sum_probs=34.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      -.++.|.|.+|+|||||+.++......++  ...++++  ...+..++++.+ .+++.
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~g--~~~~yi~--~e~~~~~~~~~~-~~~g~   76 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQNG--YSVSYVS--TQLTTTEFIKQM-MSLGY   76 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEEe--CCCCHHHHHHHH-HHhCC
Confidence            45899999999999999877666553332  3456666  333556666665 34443

>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=96.16  E-value=0.0043  Score=48.32  Aligned_cols=24  Identities=33%  Similarity=0.527  Sum_probs=20.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhccc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      |.|.|.+|+|||||.+.+....+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhc
Confidence            689999999999999999988854

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.16  E-value=0.0045  Score=49.03  Aligned_cols=25  Identities=20%  Similarity=0.422  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.|+|++|+|||||++.+.....
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~   27 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQ   27 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCC
Confidence            3789999999999999999976653

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.16  E-value=0.0056  Score=53.21  Aligned_cols=28  Identities=29%  Similarity=0.368  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+++.++|++|+||||||..+.+....
T Consensus        77 ~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       77 RKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4678999999999999999999888754

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

>PF13245 AAA_19: Part of AAA domain

Probab=96.16  E-value=0.014  Score=38.94  Aligned_cols=26  Identities=35%  Similarity=0.446  Sum_probs=18.8

Q ss_pred             CccEEEEEcCCCCcHHH-HHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTM-LAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTt-La~~v~~~~  137 (276)
                      +.++..|.|++|.|||+ ++..+.+..
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            34678889999999995 555555444

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

Probab=96.15  E-value=0.088  Score=48.57  Aligned_cols=30  Identities=30%  Similarity=0.261  Sum_probs=26.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..++=|.++|++|+|||.||+.+.++..+-
T Consensus       221 ~PprGvLlHGPPGCGKT~lA~AiAgel~vP  250 (802)
T KOG0733|consen  221 RPPRGVLLHGPPGCGKTSLANAIAGELGVP  250 (802)
T ss_pred             CCCCceeeeCCCCccHHHHHHHHhhhcCCc
Confidence            347788999999999999999999998765

>PRK12377 putative replication protein; Provisional

Probab=96.15  E-value=0.0057  Score=50.74  Aligned_cols=38  Identities=26%  Similarity=0.337  Sum_probs=29.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      ...+.++|.+|+|||+||..+.+....+  .-.+.++++.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~--g~~v~~i~~~  138 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAK--GRSVIVVTVP  138 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEHH
Confidence            4578999999999999999999998754  3335666553

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=96.14  E-value=0.011  Score=49.91  Aligned_cols=38  Identities=21%  Similarity=0.227  Sum_probs=32.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +...++...+..++.|.|.+|.|||||...+.+.....
T Consensus        94 ~~r~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~~l~~~  131 (290)
T PRK10463         94 RNRARFAARKQLVLNLVSSPGSGKTTLLTETLMRLKDS  131 (290)
T ss_pred             HHHHHHHhcCCeEEEEECCCCCCHHHHHHHHHHHhccC
Confidence            45566677788999999999999999999999887654

>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=96.14  E-value=0.0058  Score=44.29  Aligned_cols=25  Identities=24%  Similarity=0.351  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|.|+|..|+|||||.+.+.+....
T Consensus         1 kI~V~G~~g~GKTsLi~~l~~~~~~   25 (119)
T PF08477_consen    1 KIVVLGDSGVGKTSLIRRLCGGEFP   25 (119)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS--
T ss_pred             CEEEECcCCCCHHHHHHHHhcCCCc
Confidence            3789999999999999999877654

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.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.12  E-value=0.008  Score=47.38  Aligned_cols=45  Identities=18%  Similarity=0.166  Sum_probs=30.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  163 (276)
                      ++.|.|.+|+|||+|+.++......+  =..+.|++...  +...+.+.
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC--CCcEEEEECCC--CHHHHHHH
Confidence            36789999999999999987765433  24567776543  44444433

A related protein is found in archaea.

>PLN02200 adenylate kinase family protein

Probab=96.12  E-value=0.0058  Score=50.34  Aligned_cols=27  Identities=22%  Similarity=0.198  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.+|.|.|++|+||||+|+.+.....
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~g   68 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETFG   68 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999987653

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

Probab=96.11  E-value=0.17  Score=41.76  Aligned_cols=51  Identities=14%  Similarity=0.081  Sum_probs=37.8

Q ss_pred             eeCCCCCHHHHHHHHHHhhCCCCCChh--HHHHHHHHHHHcCCCcHHHHHHHH
Q 041612          214 FSIGVLNEEEAWSLFKKMAGDYIEDSE--FQSIARDVAKECAGLPVSIVTIAR  264 (276)
Q Consensus       214 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~--~~~~~~~i~~~c~G~PLai~~i~~  264 (276)
                      |++.|++.++...+++.+......+..  ..+....|.....|.|.+|..++.
T Consensus       195 ~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         195 IELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             EecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            899999999999988887752221111  134577889999999999987764

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.11  E-value=0.0073  Score=50.01  Aligned_cols=30  Identities=23%  Similarity=0.445  Sum_probs=26.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      .+..|.++||.|.||||..+.++.+...+.
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~   47 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHLHAKK   47 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHHhhcc
Confidence            466888999999999999999999988763

>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.10  E-value=0.0089  Score=46.11  Aligned_cols=34  Identities=21%  Similarity=0.339  Sum_probs=28.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEE
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVE  150 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~  150 (276)
                      -.+.+.|++|+||+||.+.+|.++...   ...+|+.
T Consensus        38 ECvvL~G~SG~GKStllr~LYaNY~~d---~G~I~v~   71 (235)
T COG4778          38 ECVVLHGPSGSGKSTLLRSLYANYLPD---EGQILVR   71 (235)
T ss_pred             cEEEeeCCCCCcHHHHHHHHHhccCCC---CceEEEE
Confidence            368899999999999999999999875   5667663

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.10  E-value=0.29  Score=42.18  Aligned_cols=154  Identities=17%  Similarity=0.152  Sum_probs=83.2

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC--------------CCCCeEEEEEe-----cCcC-------
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD--------------KLFDQVVFVEV-----SQNQ-------  155 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------~~f~~~~wv~~-----~~~~-------  155 (276)
                      .+...+..+. .+...++|+.|+||+++|..+....-..              .|.|. .|+.-     +...       
T Consensus        15 ~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl-~~i~p~~~~~g~~~~~~~~~~   93 (314)
T PRK07399         15 LLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDL-LWVEPTYQHQGKLITASEAEE   93 (314)
T ss_pred             HHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCE-EEEeccccccccccchhhhhh
Confidence            3444444454 5789999999999999998887765321              23332 33321     1000       


Q ss_pred             ---------C-HHHHHHHHHHHhCCCccc------------ccchhhhhhccc---cCCCCcEEEEEecc-ccccccCCC
Q 041612          156 ---------D-IRKIQEEIGDKLGLKFHE------------ESESGRANSLFT---HGHKGCKVLLTARS-QDVLSGKMD  209 (276)
Q Consensus       156 ---------~-~~~l~~~i~~~l~~~~~~------------~~~~~~~~~l~~---~~~~gs~IivTTR~-~~va~~~~~  209 (276)
                               . ..+-.+.|.+.+......            .-+....+.+.+   ..+ .+.+|++|.+ ..+......
T Consensus        94 ~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~~~~~Ll~TI~S  172 (314)
T PRK07399         94 AGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAPSPESLLPTIVS  172 (314)
T ss_pred             ccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEECChHhCcHHHHh
Confidence                     0 011234555554432211            011111222222   233 4456665544 344444444


Q ss_pred             CCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          210 SRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       210 ~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      ....+++.++++++..+.+.+.........    ....++..++|-|..+...
T Consensus       173 Rcq~i~f~~l~~~~~~~~L~~~~~~~~~~~----~~~~l~~~a~Gs~~~al~~  221 (314)
T PRK07399        173 RCQIIPFYRLSDEQLEQVLKRLGDEEILNI----NFPELLALAQGSPGAAIAN  221 (314)
T ss_pred             hceEEecCCCCHHHHHHHHHHhhccccchh----HHHHHHHHcCCCHHHHHHH
Confidence            456899999999999999987743111111    1346788899999655443

>PRK14738 gmk guanylate kinase; Provisional

Probab=96.09  E-value=0.0063  Score=49.08  Aligned_cols=26  Identities=19%  Similarity=0.370  Sum_probs=22.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ...+.+.|+|++|+|||||+..+...
T Consensus        11 ~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         11 AKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            35778999999999999999998754

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.09  E-value=0.0051  Score=46.93  Aligned_cols=25  Identities=24%  Similarity=0.498  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ++.|+|.+|+||||||+.+......
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~~   25 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLFQ   25 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4789999999999999999888753

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=96.09  E-value=0.0056  Score=47.07  Aligned_cols=29  Identities=41%  Similarity=0.661  Sum_probs=25.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      .++++|+|..|+|||||...+....+.++
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G   30 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARG   30 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCC
Confidence            47899999999999999999998887763

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

Probab=96.09  E-value=0.068  Score=51.59  Aligned_cols=37  Identities=27%  Similarity=0.352  Sum_probs=30.3

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +++..|......-+.++|++|+|||++|+.+.+....
T Consensus       193 ~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~  229 (731)
T TIGR02639       193 RTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAE  229 (731)
T ss_pred             HHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            5666666666667889999999999999999988744

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.09  E-value=0.019  Score=49.44  Aligned_cols=58  Identities=21%  Similarity=0.387  Sum_probs=42.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      .-.++-|+|.+|+|||+++.+++.......    .=..++|++....++...+. ++++.++.
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl  155 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGL  155 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            367889999999999999999987754210    01378999988888877654 44455544

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.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.08  E-value=0.0077  Score=49.90  Aligned_cols=58  Identities=24%  Similarity=0.380  Sum_probs=36.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe--cC--cCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV--SQ--NQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~--~~--~~~~~~l~~~i~~~l~~~  171 (276)
                      .-.+++|+|.+|+|||||++.+..-....  ...+.|-.-  ..  .....+-..++++.++.+
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~pt--~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~   99 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEPT--SGEILFEGKDITKLSKEERRERVLELLEKVGLP   99 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCCC--CceEEEcCcchhhcchhHHHHHHHHHHHHhCCC
Confidence            34689999999999999999999888764  334443211  11  112333445566666643

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.07  E-value=0.035  Score=48.35  Aligned_cols=28  Identities=29%  Similarity=0.379  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+-|.++|++|.|||-||++|+......
T Consensus       245 WkgvLm~GPPGTGKTlLAKAvATEc~tT  272 (491)
T KOG0738|consen  245 WKGVLMVGPPGTGKTLLAKAVATECGTT  272 (491)
T ss_pred             cceeeeeCCCCCcHHHHHHHHHHhhcCe
Confidence            5678899999999999999999988754

>PRK14531 adenylate kinase; Provisional

Probab=96.02  E-value=0.0065  Score=47.99  Aligned_cols=25  Identities=24%  Similarity=0.222  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|.|+|++|+||||+++.+.....
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g   27 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHG   27 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999988764

>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=96.02  E-value=0.0061  Score=43.46  Aligned_cols=22  Identities=45%  Similarity=0.398  Sum_probs=19.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      -..++|.|++|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            3579999999999999999976

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

>PRK13946 shikimate kinase; Provisional

Probab=96.02  E-value=0.0072  Score=47.81  Aligned_cols=27  Identities=19%  Similarity=0.321  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+.|.+.|++|+||||+++.+......
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~   36 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGL   36 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            357999999999999999999988743

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.00  E-value=0.02  Score=49.42  Aligned_cols=58  Identities=22%  Similarity=0.408  Sum_probs=42.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCC----CCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKL----FDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      .-.++-|+|.+|+|||+++.++.........    =..++|++....++...+. ++++.++.
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g~  162 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALGL  162 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcCC
Confidence            4678999999999999999999876533211    1478999988887877765 34455543

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.99  E-value=0.0059  Score=47.19  Aligned_cols=22  Identities=36%  Similarity=0.410  Sum_probs=17.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|+|.|..|+|||||+..+...
T Consensus         1 rI~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    1 RIVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             -EEEE--TTSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHc
Confidence            3899999999999999999977

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.98  E-value=0.024  Score=50.02  Aligned_cols=29  Identities=24%  Similarity=0.475  Sum_probs=25.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +.++|+++|++|+||||++..+......+
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~  268 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGK  268 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            46899999999999999999998877543

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=95.98  E-value=0.0083  Score=49.74  Aligned_cols=28  Identities=32%  Similarity=0.459  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|.|+.|+|||||.+.+..-.+..
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g~l~p~   55 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAGLLKPK   55 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCCCC
Confidence            4689999999999999999999877654

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.98  E-value=0.22  Score=43.36  Aligned_cols=65  Identities=18%  Similarity=0.257  Sum_probs=41.5

Q ss_pred             cCCCCcEEEEEecc-ccccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          187 HGHKGCKVLLTARS-QDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       187 ~~~~gs~IivTTR~-~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      ..++++.+|++|.+ ..+......-...+.+.+++.++..+.+.....   .  +    ....+..++|.|+.+.
T Consensus       158 EPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~~---~--~----~~~~l~~~~Gsp~~Al  223 (342)
T PRK06964        158 EPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQGV---A--D----ADALLAEAGGAPLAAL  223 (342)
T ss_pred             CCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcCC---C--h----HHHHHHHcCCCHHHHH
Confidence            55566666666655 445444334446789999999999988876511   1  1    1235677888887444

>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=95.97  E-value=0.0061  Score=48.43  Aligned_cols=23  Identities=35%  Similarity=0.442  Sum_probs=20.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |.|.|++|+||||+|+.+.....
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~   24 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYG   24 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999988753

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.97  E-value=0.0061  Score=46.83  Aligned_cols=26  Identities=35%  Similarity=0.502  Sum_probs=23.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +++|+|+.|+|||||+..+....+.+
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~~   26 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKAR   26 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            57899999999999999999987654

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.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.96  E-value=0.0065  Score=49.71  Aligned_cols=27  Identities=33%  Similarity=0.393  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      --.++|+|++|+|||||-+.+..-.+.
T Consensus        29 GEfvsilGpSGcGKSTLLriiAGL~~p   55 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIAGLEKP   55 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            348999999999999999999876654

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.96  E-value=0.01  Score=45.99  Aligned_cols=33  Identities=21%  Similarity=0.399  Sum_probs=28.4

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +..+...+|-+.|.+|.||||+|..+.......
T Consensus        18 ~~~~~~~viW~TGLSGsGKSTiA~ale~~L~~~   50 (197)
T COG0529          18 LKGQKGAVIWFTGLSGSGKSTIANALEEKLFAK   50 (197)
T ss_pred             HhCCCCeEEEeecCCCCCHHHHHHHHHHHHHHc
Confidence            445567799999999999999999999998765

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=95.95  E-value=0.0058  Score=50.83  Aligned_cols=25  Identities=28%  Similarity=0.684  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +|.++|++|+||||+|+.+......
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4789999999999999999877653

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.

>TIGR01287 nifH nitrogenase iron protein

Probab=95.95  E-value=0.0068  Score=51.20  Aligned_cols=28  Identities=36%  Similarity=0.623  Sum_probs=24.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      +.|+|+|-||+||||++..+......++
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~La~~G   28 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAALAEMG   28 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHHHHCC
Confidence            5799999999999999999888876553

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PRK13948 shikimate kinase; Provisional

Probab=95.94  E-value=0.0081  Score=47.41  Aligned_cols=27  Identities=26%  Similarity=0.453  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.|.++|+.|+||||+++.+.....
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg   35 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALM   35 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            457899999999999999999998764

>PRK14532 adenylate kinase; Provisional

Probab=95.94  E-value=0.0068  Score=48.04  Aligned_cols=24  Identities=21%  Similarity=0.271  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.+.|++|+||||+|+.+.....
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g   25 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERG   25 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            378899999999999999986653

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.93  E-value=0.015  Score=47.31  Aligned_cols=52  Identities=21%  Similarity=0.230  Sum_probs=31.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc-----CCCCCeEEEEEecCcCCHHHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS-----DKLFDQVVFVEVSQNQDIRKIQEEIGD  166 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~-----~~~f~~~~wv~~~~~~~~~~l~~~i~~  166 (276)
                      +..|.|++|+|||+++..+......     .......+-++...+.....++..+.+
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            7889999999999876666666511     112445555555556566666666655

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=95.92  E-value=0.0081  Score=47.20  Aligned_cols=26  Identities=23%  Similarity=0.447  Sum_probs=22.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++.|+|.+|+|||||++.+......
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~~   29 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFSA   29 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCC
Confidence            47899999999999999999987653

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.92  E-value=0.017  Score=49.96  Aligned_cols=30  Identities=23%  Similarity=0.471  Sum_probs=25.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+..+|+|.|.+|+|||||...+.......
T Consensus        54 ~~~~~igi~G~~GaGKSTl~~~l~~~l~~~   83 (332)
T PRK09435         54 GNALRIGITGVPGVGKSTFIEALGMHLIEQ   83 (332)
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            457799999999999999999987777654

>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=95.91  E-value=0.011  Score=45.49  Aligned_cols=27  Identities=30%  Similarity=0.569  Sum_probs=24.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++++|+|..|+|||||+..+......+
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~l~~~   28 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPALSAR   28 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999887655

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.91  E-value=0.017  Score=48.51  Aligned_cols=23  Identities=43%  Similarity=0.546  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -+.+.|.+|+|||+||+.+....
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~l   45 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARKR   45 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            56789999999999999998744

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).

>COG3899 Predicted ATPase [General function prediction only]

Probab=95.91  E-value=0.068  Score=52.33  Aligned_cols=55  Identities=15%  Similarity=0.109  Sum_probs=44.6

Q ss_pred             CCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          211 RPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       211 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ...+.|.||+..+...+.........  ....+....|.++..|.|+-+.-+-..|.
T Consensus       211 i~~I~L~PL~~~d~~~lV~~~l~~~~--~~~~p~~~~i~~kt~GnPfFi~e~lk~l~  265 (849)
T COG3899         211 ITTITLAPLSRADTNQLVAATLGCTK--LLPAPLLELIFEKTKGNPFFIEEFLKALY  265 (849)
T ss_pred             eeEEecCcCchhhHHHHHHHHhCCcc--cccchHHHHHHHHhcCCCccHHHHHHHHH
Confidence            35789999999999999998887421  22234577899999999999999988887

>PRK13695 putative NTPase; Provisional

Probab=95.90  E-value=0.013  Score=45.88  Aligned_cols=25  Identities=44%  Similarity=0.620  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++|.|.+|+|||||++.+++....
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~   26 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKE   26 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            5899999999999999999887654

>PRK00698 tmk thymidylate kinase; Validated

Probab=95.90  E-value=0.022  Score=45.62  Aligned_cols=27  Identities=22%  Similarity=0.388  Sum_probs=23.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|.|+.|+||||+++.+.+.....
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~l~~~   30 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKELLEQQ   30 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            689999999999999999999877543

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.89  E-value=0.028  Score=49.95  Aligned_cols=25  Identities=28%  Similarity=0.288  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..++.++|++|+||||++..+....
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998755

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.88  E-value=0.054  Score=46.83  Aligned_cols=29  Identities=38%  Similarity=0.566  Sum_probs=25.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++-|.++|++|+|||-||+.+..+....
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Akeaga~  154 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLAKAIAKEAGAN  154 (386)
T ss_pred             CCccceecCCCCchHHHHHHHHHHHcCCC
Confidence            46678999999999999999999887655

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.87  E-value=0.0069  Score=45.50  Aligned_cols=26  Identities=35%  Similarity=0.433  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+-|.|.|.||+|||||+..+.....
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~   32 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTG   32 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhC
Confidence            46789999999999999999985544

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.87  E-value=0.028  Score=46.01  Aligned_cols=53  Identities=25%  Similarity=0.369  Sum_probs=35.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      -..+.|.|.+|+|||+|+..+......+  -...+|++...  +...+... +.+++.
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~~~~~--g~~~~~is~e~--~~~~i~~~-~~~~g~   72 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYKGLRD--GDPVIYVTTEE--SRESIIRQ-AAQFGM   72 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHHHHhc--CCeEEEEEccC--CHHHHHHH-HHHhCC
Confidence            4689999999999999999876654323  35678887643  33444433 444543

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.

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=95.86  E-value=0.4  Score=39.52  Aligned_cols=35  Identities=31%  Similarity=0.473  Sum_probs=30.4

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|...|.--.++=+.++|++|.|||-||+.++++-
T Consensus       171 ELF~aLGIaQPKGvlLygppgtGktLlaraVahht  205 (404)
T KOG0728|consen  171 ELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT  205 (404)
T ss_pred             HHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc
Confidence            77777777778889999999999999999999654

>PRK06761 hypothetical protein; Provisional

Probab=95.86  E-value=0.019  Score=48.48  Aligned_cols=27  Identities=22%  Similarity=0.421  Sum_probs=24.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|.|.|++|+||||+++.+.......
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~   30 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQN   30 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcC
Confidence            589999999999999999999988643

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.86  E-value=0.021  Score=43.86  Aligned_cols=48  Identities=23%  Similarity=0.278  Sum_probs=33.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF  172 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  172 (276)
                      .+++.|+|.+|+||||+.+...... .   +..        ..+...++-+++...|...
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l-~---~~~--------ivNyG~~Mle~A~k~glve   51 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL-V---KHK--------IVNYGDLMLEIAKKKGLVE   51 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH-h---hce--------eeeHhHHHHHHHHHhCCcc
Confidence            5799999999999999998877666 1   111        1255666667766666543

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

Probab=95.85  E-value=0.0083  Score=52.20  Aligned_cols=30  Identities=30%  Similarity=0.449  Sum_probs=26.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .-++.++|+|++|+|||.+|+.+++.....
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~  175 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIE  175 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCC
Confidence            457899999999999999999999998754

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.84  E-value=0.0088  Score=49.03  Aligned_cols=25  Identities=28%  Similarity=0.522  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..|.|.|++|+||||+|+.+...+.
T Consensus         7 mrIvl~G~PGsGK~T~a~~La~~~g   31 (229)
T PTZ00088          7 LKIVLFGAPGVGKGTFAEILSKKEN   31 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4599999999999999999988764

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=95.83  E-value=0.0082  Score=51.31  Aligned_cols=24  Identities=33%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+|.+.|++|+||||+|+.+....
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHC
Confidence            578889999999999999998765

>TIGR02012 tigrfam_recA protein RecA

Probab=95.83  E-value=0.015  Score=50.08  Aligned_cols=43  Identities=23%  Similarity=0.337  Sum_probs=31.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD  156 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~  156 (276)
                      .-+++-|+|++|+||||||.++.......  -..++|++....++
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~~~~   96 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALD   96 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccchhH
Confidence            35699999999999999999987766443  24556775544433

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.

>PRK01184 hypothetical protein; Provisional

Probab=95.83  E-value=0.0087  Score=47.24  Aligned_cols=22  Identities=41%  Similarity=0.789  Sum_probs=18.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .+|+|+|++|+||||+++ +...
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~~   23 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IARE   23 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHHH
Confidence            589999999999999987 4433

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=95.83  E-value=0.0085  Score=50.49  Aligned_cols=28  Identities=29%  Similarity=0.488  Sum_probs=25.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      ++|+|+|.+|+|||||+..+......++
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L~~~G   29 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRLSGRG   29 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhCC
Confidence            5899999999999999999999987763

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=95.83  E-value=0.02  Score=49.27  Aligned_cols=49  Identities=22%  Similarity=0.396  Sum_probs=35.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  163 (276)
                      .+++.+.|.||+||||+|-...-.....+  ..+.-++.....+..+++..
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g--~kvLlvStDPAhsL~d~f~~   50 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESG--KKVLLVSTDPAHSLGDVFDL   50 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcC--CcEEEEEeCCCCchHhhhcc
Confidence            47889999999999999999777766553  34666666666565555433

>PRK08356 hypothetical protein; Provisional

Probab=95.83  E-value=0.0081  Score=47.97  Aligned_cols=22  Identities=27%  Similarity=0.359  Sum_probs=19.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      .++|+|+|++|+||||+|+.+.
T Consensus         5 ~~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          5 KMIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             cEEEEEECCCCCCHHHHHHHHH
Confidence            4679999999999999999994

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.81  E-value=0.19  Score=44.67  Aligned_cols=143  Identities=15%  Similarity=0.129  Sum_probs=72.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc-------------cc--c--
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH-------------EE--S--  176 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~-------------~~--~--  176 (276)
                      |=-.++|+||+|||++..++.+...-.     ++=+.++...+-.+ ++.++........             +.  .  
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L~yd-----IydLeLt~v~~n~d-Lr~LL~~t~~kSIivIEDIDcs~~l~~~~~~~~  309 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYLNYD-----IYDLELTEVKLDSD-LRHLLLATPNKSILLIEDIDCSFDLRERRKKKK  309 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhcCCc-----eEEeeeccccCcHH-HHHHHHhCCCCcEEEEeeccccccccccccccc
Confidence            446789999999999999999888633     33334444433333 5555544332100             00  0  


Q ss_pred             -c-h---------hhhhhccc-c-CCCCcEEEE-Eecccccccc-CCCC---CCceeCCCCCHHHHHHHHHHhhCCCCCC
Q 041612          177 -E-S---------GRANSLFT-H-GHKGCKVLL-TARSQDVLSG-KMDS---RPNFSIGVLNEEEAWSLFKKMAGDYIED  238 (276)
Q Consensus       177 -~-~---------~~~~~l~~-~-~~~gs~Iiv-TTR~~~va~~-~~~~---~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  238 (276)
                       . .         +.+..+-. + .+.+-|||| ||-..+-+.. .+..   +--+.+..=+.+....||....+...++
T Consensus       310 ~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h  389 (457)
T KOG0743|consen  310 ENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDH  389 (457)
T ss_pred             ccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCc
Confidence             0 0         00111111 1 222356665 5544433221 2222   2246677778888888888887632222


Q ss_pred             hhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 041612          239 SEFQSIARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      +    +..+|.+...|.-+.-..|+..|
T Consensus       390 ~----L~~eie~l~~~~~~tPA~V~e~l  413 (457)
T KOG0743|consen  390 R----LFDEIERLIEETEVTPAQVAEEL  413 (457)
T ss_pred             c----hhHHHHHHhhcCccCHHHHHHHH
Confidence            2    34445555555544444444433

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

Probab=95.81  E-value=0.014  Score=50.18  Aligned_cols=43  Identities=26%  Similarity=0.316  Sum_probs=32.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      -+++-|+|++|+||||||.+++......  -...+|++....++.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~--g~~~vyId~E~~~~~   97 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKL--GGTVAFIDAEHALDP   97 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCCEEEECccccHHH
Confidence            5689999999999999999987766443  345677766554443

RecA couples ATP hydrolysis to DNA strand exchange.

>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=95.81  E-value=0.0064  Score=45.36  Aligned_cols=34  Identities=21%  Similarity=0.388  Sum_probs=27.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEE
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVE  150 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~  150 (276)
                      .+++|+|..|+|||||.+.+......   ....+++.
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~~~~---~~G~i~~~   45 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGLLPP---DSGSILIN   45 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTSSHE---SEEEEEET
T ss_pred             CEEEEEccCCCccccceeeecccccc---cccccccc
Confidence            58999999999999999999888765   24455443

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 ....

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=95.80  E-value=0.0098  Score=46.10  Aligned_cols=27  Identities=19%  Similarity=0.364  Sum_probs=23.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +.|.++|+.|+||||+.+.+.......
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~   29 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLP   29 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCC
Confidence            468899999999999999999888765

>PLN02348 phosphoribulokinase

Probab=95.80  E-value=0.01  Score=52.13  Aligned_cols=28  Identities=14%  Similarity=0.305  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.+.+|+|.|.+|+||||+|+.+.+...
T Consensus        47 ~~p~IIGIaG~SGSGKSTfA~~L~~~Lg   74 (395)
T PLN02348         47 DGTVVIGLAADSGCGKSTFMRRLTSVFG   74 (395)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4678999999999999999999998874

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.78  E-value=0.012  Score=43.79  Aligned_cols=27  Identities=22%  Similarity=0.294  Sum_probs=23.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+|.+.|..|+||||+++.+.......
T Consensus        23 ~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        23 TVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            489999999999999999999987543

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.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.77  E-value=0.014  Score=44.88  Aligned_cols=32  Identities=19%  Similarity=0.368  Sum_probs=26.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|...+.+   +++.++|.+|+|||||...+....
T Consensus        28 ~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   28 ELKELLKG---KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             HHHHHHTT---SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             HHHHHhcC---CEEEEECCCCCCHHHHHHHHHhhc
Confidence            55555555   689999999999999999998765

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.

>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=95.77  E-value=0.021  Score=44.55  Aligned_cols=26  Identities=31%  Similarity=0.517  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++.++|++|+||||++..+.......
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~   27 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK   27 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            67899999999999999998877654

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.77  E-value=0.032  Score=46.01  Aligned_cols=54  Identities=13%  Similarity=0.292  Sum_probs=37.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      .-.++.|.|.+|+|||+++.++......+  -...+|++...  +..++.+.+ .+++.
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~--ge~~lyvs~ee--~~~~i~~~~-~~~g~   73 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGIYVALEE--HPVQVRRNM-AQFGW   73 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEEEeeC--CHHHHHHHH-HHhCC
Confidence            35689999999999999999876554332  35788888754  555555553 34443

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.

>PRK02496 adk adenylate kinase; Provisional

Probab=95.76  E-value=0.01  Score=46.88  Aligned_cols=25  Identities=28%  Similarity=0.287  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.|.|++|+||||+++.+.....
T Consensus         2 ~~i~i~G~pGsGKst~a~~la~~~~   26 (184)
T PRK02496          2 TRLIFLGPPGAGKGTQAVVLAEHLH   26 (184)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3588999999999999999987663

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

Probab=95.76  E-value=0.0096  Score=46.86  Aligned_cols=37  Identities=35%  Similarity=0.428  Sum_probs=26.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      ..-+.++|.+|+|||.||..+.+....++  -.+.|++.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g--~~v~f~~~   83 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKG--YSVLFITA   83 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT----EEEEEH
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCC--cceeEeec
Confidence            35699999999999999999998876542  23555544

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.

>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=95.75  E-value=0.013  Score=47.52  Aligned_cols=27  Identities=22%  Similarity=0.321  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+......
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~Gl~~~   56 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGGLDRP   56 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCCcCC
Confidence            358999999999999999999987654

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.

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=95.75  E-value=0.018  Score=49.39  Aligned_cols=44  Identities=23%  Similarity=0.400  Sum_probs=28.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRK  159 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~  159 (276)
                      +++.+.|.||+||||+|....-....++  ..+.-++.....++.+
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~G--~rtLlvS~Dpa~~L~d   45 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARRG--KRTLLVSTDPAHSLSD   45 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTT--S-EEEEESSTTTHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhCC--CCeeEeecCCCccHHH
Confidence            6889999999999999988776665542  2244444443333333

...

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=95.75  E-value=0.028  Score=47.77  Aligned_cols=36  Identities=19%  Similarity=0.347  Sum_probs=27.9

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+...+.. ..+.+|.|.|.+|+||||+|..+.+...
T Consensus        81 ~~~~~i~~~~~p~iIlI~G~sgsGKStlA~~La~~l~  117 (301)
T PRK04220         81 LLWRRIRKSKEPIIILIGGASGVGTSTIAFELASRLG  117 (301)
T ss_pred             HHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34444444 4567899999999999999999998873

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.06  Score=42.29  Aligned_cols=34  Identities=32%  Similarity=0.428  Sum_probs=26.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      -.+.|.|+.|+|||||-+.+..-.+..  -..+.|-
T Consensus        29 e~~~i~G~NG~GKTtLLRilaGLl~p~--~G~v~~~   62 (209)
T COG4133          29 EALQITGPNGAGKTTLLRILAGLLRPD--AGEVYWQ   62 (209)
T ss_pred             CEEEEECCCCCcHHHHHHHHHcccCCC--CCeEEec
Confidence            378899999999999999998877665  3445554

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=95.72  E-value=0.014  Score=47.06  Aligned_cols=27  Identities=26%  Similarity=0.384  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||++.+......
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~~~~   52 (210)
T cd03269          26 GEIFGLLGPNGAGKTTTIRMILGIILP   52 (210)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987643

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.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=95.72  E-value=0.01  Score=52.86  Aligned_cols=29  Identities=24%  Similarity=0.285  Sum_probs=25.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+.|+|+|.+|+|||||++.+......
T Consensus       217 ~~~~~IvI~G~~gsGKTTL~~~La~~~g~  245 (399)
T PRK08099        217 FFVRTVAILGGESSGKSTLVNKLANIFNT  245 (399)
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            35889999999999999999999987543

>PLN02796 D-glycerate 3-kinase

Probab=95.71  E-value=0.018  Score=49.87  Aligned_cols=29  Identities=24%  Similarity=0.267  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+-+|+|.|..|+|||||++.+.......
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~lL~~~  127 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYLFNAT  127 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHhccc
Confidence            45689999999999999999999887643

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.71  E-value=0.011  Score=48.09  Aligned_cols=24  Identities=38%  Similarity=0.321  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~   25 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYG   25 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999987764

>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=95.70  E-value=0.015  Score=45.67  Aligned_cols=27  Identities=30%  Similarity=0.458  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p   51 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQLIP   51 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCC
Confidence            458999999999999999999987654

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.

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

Probab=95.70  E-value=0.022  Score=47.46  Aligned_cols=38  Identities=29%  Similarity=0.334  Sum_probs=29.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      ...-+.++|.+|+|||.||..+.+... +. --.+.++++
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~-g~sv~f~~~  141 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KA-GISVLFITA  141 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-Hc-CCeEEEEEH
Confidence            556799999999999999999999988 42 234455543

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=95.70  E-value=0.011  Score=46.11  Aligned_cols=26  Identities=27%  Similarity=0.339  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..|.|+|++|+||||+++.+......
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~   28 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGY   28 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            35888999999999999999987643

>PRK13236 nitrogenase reductase; Reviewed

Probab=95.69  E-value=0.012  Score=50.32  Aligned_cols=31  Identities=26%  Similarity=0.560  Sum_probs=26.2

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +++.+++++.|-||+||||.+-.+.......
T Consensus         3 ~~~~~~~~~~GKGGVGKTt~a~NLA~~La~~   33 (296)
T PRK13236          3 DENIRQIAFYGKGGIGKSTTSQNTLAAMAEM   33 (296)
T ss_pred             CcCceEEEEECCCcCCHHHHHHHHHHHHHHC
Confidence            4567999999999999999988887776654

>PRK14528 adenylate kinase; Provisional

Probab=95.69  E-value=0.011  Score=46.80  Aligned_cols=25  Identities=20%  Similarity=0.292  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|.|.|++|+||||+|+.+.....
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~~   26 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERLS   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            5689999999999999999987664

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=95.68  E-value=0.01  Score=44.57  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|.++|..|+|||||++.+....
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            578899999999999999998765

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.68  E-value=0.018  Score=46.18  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++.|+|+.|+||||++..+.....
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4789999999999999998777664

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.

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=95.66  E-value=0.011  Score=50.02  Aligned_cols=27  Identities=33%  Similarity=0.556  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|+|-||+||||++..+.......
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~La~~   28 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAALAES   28 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHhC
Confidence            578999999999999999988887654

>PLN02924 thymidylate kinase

Probab=95.66  E-value=0.031  Score=45.55  Aligned_cols=29  Identities=14%  Similarity=0.186  Sum_probs=25.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      ...|+|.|..|+||||+++.+......++
T Consensus        16 g~~IviEGiDGsGKsTq~~~L~~~l~~~g   44 (220)
T PLN02924         16 GALIVLEGLDRSGKSTQCAKLVSFLKGLG   44 (220)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            45899999999999999999999987653

>PLN02165 adenylate isopentenyltransferase

Probab=95.65  E-value=0.012  Score=50.74  Aligned_cols=30  Identities=23%  Similarity=0.395  Sum_probs=25.4

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+....+++|+|+.|+|||+||..+.....
T Consensus        39 ~~~~g~iivIiGPTGSGKStLA~~LA~~l~   68 (334)
T PLN02165         39 QNCKDKVVVIMGATGSGKSRLSVDLATRFP   68 (334)
T ss_pred             cCCCCCEEEEECCCCCcHHHHHHHHHHHcC
Confidence            444566999999999999999999988854

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=95.63  E-value=0.017  Score=47.34  Aligned_cols=38  Identities=26%  Similarity=0.394  Sum_probs=31.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +|-..+.-+.++=+.++|++|+|||-||+.+.++-...
T Consensus       179 ~ly~qigidpprgvllygppg~gktml~kava~~t~a~  216 (408)
T KOG0727|consen  179 DLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA  216 (408)
T ss_pred             HHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchh
Confidence            44455556778889999999999999999999887654

>smart00072 GuKc Guanylate kinase homologues

Probab=95.62  E-value=0.015  Score=46.00  Aligned_cols=25  Identities=24%  Similarity=0.440  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+.+.|+|++|+||+||+..+....
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcC
Confidence            4689999999999999999998775

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.

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

Probab=95.61  E-value=0.26  Score=40.57  Aligned_cols=56  Identities=16%  Similarity=0.270  Sum_probs=37.5

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHH
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIG  165 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  165 (276)
                      +......-+.++|..|+|||+|++.+.+....++  =..+-|.-.+-.++..++..+.
T Consensus        47 l~G~pannvLL~G~rGtGKSSlVkall~~y~~~G--LRlIev~k~~L~~l~~l~~~l~  102 (249)
T PF05673_consen   47 LQGLPANNVLLWGARGTGKSSLVKALLNEYADQG--LRLIEVSKEDLGDLPELLDLLR  102 (249)
T ss_pred             HcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC--ceEEEECHHHhccHHHHHHHHh
Confidence            3444566788999999999999999999987763  1233333333345666655544

>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=95.61  E-value=0.011  Score=48.70  Aligned_cols=23  Identities=26%  Similarity=0.504  Sum_probs=20.2

Q ss_pred             EEcCCCCcHHHHHHHHHHhcccC
Q 041612          118 IYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       118 I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      |+|++|+||||+++.+.+.....
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~   23 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESN   23 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhc
Confidence            68999999999999999988765

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK10536 hypothetical protein; Provisional

Probab=95.61  E-value=0.028  Score=46.66  Aligned_cols=44  Identities=25%  Similarity=0.356  Sum_probs=30.2

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEE
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVF  148 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~w  148 (276)
                      .++..+.+.  .++.+.|..|+|||+||..+..+.-..+.|+.++.
T Consensus        66 ~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI  109 (262)
T PRK10536         66 HYLKAIESK--QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIV  109 (262)
T ss_pred             HHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEE
Confidence            555555553  48999999999999999998885322223554443

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

Probab=95.59  E-value=0.034  Score=46.68  Aligned_cols=52  Identities=23%  Similarity=0.441  Sum_probs=38.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCC-CeEEEEEecCcCC-HHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLF-DQVVFVEVSQNQD-IRKIQEEIGD  166 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f-~~~~wv~~~~~~~-~~~l~~~i~~  166 (276)
                      -..++|.|.+|+|||+|++.++++.+.+  | +..+++.+++... ..++...+..
T Consensus        69 GQr~~If~~~G~GKTtLa~~i~~~i~~~--~~~~~V~~~iGer~~Ev~e~~~~~~~  122 (274)
T cd01133          69 GGKIGLFGGAGVGKTVLIMELINNIAKA--HGGYSVFAGVGERTREGNDLYHEMKE  122 (274)
T ss_pred             CCEEEEecCCCCChhHHHHHHHHHHHhc--CCCEEEEEEeccCcHHHHHHHHHHHh
Confidence            4579999999999999999999998765  4 4566667766653 4555555543

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.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=95.59  E-value=0.016  Score=45.98  Aligned_cols=27  Identities=22%  Similarity=0.421  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|.|||||.+.+......
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G~~~~   44 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNGLLRP   44 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999887654

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.

>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=95.58  E-value=0.021  Score=43.13  Aligned_cols=42  Identities=12%  Similarity=0.174  Sum_probs=33.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN  154 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~  154 (276)
                      --++.+.|++|+||+||-.-+......+-.|...+|+.-.+-
T Consensus        28 GeivtlMGPSGcGKSTLls~~~G~La~~F~~~G~~~l~~~~l   69 (213)
T COG4136          28 GEIVTLMGPSGCGKSTLLSWMIGALAGQFSCTGELWLNEQRL   69 (213)
T ss_pred             CcEEEEECCCCccHHHHHHHHHhhcccCcceeeEEEECCeec
Confidence            358999999999999999999999988733346788865443

>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=95.58  E-value=0.012  Score=42.63  Aligned_cols=22  Identities=27%  Similarity=0.472  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|+|.|.+|+|||||...+.+.
T Consensus         1 ~V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    1 RVAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEECCCCCCHHHHHHHHhcc
Confidence            3789999999999999999974

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 ....

>cd03114 ArgK-like The function of this protein family is unkown

Probab=95.58  E-value=0.016  Score=44.16  Aligned_cols=26  Identities=27%  Similarity=0.626  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++++.|.+|+||||++..+.......
T Consensus         1 ~i~~~G~~GsGKTt~~~~l~~~~~~~   26 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITALRAR   26 (148)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            47899999999999999998887654

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=95.57  E-value=0.016  Score=46.96  Aligned_cols=27  Identities=26%  Similarity=0.285  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+......
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl~~~   55 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGIEKP   55 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987654

>PF00142 Fer4_NifH: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family; InterPro: IPR000392 This entry represents members of the NifH/BchL/ChlL family

Probab=95.57  E-value=0.028  Score=46.60  Aligned_cols=39  Identities=26%  Similarity=0.494  Sum_probs=28.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN  154 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~  154 (276)
                      +.|+|+|-|||||||.+..+.-.....+  ..+.-+.....
T Consensus         1 r~IAiYGKGGIGKST~~~Nlsaala~~G--~kVl~iGCDPK   39 (273)
T PF00142_consen    1 RKIAIYGKGGIGKSTTASNLSAALAEMG--KKVLQIGCDPK   39 (273)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTT----EEEEEESSS
T ss_pred             CeEEEEcCCCcccChhhhHHHHHHHhcc--ceeeEecccCC
Confidence            4799999999999999999888777652  45555644433

Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [, , ]. The nitrogenase enzyme complex consists of two components: Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits. Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene []. Component II has 2 ATP-binding domains and one 4Fe-4S cluster per homodimer: it supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component I for the reduction of molecular nitrogen to ammonia []. There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) IPR001687 from INTERPRO and in the central section there are two conserved cysteines which have been shown, in nifH, to be the ligands of the 4Fe-4S cluster. Protochlorophyllide reductase is involved in light-independent chlorophyll biosynthesis. The light-independent reaction uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This enzyme complex is composed of three subunits: ChlL, ChlN and ChlB. ChlL is present as a homodimer, and binds one 4Fe-4S cluster per dimer. The conserved domains, including the ATP-binding motif and the Fe-S binding motif found in the three subunits, are similar to those in nitrogenases []. ; GO: 0005524 ATP binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1CP2_A 2AFI_F 1N2C_F 1FP6_C 2AFK_G 1M34_M 1XD8_A 1NIP_A 1M1Y_N 1G21_H ....

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=95.57  E-value=0.013  Score=40.41  Aligned_cols=25  Identities=36%  Similarity=0.647  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ++.+.|.+|+||||++..+......
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l~~   25 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAALAK   25 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4788999999999999999988865

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>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=95.55  E-value=0.018  Score=46.85  Aligned_cols=27  Identities=26%  Similarity=0.460  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G~~~~   52 (220)
T cd03265          26 GEIFGLLGPNGAGKTTTIKMLTTLLKP   52 (220)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987543

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.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=95.55  E-value=0.012  Score=47.58  Aligned_cols=27  Identities=22%  Similarity=0.255  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||++.+......
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G~~~~   53 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNGLLGP   53 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999987653

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.

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=95.55  E-value=1.2  Score=37.14  Aligned_cols=27  Identities=30%  Similarity=0.431  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++=+.++|++|.|||-+|+....+-.
T Consensus       204 pPKGvLmYGPPGTGKTlmARAcAaqT~  230 (424)
T KOG0652|consen  204 PPKGVLMYGPPGTGKTLMARACAAQTN  230 (424)
T ss_pred             CCCceEeeCCCCCcHHHHHHHHHHhcc
Confidence            466788999999999999998776544

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=95.55  E-value=0.012  Score=44.93  Aligned_cols=23  Identities=26%  Similarity=0.455  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58899999999999999998654

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

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=95.55  E-value=0.011  Score=47.76  Aligned_cols=27  Identities=26%  Similarity=0.422  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..|+++|.+|+|||||...+.++....
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~~~~   32 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDEFPE   32 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCcCcc
Confidence            578999999999999999999887653

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.55  E-value=0.024  Score=47.49  Aligned_cols=39  Identities=28%  Similarity=0.468  Sum_probs=30.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ  153 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~  153 (276)
                      -.++.|.|.+|+|||+++.++......+  =..++|++...
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~Ee   74 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASR--GNPVLFVTVES   74 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecC
Confidence            5689999999999999999986654333  24677787754

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd01878 HflX HflX subfamily

Probab=95.54  E-value=0.058  Score=43.17  Aligned_cols=27  Identities=15%  Similarity=0.290  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++...|+|+|.+|+|||||...+.+..
T Consensus        39 ~~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          39 SGIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHhcch
Confidence            445789999999999999999988764

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>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=95.54  E-value=0.016  Score=46.44  Aligned_cols=38  Identities=24%  Similarity=0.442  Sum_probs=27.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      +..++.+.|+.|+|||.||....-+.-..+.|+.++++
T Consensus        18 ~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~   55 (205)
T PF02562_consen   18 NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIIT   55 (205)
T ss_dssp             H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE
T ss_pred             hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            34589999999999999999988766555678888777

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

>TIGR01351 adk adenylate kinases

Probab=95.54  E-value=0.012  Score=47.54  Aligned_cols=23  Identities=39%  Similarity=0.424  Sum_probs=20.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |.|.|++|+||||+|+.+.....
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g   24 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYG   24 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999987654

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.

>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=95.53  E-value=0.011  Score=49.68  Aligned_cols=26  Identities=23%  Similarity=0.378  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.|.|+|.||+||||+|+.+......
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHh
Confidence            57999999999999999999887665

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=95.52  E-value=0.016  Score=46.76  Aligned_cols=25  Identities=36%  Similarity=0.527  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +++|+|+.|.|||||++.+......
T Consensus        27 ~~~i~G~nGsGKSTLl~~l~Gl~~~   51 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILATLTPP   51 (211)
T ss_pred             cEEEECCCCCCHHHHHHHHhCCCCC
Confidence            8999999999999999999977653

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.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=95.51  E-value=0.019  Score=47.27  Aligned_cols=26  Identities=23%  Similarity=0.356  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|.|||||++.+.....
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (236)
T TIGR03864        27 GEFVALLGPNGAGKSTLFSLLTRLYV   52 (236)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCcC
Confidence            45899999999999999999987654

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.

>PRK15453 phosphoribulokinase; Provisional

Probab=95.51  E-value=0.016  Score=48.73  Aligned_cols=27  Identities=15%  Similarity=0.382  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|+|.|.+|+||||+++.+.....
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~if~   30 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            457999999999999999999886553

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=95.51  E-value=0.014  Score=47.29  Aligned_cols=27  Identities=30%  Similarity=0.635  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|.|-||+||||++-.+.......
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~la~~   27 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAALAEM   27 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHHHHHC
Confidence            578999999999999888887776654

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=95.50  E-value=0.014  Score=49.09  Aligned_cols=27  Identities=30%  Similarity=0.629  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|.|-||+||||++..+......+
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~La~~   28 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAALAEM   28 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHHHHhC
Confidence            578888999999999999988877654

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.50  E-value=0.019  Score=45.75  Aligned_cols=28  Identities=29%  Similarity=0.335  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|..|.|||||++.+.......
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~~~~~   53 (195)
T PRK13541         26 SAITYIKGANGCGKSSLLRMIAGIMQPS   53 (195)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            3489999999999999999999876543

>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=95.50  E-value=0.017  Score=47.44  Aligned_cols=27  Identities=30%  Similarity=0.425  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||++.+......
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~~~p   52 (235)
T cd03261          26 GEILAIIGPSGSGKSTLLRLIVGLLRP   52 (235)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987653

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.

>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=95.49  E-value=0.02  Score=46.65  Aligned_cols=27  Identities=26%  Similarity=0.359  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        30 G~~~~i~G~nGsGKSTLl~~l~Gl~~~   56 (220)
T cd03293          30 GEFVALVGPSGCGKSTLLRIIAGLERP   56 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987643

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.

>PRK12338 hypothetical protein; Provisional

Probab=95.48  E-value=0.015  Score=49.89  Aligned_cols=26  Identities=35%  Similarity=0.511  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.+|.|.|.+|+||||+|+.+.....
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~   29 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLN   29 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCC
Confidence            56899999999999999999988864

>PRK05973 replicative DNA helicase; Provisional

Probab=95.47  E-value=0.028  Score=46.26  Aligned_cols=39  Identities=23%  Similarity=0.220  Sum_probs=28.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ  153 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~  153 (276)
                      -.++.|.|.+|+|||+++.++......+  =..++|++...
T Consensus        64 Gsl~LIaG~PG~GKT~lalqfa~~~a~~--Ge~vlyfSlEe  102 (237)
T PRK05973         64 GDLVLLGARPGHGKTLLGLELAVEAMKS--GRTGVFFTLEY  102 (237)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEEEeC
Confidence            3589999999999999999987765433  23455665543

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=95.47  E-value=0.019  Score=47.33  Aligned_cols=26  Identities=31%  Similarity=0.400  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|+|||||++.+.....
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   53 (239)
T cd03296          28 GELVALLGPSGSGKTTLLRLIAGLER   53 (239)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45899999999999999999988764

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.

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=95.47  E-value=0.018  Score=46.63  Aligned_cols=27  Identities=33%  Similarity=0.455  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~G~~~p   51 (213)
T cd03235          25 GEFLAIVGPNGAGKSTLLKAILGLLKP   51 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCC
Confidence            458999999999999999999887654

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.

>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=95.45  E-value=0.012  Score=44.88  Aligned_cols=21  Identities=33%  Similarity=0.482  Sum_probs=19.1

Q ss_pred             EEcCCCCcHHHHHHHHHHhcc
Q 041612          118 IYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       118 I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |.|+||+||||+|+.+.....
T Consensus         1 i~G~PgsGK~t~~~~la~~~~   21 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYG   21 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHT
T ss_pred             CcCCCCCChHHHHHHHHHhcC
Confidence            689999999999999998763

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 ....

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.45  E-value=0.074  Score=44.86  Aligned_cols=26  Identities=31%  Similarity=0.487  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+-|.++|++|.||+.||+.+.....
T Consensus       166 wrgiLLyGPPGTGKSYLAKAVATEAn  191 (439)
T KOG0739|consen  166 WRGILLYGPPGTGKSYLAKAVATEAN  191 (439)
T ss_pred             ceeEEEeCCCCCcHHHHHHHHHhhcC
Confidence            67889999999999999999987765

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.45  E-value=0.02  Score=45.85  Aligned_cols=35  Identities=29%  Similarity=0.410  Sum_probs=27.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVE  150 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~  150 (276)
                      -.+++|+|..|.|||||.+.+.......   ...+++.
T Consensus        27 Ge~~~l~G~nGsGKSTLl~~i~G~~~~~---~G~v~~~   61 (200)
T PRK13540         27 GGLLHLKGSNGAGKTTLLKLIAGLLNPE---KGEILFE   61 (200)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCC---CeeEEEC
Confidence            4589999999999999999998876543   4445543

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=95.45  E-value=0.014  Score=44.75  Aligned_cols=23  Identities=30%  Similarity=0.546  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+|+|.+|+|||||...+.+..
T Consensus         2 ki~v~G~~~~GKTsli~~~~~~~   24 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQGH   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            57899999999999999987654

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>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=95.44  E-value=0.013  Score=45.96  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhh
Confidence            45899999999999999999864

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.

>cd04155 Arl3 Arl3 subfamily

Probab=95.43  E-value=0.019  Score=44.56  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +...|+|+|.+|+|||||...+.+.
T Consensus        13 ~~~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          13 EEPRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             CccEEEEEccCCCCHHHHHHHHhcC
Confidence            4567999999999999999999876

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.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.43  E-value=0.38  Score=42.72  Aligned_cols=71  Identities=17%  Similarity=0.273  Sum_probs=47.0

Q ss_pred             HHHHhhcC---------CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc
Q 041612          103 NILSALED---------PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       103 ~l~~~L~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  173 (276)
                      +|++.|..         ..+.+|-++|.=|.||||-+..+.+.++.+++-...+-.++ ..|..-+-++.+.++++.+..
T Consensus        81 ELv~llG~~~~~~~l~~~~P~vImmvGLQGsGKTTt~~KLA~~lkk~~~kvllVaaD~-~RpAA~eQL~~La~q~~v~~f  159 (451)
T COG0541          81 ELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAADT-YRPAAIEQLKQLAEQVGVPFF  159 (451)
T ss_pred             HHHHHhCCCCcccccCCCCCeEEEEEeccCCChHhHHHHHHHHHHHcCCceEEEeccc-CChHHHHHHHHHHHHcCCcee
Confidence            77777763         23678999999999999999998888876432222222222 223445556778888877654


Q ss_pred             c
Q 041612          174 E  174 (276)
Q Consensus       174 ~  174 (276)
                      .
T Consensus       160 ~  160 (451)
T COG0541         160 G  160 (451)
T ss_pred             c
Confidence            4

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.43  E-value=0.017  Score=50.00  Aligned_cols=36  Identities=31%  Similarity=0.489  Sum_probs=29.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      .-+.++|.+|+|||+||..+.+....++  ..++|+++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g--~~V~y~t~  219 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRG--KSVIYRTA  219 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCC--CeEEEEEH
Confidence            6799999999999999999999886552  34566654

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=95.42  E-value=0.011  Score=47.95  Aligned_cols=22  Identities=41%  Similarity=0.511  Sum_probs=19.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      ...+.|+|.+|+||||+|+.+-
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~   33 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLP   33 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcC
Confidence            5679999999999999999874

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.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=95.42  E-value=0.02  Score=46.27  Aligned_cols=27  Identities=26%  Similarity=0.294  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||++.+......
T Consensus        28 G~~~~l~G~nGsGKSTLl~~i~Gl~~~   54 (214)
T TIGR02673        28 GEFLFLTGPSGAGKTTLLKLLYGALTP   54 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999887643

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.

>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=95.41  E-value=0.02  Score=46.29  Aligned_cols=27  Identities=22%  Similarity=0.272  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        27 G~~~~i~G~nGsGKSTLl~~l~G~~~~   53 (214)
T cd03292          27 GEFVFLVGPSGAGKSTLLKLIYKEELP   53 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999987654

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=95.41  E-value=0.035  Score=45.27  Aligned_cols=40  Identities=23%  Similarity=0.340  Sum_probs=32.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      -.+.+|.|.+|+|||||.+.+....+..   ...+|+.-...+
T Consensus        34 Gei~~iiGgSGsGKStlLr~I~Gll~P~---~GeI~i~G~~i~   73 (263)
T COG1127          34 GEILAILGGSGSGKSTLLRLILGLLRPD---KGEILIDGEDIP   73 (263)
T ss_pred             CcEEEEECCCCcCHHHHHHHHhccCCCC---CCeEEEcCcchh
Confidence            4689999999999999999999988765   567777554443

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.41  E-value=0.055  Score=44.49  Aligned_cols=53  Identities=13%  Similarity=0.223  Sum_probs=36.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      .-.++.|+|.+|+|||+|+.++......+  =..++|++..+.  ...+.+.+ .+++
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~~--~~~~~~~~-~~~g   76 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ--GKKVYVITTENT--SKSYLKQM-ESVK   76 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC--CCEEEEEEcCCC--HHHHHHHH-HHCC
Confidence            35689999999999999999986554322  357888887543  45555543 3444

>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=0.015  Score=45.74  Aligned_cols=26  Identities=27%  Similarity=0.362  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|.|..|.|||||++.+.....
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~~~   51 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGLEE   51 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            35899999999999999999987654

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.

>PRK13973 thymidylate kinase; Provisional

Probab=95.40  E-value=0.052  Score=43.99  Aligned_cols=27  Identities=19%  Similarity=0.366  Sum_probs=24.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..|+|-|+.|+||||+++.++.....+
T Consensus         4 ~~IviEG~dGsGKtTq~~~l~~~l~~~   30 (213)
T PRK13973          4 RFITFEGGEGAGKSTQIRLLAERLRAA   30 (213)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            579999999999999999999998765

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=95.40  E-value=0.022  Score=46.79  Aligned_cols=27  Identities=26%  Similarity=0.340  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.++.....
T Consensus        35 Ge~~~l~G~nGsGKSTLl~~l~Gl~~~   61 (233)
T PRK11629         35 GEMMAIVGSSGSGKSTLLHLLGGLDTP   61 (233)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999987643

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.40  E-value=0.015  Score=53.73  Aligned_cols=28  Identities=25%  Similarity=0.551  Sum_probs=24.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+++.+|+|.|.+|+||||||+.+....
T Consensus        62 ~~~riIIGIaGpSGSGKTTLAk~LaglL   89 (656)
T PLN02318         62 NDGIILVGVAGPSGAGKTVFTEKVLNFM   89 (656)
T ss_pred             CCCeEEEEEECCCCCcHHHHHHHHHhhC
Confidence            3467899999999999999999998765

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=95.40  E-value=0.023  Score=43.04  Aligned_cols=27  Identities=30%  Similarity=0.511  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|.|||||.+.+......
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~   52 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELEP   52 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCC
Confidence            358999999999999999999887654

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=95.40  E-value=0.26  Score=46.85  Aligned_cols=27  Identities=37%  Similarity=0.427  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+-+.++|++|+|||++|+.+.+....
T Consensus       185 ~~gill~G~~G~GKt~~~~~~a~~~~~  211 (644)
T PRK10733        185 PKGVLMVGPPGTGKTLLAKAIAGEAKV  211 (644)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHcCC
Confidence            345999999999999999999887754

>PRK09354 recA recombinase A; Provisional

Probab=95.39  E-value=0.027  Score=48.93  Aligned_cols=44  Identities=23%  Similarity=0.302  Sum_probs=32.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      .-+++-|+|++|+|||||+.++.......  -...+|++.-..++.
T Consensus        59 ~G~IteI~G~~GsGKTtLal~~~~~~~~~--G~~~~yId~E~s~~~  102 (349)
T PRK09354         59 RGRIVEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDP  102 (349)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchHH
Confidence            35689999999999999999987766543  345677766555443

>PRK06851 hypothetical protein; Provisional

Probab=95.39  E-value=0.029  Score=49.17  Aligned_cols=44  Identities=23%  Similarity=0.294  Sum_probs=32.9

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN  154 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~  154 (276)
                      ....+++.|.|.+|+|||||.+.+.+.....+ |+...++|-+.+
T Consensus        27 ~~~~~~~il~G~pGtGKStl~~~i~~~~~~~g-~~Ve~~~~~~d~   70 (367)
T PRK06851         27 DGANRIFILKGGPGTGKSTLMKKIGEEFLEKG-YDVEFLHCSSDN   70 (367)
T ss_pred             cccceEEEEECCCCCCHHHHHHHHHHHHHHcC-CeEEEEEcCCCC
Confidence            44567899999999999999999998886542 555555544443

>PRK13768 GTPase; Provisional

Probab=95.38  E-value=0.016  Score=48.33  Aligned_cols=27  Identities=22%  Similarity=0.393  Sum_probs=22.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++.|.|+||+||||++..+......+
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~~l~~~   29 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSDWLEEQ   29 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHHHHHhc
Confidence            578999999999999998888776543

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.38  E-value=0.024  Score=48.52  Aligned_cols=30  Identities=27%  Similarity=0.499  Sum_probs=25.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ....+|+|.|.+|+|||||+..+......+
T Consensus        32 ~~~~~i~i~G~~G~GKttl~~~l~~~~~~~   61 (300)
T TIGR00750        32 GNAHRVGITGTPGAGKSTLLEALGMELRRR   61 (300)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            356799999999999999999988876543

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.37  E-value=0.022  Score=45.75  Aligned_cols=27  Identities=30%  Similarity=0.367  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        27 Ge~~~l~G~nGsGKSTLl~~l~G~~~p   53 (204)
T PRK13538         27 GELVQIEGPNGAGKTSLLRILAGLARP   53 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987654

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=95.37  E-value=0.014  Score=45.98  Aligned_cols=21  Identities=29%  Similarity=0.513  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      +|+|.|.+|+||||+++.+.+
T Consensus         1 ii~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999876

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=95.37  E-value=0.022  Score=47.05  Aligned_cols=27  Identities=22%  Similarity=0.217  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|.|||||++.+......
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G~~~~   54 (242)
T PRK11124         28 GETLVLLGPSGAGKSSLLRVLNLLEMP   54 (242)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987643

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=95.37  E-value=0.022  Score=46.32  Aligned_cols=27  Identities=22%  Similarity=0.314  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.++.....
T Consensus        31 G~~~~i~G~nGsGKSTLl~~i~G~~~~   57 (221)
T TIGR02211        31 GEIVAIVGSSGSGKSTLLHLLGGLDNP   57 (221)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987653

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.

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=95.36  E-value=0.014  Score=44.76  Aligned_cols=23  Identities=17%  Similarity=0.284  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         2 ki~~vG~~~vGKTsli~~l~~~~   24 (168)
T cd04119           2 KVISMGNSGVGKSCIIKRYCEGR   24 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999999998765

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.36  E-value=0.038  Score=49.07  Aligned_cols=28  Identities=25%  Similarity=0.396  Sum_probs=24.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++.|.++|++|+|||++|+.+.......
T Consensus        47 p~~ILLiGppG~GKT~lAraLA~~l~~~   74 (441)
T TIGR00390        47 PKNILMIGPTGVGKTEIARRLAKLANAP   74 (441)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCe
Confidence            5679999999999999999999887643

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.

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

Probab=95.36  E-value=0.2  Score=38.66  Aligned_cols=97  Identities=20%  Similarity=0.224  Sum_probs=54.6

Q ss_pred             HHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC-------------------CCCeEEEEEecCc---CCHHHH
Q 041612          104 ILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK-------------------LFDQVVFVEVSQN---QDIRKI  160 (276)
Q Consensus       104 l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~~~~~---~~~~~l  160 (276)
                      |.+.+..+. ++.+.++|+.|+||+++|..+.+..--..                   |.| ..|+.-...   ...+++
T Consensus         9 L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~~~i~i~~i   87 (162)
T PF13177_consen    9 LKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPD-FIIIKPDKKKKSIKIDQI   87 (162)
T ss_dssp             HHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTT-EEEEETTTSSSSBSHHHH
T ss_pred             HHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcc-eEEEecccccchhhHHHH
Confidence            344444454 45689999999999999999887754321                   233 344443332   355555


Q ss_pred             HHHHHHHhCCCcccc------------cchhhhh---hccccCCCCcEEEEEecccc
Q 041612          161 QEEIGDKLGLKFHEE------------SESGRAN---SLFTHGHKGCKVLLTARSQD  202 (276)
Q Consensus       161 ~~~i~~~l~~~~~~~------------~~~~~~~---~l~~~~~~gs~IivTTR~~~  202 (276)
                      . .+.+.+.......            -......   +..+..+..+.+|++|.+..
T Consensus        88 r-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   88 R-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             H-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             H-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChH
Confidence            4 6766665442220            1111122   22226677899999998765

...

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=95.36  E-value=0.021  Score=47.41  Aligned_cols=27  Identities=37%  Similarity=0.619  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        25 Ge~~~i~G~NGsGKSTLlk~L~G~~~p   51 (246)
T cd03237          25 SEVIGILGPNGIGKTTFIKMLAGVLKP   51 (246)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCcC
Confidence            358999999999999999999887654

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. 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 of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed

Probab=95.36  E-value=0.062  Score=48.76  Aligned_cols=53  Identities=15%  Similarity=0.199  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhhccccchHHHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612           73 NWLARANNVIEAADNFTKDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus        73 ~wl~~l~~~~~~~ed~ld~~~~~~~~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....++..+..+.+++++.....          ..+ .++ ..|+|+|.+|+|||||...+....
T Consensus       187 ~i~~~i~~l~~~l~~l~~~~~~~----------~~~-~~~-~kV~ivG~~nvGKSSLln~L~~~~  239 (449)
T PRK05291        187 KILEKLEELIAELEALLASARQG----------EIL-REG-LKVVIAGRPNVGKSSLLNALLGEE  239 (449)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----------HHh-hcC-CEEEEECCCCCCHHHHHHHHhCCC
Confidence            34455555555555555444221          111 122 468999999999999999998754

>TIGR00017 cmk cytidylate kinase

Probab=95.35  E-value=0.018  Score=46.90  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+|+|.|+.|+||||+++.+.....
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~~~   27 (217)
T TIGR00017         3 MIIAIDGPSGAGKSTVAKAVAEKLG   27 (217)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999987665

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.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=95.35  E-value=0.016  Score=46.41  Aligned_cols=23  Identities=30%  Similarity=0.491  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      ..+|+|+|+.|+||||.|+.+-+
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            46899999999999999988766

>TIGR00101 ureG urease accessory protein UreG

Probab=95.35  E-value=0.019  Score=46.06  Aligned_cols=26  Identities=35%  Similarity=0.544  Sum_probs=22.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..++|.|+.|.|||||.+.+.+....
T Consensus         2 ~~i~i~G~~GsGKTTll~~l~~~l~~   27 (199)
T TIGR00101         2 LKIGVAGPVGSGKTALIEALTRALRQ   27 (199)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhhCc
Confidence            46899999999999999999987654

This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=95.35  E-value=0.025  Score=43.66  Aligned_cols=49  Identities=16%  Similarity=0.297  Sum_probs=33.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe-cCcCCHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV-SQNQDIRKIQEEI  164 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~-~~~~~~~~l~~~i  164 (276)
                      -.++|.|++|+||+||-+.+++-....  -....|-.- -+..+++..-+++
T Consensus        30 e~iaitGPSG~GKStllk~va~Lisp~--~G~l~f~Ge~vs~~~pea~Rq~V   79 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLISPT--SGTLLFEGEDVSTLKPEAYRQQV   79 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhccCCC--CceEEEcCccccccChHHHHHHH
Confidence            369999999999999999999887665  334445321 1234556655555

>PRK04328 hypothetical protein; Provisional

Probab=95.34  E-value=0.036  Score=46.11  Aligned_cols=54  Identities=15%  Similarity=0.226  Sum_probs=36.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      -.++.|.|.+|+|||+|+.++......+  -...+|++....  +..+.+ .++.++.+
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee~--~~~i~~-~~~~~g~d   76 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGVYVALEEH--PVQVRR-NMRQFGWD   76 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeCC--HHHHHH-HHHHcCCC
Confidence            5689999999999999999977664333  356788887653  334433 34555543

>PRK07933 thymidylate kinase; Validated

Probab=95.34  E-value=0.032  Score=45.22  Aligned_cols=28  Identities=25%  Similarity=0.482  Sum_probs=24.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      +.|+|-|+.|+||||+++.+.+....++
T Consensus         1 ~~IviEG~dGsGKST~~~~L~~~L~~~g   28 (213)
T PRK07933          1 MLIAIEGVDGAGKRTLTEALRAALEARG   28 (213)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCC
Confidence            3689999999999999999999987653

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=95.34  E-value=0.027  Score=43.97  Aligned_cols=27  Identities=33%  Similarity=0.405  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~~~   54 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLLRP   54 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccCC
Confidence            358999999999999999999987654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.33  E-value=0.014  Score=46.42  Aligned_cols=27  Identities=30%  Similarity=0.594  Sum_probs=23.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +.|.+.|.+|+||||+|+.+....+.+
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHh
Confidence            578889999999999999998877654

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=95.32  E-value=0.016  Score=47.12  Aligned_cols=27  Identities=26%  Similarity=0.326  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      --.++|+|++|+|||||...+..-.+.
T Consensus        31 Ge~vaI~GpSGSGKSTLLniig~ld~p   57 (226)
T COG1136          31 GEFVAIVGPSGSGKSTLLNLLGGLDKP   57 (226)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcccCC
Confidence            348999999999999999888765544

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=95.31  E-value=0.02  Score=52.78  Aligned_cols=30  Identities=27%  Similarity=0.368  Sum_probs=25.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +...+++.++|++|+|||+||+.+..-...
T Consensus       100 ~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455        100 EEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             CCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            345679999999999999999999887654

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=95.31  E-value=0.024  Score=45.58  Aligned_cols=26  Identities=35%  Similarity=0.374  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|..|.|||||.+.+......
T Consensus        25 e~~~i~G~nGsGKSTLl~~l~G~~~~   50 (206)
T TIGR03608        25 KMYAIIGESGSGKSTLLNIIGLLEKF   50 (206)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            58999999999999999999987653

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.

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=95.30  E-value=0.023  Score=46.43  Aligned_cols=27  Identities=22%  Similarity=0.287  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||++.++.....
T Consensus        36 Ge~~~i~G~nGsGKSTLl~~i~Gl~~p   62 (228)
T PRK10584         36 GETIALIGESGSGKSTLLAILAGLDDG   62 (228)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCCCC
Confidence            469999999999999999999987653

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=95.30  E-value=0.024  Score=46.56  Aligned_cols=26  Identities=23%  Similarity=0.445  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|..|+|||||.+.+......
T Consensus        12 e~~~i~G~nGsGKSTLl~~l~Gl~~p   37 (230)
T TIGR01184        12 EFISLIGHSGCGKSTLLNLISGLAQP   37 (230)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            58999999999999999999887653

This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=95.30  E-value=0.025  Score=45.74  Aligned_cols=27  Identities=26%  Similarity=0.263  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|+|||||.+.+......
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~~~~   52 (213)
T cd03301          26 GEFVVLLGPSGCGKTTTLRMIAGLEEP   52 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987643

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

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

Probab=95.30  E-value=0.05  Score=45.44  Aligned_cols=57  Identities=28%  Similarity=0.447  Sum_probs=41.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      -.+.-|+|.+|+|||.|+.+++-.....    +.=..++|++-...++...+. +|++..+.
T Consensus        38 g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~   98 (256)
T PF08423_consen   38 GSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGL   98 (256)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS
T ss_pred             CcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhcccc
Confidence            4689999999999999998887554321    112468999988888888775 56666543

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 ....

>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=95.30  E-value=0.025  Score=45.77  Aligned_cols=28  Identities=36%  Similarity=0.557  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .. .+++|+|..|+|||||.+.+......
T Consensus        22 ~~-e~~~i~G~nGsGKSTLl~~l~G~~~~   49 (214)
T cd03297          22 NE-EVTGIFGASGAGKSTLLRCIAGLEKP   49 (214)
T ss_pred             cc-eeEEEECCCCCCHHHHHHHHhCCCCC
Confidence            35 79999999999999999999887653

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.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=95.30  E-value=0.016  Score=47.16  Aligned_cols=27  Identities=22%  Similarity=0.493  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.++.-...
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~~~   54 (220)
T cd03263          28 GEIFGLLGHNGAGKTTTLKMLTGELRP   54 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987654

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.

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=95.30  E-value=0.015  Score=47.90  Aligned_cols=27  Identities=22%  Similarity=0.363  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||++.+......
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl~~~   53 (241)
T cd03256          27 GEFVALIGPSGAGKSTLLRCLNGLVEP   53 (241)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCcCC
Confidence            358999999999999999999877643

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.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=95.30  E-value=0.023  Score=47.40  Aligned_cols=27  Identities=37%  Similarity=0.370  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p   53 (255)
T PRK11248         27 GELLVVLGPSGCGKTTLLNLIAGFVPY   53 (255)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987643

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=95.30  E-value=0.023  Score=46.63  Aligned_cols=26  Identities=35%  Similarity=0.420  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|+|||||.+.+.....
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~Gl~~   51 (232)
T cd03218          26 GEIVGLLGPNGAGKTTTFYMIVGLVK   51 (232)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC
Confidence            35899999999999999999987654

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.30  E-value=0.02  Score=45.16  Aligned_cols=28  Identities=25%  Similarity=0.487  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...++.|.|.+|+||||+|+.+......
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l~~   44 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKLES   44 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3569999999999999999999987653

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>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=95.30  E-value=0.039  Score=43.10  Aligned_cols=42  Identities=21%  Similarity=0.311  Sum_probs=31.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc-CCCCCeEEEEEecCcCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS-DKLFDQVVFVEVSQNQD  156 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~f~~~~wv~~~~~~~  156 (276)
                      ...+.+.|+.|+|||.||+.+...... .  ....+-++.+.-..
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~--~~~~~~~d~s~~~~   45 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGS--ERPLIRIDMSEYSE   45 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SS--CCEEEEEEGGGHCS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCC--ccchHHHhhhcccc
Confidence            357888999999999999999998873 3  45566666654433

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 ....

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=95.29  E-value=0.016  Score=44.21  Aligned_cols=23  Identities=30%  Similarity=0.580  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         3 ki~iiG~~~vGKTsl~~~~~~~~   25 (162)
T cd04138           3 KLVVVGAGGVGKSALTIQLIQNH   25 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999999988754

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=95.28  E-value=0.024  Score=45.59  Aligned_cols=27  Identities=33%  Similarity=0.506  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+......
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p   52 (205)
T cd03226          26 GEIIALTGKNGAGKTTLAKILAGLIKE   52 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999987653

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.

>cd01862 Rab7 Rab7 subfamily

Probab=95.28  E-value=0.016  Score=44.83  Aligned_cols=23  Identities=35%  Similarity=0.459  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+|+|.+|+|||||+..+.+..
T Consensus         2 ki~viG~~~~GKSsl~~~l~~~~   24 (172)
T cd01862           2 KVIILGDSGVGKTSLMNQYVNKK   24 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            48899999999999999987663

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-

>cd04163 Era Era subfamily

Probab=95.28  E-value=0.015  Score=44.20  Aligned_cols=25  Identities=20%  Similarity=0.389  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+|+++|.+|+|||||...+....
T Consensus         3 ~~~i~~~G~~g~GKttl~~~l~~~~   27 (168)
T cd04163           3 SGFVAIVGRPNVGKSTLLNALVGQK   27 (168)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCCc
Confidence            4579999999999999999987653

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.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=95.28  E-value=0.016  Score=46.84  Aligned_cols=27  Identities=33%  Similarity=0.411  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G~~~p   52 (213)
T cd03259          26 GEFLALLGPSGCGKTTLLRLIAGLERP   52 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999886543

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.

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=95.27  E-value=0.016  Score=47.92  Aligned_cols=27  Identities=33%  Similarity=0.463  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||++.+......
T Consensus        28 Ge~~~l~G~nGsGKSTLl~~l~Gl~~~   54 (243)
T TIGR02315        28 GEFVAIIGPSGAGKSTLLRCINRLVEP   54 (243)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCcCC
Confidence            358999999999999999999876643

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.

>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=95.27  E-value=0.022  Score=46.29  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~Gl~~~   52 (222)
T cd03224          26 GEIVALLGRNGAGKTTLLKTIMGLLPP   52 (222)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999877643

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=95.27  E-value=0.045  Score=47.10  Aligned_cols=59  Identities=15%  Similarity=0.318  Sum_probs=42.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      .-+++-|+|.+|+|||+|+.+++-.....    ..=..++|++....++++.+. ++++.++.+
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d  157 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVD  157 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCC
Confidence            35688899999999999998876443211    112478999988888888875 456666554

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.

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=95.27  E-value=0.026  Score=46.15  Aligned_cols=26  Identities=27%  Similarity=0.300  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|+|||||.+.+.....
T Consensus        33 Ge~~~i~G~nGsGKSTLl~~l~G~~~   58 (225)
T PRK10247         33 GEFKLITGPSGCGKSTLLKIVASLIS   58 (225)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcccC
Confidence            35899999999999999999998654

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

Probab=95.27  E-value=0.049  Score=45.85  Aligned_cols=50  Identities=20%  Similarity=0.306  Sum_probs=40.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  163 (276)
                      .-+++-|+|+.|+||||+|.+++-.....  -...+|++.-..++++.+.+-
T Consensus        59 ~g~ItEiyG~~gsGKT~lal~~~~~aq~~--g~~a~fIDtE~~l~p~r~~~l  108 (279)
T COG0468          59 RGRITEIYGPESSGKTTLALQLVANAQKP--GGKAAFIDTEHALDPERAKQL  108 (279)
T ss_pred             cceEEEEecCCCcchhhHHHHHHHHhhcC--CCeEEEEeCCCCCCHHHHHHH
Confidence            46799999999999999999987666544  458899999888888776433

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=95.25  E-value=1.1  Score=39.77  Aligned_cols=85  Identities=16%  Similarity=0.188  Sum_probs=46.8

Q ss_pred             CccEEEEEcCCCCcHHH-HHHHHHHhc-ccCCCCCeEEEEEecCc-CCHHHHHHHHHHHhCCCcccccchhhhhhccccC
Q 041612          112 DVNMLGIYGMGGIGKTM-LAEEIARKV-KSDKLFDQVVFVEVSQN-QDIRKIQEEIGDKLGLKFHEESESGRANSLFTHG  188 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTt-La~~v~~~~-~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~~  188 (276)
                      ..+++.++|+.|+|||| ||+.-..-. ...  -..+..++...- -...+-++.-++-++.+..-..+...........
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~--~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l  279 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKK--KKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEAL  279 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhcc--CcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHh
Confidence            37899999999999998 665543333 111  234566655432 2344445666777777655544443333333322


Q ss_pred             CCCcEEEEEe
Q 041612          189 HKGCKVLLTA  198 (276)
Q Consensus       189 ~~gs~IivTT  198 (276)
                      ..---|+|-|
T Consensus       280 ~~~d~ILVDT  289 (407)
T COG1419         280 RDCDVILVDT  289 (407)
T ss_pred             hcCCEEEEeC
Confidence            2223455544

>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=95.25  E-value=0.017  Score=47.22  Aligned_cols=25  Identities=24%  Similarity=0.341  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.+++|+|..|+|||||.+.+....
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G~~   50 (227)
T cd03260          26 GEITALIGPSGCGKSTLLRLLNRLN   50 (227)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3589999999999999999999876

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).

>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.24  E-value=0.045  Score=44.56  Aligned_cols=28  Identities=29%  Similarity=0.426  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      --.|+|+|.+|.|||||.+.+..-....
T Consensus        30 GE~VaiIG~SGaGKSTLLR~lngl~d~t   57 (258)
T COG3638          30 GEMVAIIGPSGAGKSTLLRSLNGLVDPT   57 (258)
T ss_pred             CcEEEEECCCCCcHHHHHHHHhcccCCC
Confidence            3489999999999999999998855443

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.24  E-value=0.041  Score=44.00  Aligned_cols=31  Identities=23%  Similarity=0.330  Sum_probs=25.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++-++..|.|.+|+||||+...+.......
T Consensus        15 ~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~   45 (196)
T PF13604_consen   15 TSGDRVSVLQGPAGTGKTTLLKALAEALEAA   45 (196)
T ss_dssp             HCTCSEEEEEESTTSTHHHHHHHHHHHHHHT
T ss_pred             hcCCeEEEEEECCCCCHHHHHHHHHHHHHhC
Confidence            3444688999999999999999988877765

>TIGR00763 lon ATP-dependent protease La

Probab=95.23  E-value=0.064  Score=52.14  Aligned_cols=27  Identities=33%  Similarity=0.522  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+.+.++|++|+|||++|+.+.+....
T Consensus       347 ~~~lll~GppG~GKT~lAk~iA~~l~~  373 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLGKSIAKALNR  373 (775)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            457999999999999999999988753

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.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.23  E-value=0.027  Score=45.23  Aligned_cols=26  Identities=23%  Similarity=0.368  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|+|||||.+.+.....
T Consensus        33 Ge~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          33 GEMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             CcEEEEECCCCCCHHHHHHHhcccCC
Confidence            35899999999999999999998765

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.23  E-value=0.054  Score=47.18  Aligned_cols=59  Identities=17%  Similarity=0.251  Sum_probs=42.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc----CCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS----DKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      .-.++-|+|.+|+|||+|+.+++-....    ...-..++|++-...++++.+.+ +++.++.+
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d  187 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMD  187 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCC
Confidence            3568889999999999999988644321    11124789999998888888754 56666654

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=95.22  E-value=0.029  Score=44.12  Aligned_cols=34  Identities=21%  Similarity=0.273  Sum_probs=28.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      -..+-++|++|.|||||.+.+|...+..   ...+|+
T Consensus        28 Gef~fl~GpSGAGKSTllkLi~~~e~pt---~G~i~~   61 (223)
T COG2884          28 GEFVFLTGPSGAGKSTLLKLIYGEERPT---RGKILV   61 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhhcCC---CceEEE
Confidence            4578999999999999999999998765   445555

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=95.22  E-value=0.11  Score=43.79  Aligned_cols=28  Identities=32%  Similarity=0.512  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++=|-++|.+|.|||-||+++.|+-..
T Consensus       218 pPKGVIlyG~PGTGKTLLAKAVANqTSA  245 (440)
T KOG0726|consen  218 PPKGVILYGEPGTGKTLLAKAVANQTSA  245 (440)
T ss_pred             CCCeeEEeCCCCCchhHHHHHHhcccch
Confidence            3667888999999999999999987653

>PRK10908 cell division protein FtsE; Provisional

Probab=95.22  E-value=0.027  Score=45.85  Aligned_cols=27  Identities=26%  Similarity=0.278  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G~~~~   54 (222)
T PRK10908         28 GEMAFLTGHSGAGKSTLLKLICGIERP   54 (222)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999877653

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=95.21  E-value=0.016  Score=48.93  Aligned_cols=25  Identities=24%  Similarity=0.493  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +++|.|.+|+|||||++.+......
T Consensus         1 iigI~G~sGsGKSTl~~~L~~ll~~   25 (273)
T cd02026           1 IIGVAGDSGCGKSTFLRRLTSLFGS   25 (273)
T ss_pred             CEEEECCCCCCHHHHHHHHHHhhCC
Confidence            5899999999999999999877653

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.

>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

Probab=95.21  E-value=0.017  Score=45.93  Aligned_cols=23  Identities=35%  Similarity=0.538  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|+|.|+.|+||||+++.+....
T Consensus         1 ~I~ieG~~GsGKSTl~~~L~~~~   23 (193)
T cd01673           1 VIVVEGNIGAGKSTLAKELAEHL   23 (193)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998764

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=95.20  E-value=0.029  Score=43.85  Aligned_cols=26  Identities=35%  Similarity=0.488  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|.|||||.+.+.....
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~   51 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLLK   51 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC
Confidence            35899999999999999999988764

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=95.20  E-value=0.027  Score=45.02  Aligned_cols=27  Identities=33%  Similarity=0.439  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G~~~~   52 (198)
T TIGR01189        26 GEALQVTGPNGIGKTTLLRILAGLLRP   52 (198)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987654

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=95.20  E-value=0.027  Score=45.62  Aligned_cols=27  Identities=30%  Similarity=0.433  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|.|||||.+.++.....
T Consensus        24 Ge~~~i~G~nGsGKSTLl~~l~G~~~~   50 (213)
T TIGR01277        24 GEIVAIMGPSGAGKSTLLNLIAGFIEP   50 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999987654

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=95.20  E-value=0.024  Score=46.66  Aligned_cols=26  Identities=31%  Similarity=0.438  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|.|||||.+.+.....
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~Gl~~   51 (236)
T cd03219          26 GEIHGLIGPNGAGKTTLFNLISGFLR   51 (236)
T ss_pred             CcEEEEECCCCCCHHHHHHHHcCCCC
Confidence            35899999999999999999987654

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (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).

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=95.19  E-value=0.019  Score=44.93  Aligned_cols=24  Identities=17%  Similarity=0.358  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|+|+|.+|+|||||...+.+..
T Consensus         2 ~kv~l~G~~g~GKTtl~~~~~~~~   25 (180)
T cd04137           2 RKIAVLGSRSVGKSSLTVQFVEGH   25 (180)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            468899999999999999987554

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=95.19  E-value=0.027  Score=46.43  Aligned_cols=26  Identities=27%  Similarity=0.321  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|.|||||.+.+.....
T Consensus        27 Ge~~~l~G~nGsGKSTLl~~l~G~~~   52 (240)
T PRK09493         27 GEVVVIIGPSGSGKSTLLRCINKLEE   52 (240)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45899999999999999999987764

>PLN03046 D-glycerate 3-kinase; Provisional

Probab=95.19  E-value=0.037  Score=49.15  Aligned_cols=29  Identities=21%  Similarity=0.226  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+-+|+|.|..|+|||||++.+..-.+..
T Consensus       211 ~PlIIGIsG~qGSGKSTLa~~L~~lL~~~  239 (460)
T PLN03046        211 PPLVIGFSAPQGCGKTTLVFALDYLFRVT  239 (460)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            56799999999999999999997666543

>cd04159 Arl10_like Arl10-like subfamily

Probab=95.18  E-value=0.015  Score=44.01  Aligned_cols=21  Identities=33%  Similarity=0.469  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHh
Q 041612          116 LGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~  136 (276)
                      |+|+|.+|+|||||.+.+.+.
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            789999999999999999876

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.

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=95.18  E-value=0.063  Score=43.28  Aligned_cols=29  Identities=28%  Similarity=0.375  Sum_probs=26.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      .+.|+|-|+-|+||||.++.++.....+.
T Consensus         3 g~fI~iEGiDGaGKTT~~~~L~~~l~~~g   31 (208)
T COG0125           3 GMFIVIEGIDGAGKTTQAELLKERLEERG   31 (208)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            35799999999999999999999998874

>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein

Probab=95.17  E-value=0.032  Score=46.26  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|+|||||++.+.....
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (247)
T TIGR00972        27 NQVTALIGPSGCGKSTLLRSLNRMND   52 (247)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCC
Confidence            45899999999999999999987664

This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters.

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=95.17  E-value=0.028  Score=46.98  Aligned_cols=27  Identities=22%  Similarity=0.321  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        38 Ge~~~I~G~NGsGKSTLlk~l~Gl~~p   64 (257)
T PRK11247         38 GQFVAVVGRSGCGKSTLLRLLAGLETP   64 (257)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999887643

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=95.17  E-value=0.016  Score=43.33  Aligned_cols=23  Identities=26%  Similarity=0.352  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||+|...+....
T Consensus         2 kv~liG~~~vGKSsL~~~l~~~~   24 (142)
T TIGR02528         2 RIMFIGSVGCGKTTLTQALQGEE   24 (142)
T ss_pred             eEEEECCCCCCHHHHHHHHcCCc
Confidence            58899999999999999987664

This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.17  E-value=0.027  Score=46.60  Aligned_cols=26  Identities=31%  Similarity=0.428  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|+|||||++.+.....
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   54 (241)
T PRK14250         29 GAIYTIVGPSGAGKSTLIKLINRLID   54 (241)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            35899999999999999999998754

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.17  E-value=0.036  Score=45.31  Aligned_cols=47  Identities=26%  Similarity=0.348  Sum_probs=31.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc-cc-CCCCCeEEEEEecCcCCHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV-KS-DKLFDQVVFVEVSQNQDIRKIQEEI  164 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~-~~-~~~f~~~~wv~~~~~~~~~~l~~~i  164 (276)
                      -.++.|.|.+|+|||+|+.++.... .. .   ..++|++...+  ...+.+.+
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~~~~~~g---e~vlyvs~ee~--~~~l~~~~   67 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYNGLKNFG---EKVLYVSFEEP--PEELIENM   67 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHT-----EEEEESSS---HHHHHHHH
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHhhhhcC---CcEEEEEecCC--HHHHHHHH
Confidence            5689999999999999999876554 33 2   35677776444  34444443

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=95.17  E-value=0.026  Score=44.02  Aligned_cols=33  Identities=18%  Similarity=0.138  Sum_probs=24.8

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +.+++.......|+++|.+|+|||||...+...
T Consensus         6 ~~~~~~~~~~~kv~~~G~~~~GKTsl~~~l~~~   38 (174)
T cd04153           6 LWSLFFPRKEYKVIIVGLDNAGKTTILYQFLLG   38 (174)
T ss_pred             HHHHhcCCCccEEEEECCCCCCHHHHHHHHccC
Confidence            334444444567899999999999999998654

Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=95.16  E-value=0.027  Score=46.57  Aligned_cols=26  Identities=31%  Similarity=0.397  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|..|.|||||.+.+.....
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (242)
T cd03295          27 GEFLVLIGPSGSGKTTTMKMINRLIE   52 (242)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35899999999999999999987754

ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. 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.

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=95.16  E-value=0.02  Score=48.36  Aligned_cols=27  Identities=30%  Similarity=0.645  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|+|-||+||||++..+.......
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~~La~~   28 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTAALSTM   28 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHhh
Confidence            578888999999999998887777544

>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=0.028  Score=46.17  Aligned_cols=27  Identities=30%  Similarity=0.448  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~G~~~~   57 (233)
T cd03258          31 GEIFGIIGRSGAGKSTLIRCINGLERP   57 (233)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999887654

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.

>PRK13976 thymidylate kinase; Provisional

Probab=95.15  E-value=0.06  Score=43.53  Aligned_cols=26  Identities=23%  Similarity=0.341  Sum_probs=23.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .|+|-|+.|+||||+++.++......
T Consensus         2 fIv~EGiDGsGKsTq~~~L~~~L~~~   27 (209)
T PRK13976          2 FITFEGIDGSGKTTQSRLLAEYLSDI   27 (209)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            68999999999999999999998754

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.15  E-value=0.057  Score=46.58  Aligned_cols=58  Identities=17%  Similarity=0.274  Sum_probs=40.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc---CC-CCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS---DK-LFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~-~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      .-.++.|+|.+|+|||+|+..++.....   .. .-..++|++....++...+ ..+++.++.
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~  156 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGL  156 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCC
Confidence            3678999999999999999988764321   11 1235789988877777664 345555544

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).

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.15  E-value=0.029  Score=45.24  Aligned_cols=28  Identities=32%  Similarity=0.294  Sum_probs=24.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+++|+|..|.|||||.+.+......
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~~   54 (207)
T PRK13539         27 AGEALVLTGPNGSGKTTLLRLIAGLLPP   54 (207)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            3458999999999999999999987653

>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL

Probab=95.15  E-value=0.028  Score=45.81  Aligned_cols=27  Identities=19%  Similarity=0.288  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        34 Ge~~~l~G~nGsGKSTLl~~i~G~~~~   60 (224)
T TIGR02324        34 GECVALSGPSGAGKSTLLKSLYANYLP   60 (224)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987654

Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=95.15  E-value=0.029  Score=45.35  Aligned_cols=27  Identities=26%  Similarity=0.254  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        26 G~~~~l~G~nGsGKSTLl~~l~G~~~~   52 (213)
T cd03262          26 GEVVVIIGPSGSGKSTLLRCINLLEEP   52 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987654

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=95.14  E-value=0.027  Score=45.66  Aligned_cols=27  Identities=26%  Similarity=0.382  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|+|||||.+.+..-...
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl~~~   57 (218)
T cd03266          31 GEVTGLLGPNGAGKTTTLRMLAGLLEP   57 (218)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCcCC
Confidence            358999999999999999999877543

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=95.13  E-value=0.027  Score=45.95  Aligned_cols=27  Identities=37%  Similarity=0.516  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~G~~~~   57 (228)
T cd03257          31 GETLGLVGESGSGKSTLARAILGLLKP   57 (228)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987653

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.

>COG0410 LivF ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=95.13  E-value=0.029  Score=45.37  Aligned_cols=28  Identities=29%  Similarity=0.457  Sum_probs=25.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++++|..|+|||||.+.++...+..
T Consensus        29 Geiv~llG~NGaGKTTlLkti~Gl~~~~   56 (237)
T COG0410          29 GEIVALLGRNGAGKTTLLKTIMGLVRPR   56 (237)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCC
Confidence            4589999999999999999999988764

>PTZ00035 Rad51 protein; Provisional

Probab=95.12  E-value=0.09  Score=45.77  Aligned_cols=58  Identities=17%  Similarity=0.308  Sum_probs=39.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc---C-CCCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS---D-KLFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~-~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      .-.++.|+|.+|+|||+|+..++.....   . ..-..++|++-...++.+.+ ..+++.++.
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~  178 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGL  178 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCC
Confidence            3568999999999999999988755431   1 01235678888777777664 344555554

>cd02032 Bchl_like This family of proteins contains bchL and chlL

Probab=95.12  E-value=0.021  Score=47.99  Aligned_cols=27  Identities=30%  Similarity=0.636  Sum_probs=22.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|++.|-||+||||++..+......+
T Consensus         1 ~~i~v~gKGGvGKTT~a~nLA~~la~~   27 (267)
T cd02032           1 MVLAVYGKGGIGKSTTSSNLSVALAKR   27 (267)
T ss_pred             CEEEEecCCCCCHHHHHHHHHHHHHHC
Confidence            368899999999999998887777644

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.

>smart00178 SAR Sar1p-like members of the Ras-family of small GTPases

Probab=95.12  E-value=0.029  Score=44.24  Aligned_cols=34  Identities=24%  Similarity=0.316  Sum_probs=25.8

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ++..++.. +....|+++|.+|+|||||...+...
T Consensus         6 ~~~~~~~~~~~~~~i~ivG~~~~GKTsli~~l~~~   40 (184)
T smart00178        6 DILASLGLWNKHAKILFLGLDNAGKTTLLHMLKND   40 (184)
T ss_pred             HHHHHhccccccCEEEEECCCCCCHHHHHHHHhcC
Confidence            34445532 45567899999999999999998765

Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=95.12  E-value=0.031  Score=45.04  Aligned_cols=27  Identities=30%  Similarity=0.405  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|+|||||.+.+......
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~Gl~~~   52 (208)
T cd03268          26 GEIYGFLGPNGAGKTTTMKIILGLIKP   52 (208)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCcCC
Confidence            458999999999999999999877643

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein

Probab=95.11  E-value=0.021  Score=47.98  Aligned_cols=26  Identities=31%  Similarity=0.631  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +|++.|-||+||||++-.+......+
T Consensus         2 ~i~~~gKGGVGKTT~~~nLA~~La~~   27 (268)
T TIGR01281         2 ILAVYGKGGIGKSTTSSNLSVAFAKL   27 (268)
T ss_pred             EEEEEcCCcCcHHHHHHHHHHHHHhC
Confidence            68888999999999988877766543

The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit.

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=95.11  E-value=0.019  Score=46.51  Aligned_cols=27  Identities=26%  Similarity=0.313  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|.|||||.+.+..-...
T Consensus        13 Ge~~~l~G~NGsGKSTLlk~i~Gl~~~   39 (213)
T PRK15177         13 HEHIGILAAPGSGKTTLTRLLCGLDAP   39 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCccC
Confidence            368999999999999999999987543

>cd04113 Rab4 Rab4 subfamily

Probab=95.11  E-value=0.019  Score=43.96  Aligned_cols=23  Identities=26%  Similarity=0.372  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         2 ki~v~G~~~vGKTsli~~l~~~~   24 (161)
T cd04113           2 KFIIIGSSGTGKSCLLHRFVENK   24 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999999987654

Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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 p

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=95.10  E-value=0.032  Score=43.32  Aligned_cols=27  Identities=30%  Similarity=0.213  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||++.+......
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~~   53 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWPW   53 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999987654

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=95.10  E-value=0.03  Score=45.77  Aligned_cols=27  Identities=26%  Similarity=0.377  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|+|||||.+.+......
T Consensus        48 Ge~~~i~G~nGsGKSTLl~~l~G~~~p   74 (224)
T cd03220          48 GERIGLIGRNGAGKSTLLRLLAGIYPP   74 (224)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987653

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>smart00175 RAB Rab subfamily of small GTPases

Probab=95.10  E-value=0.018  Score=44.05  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         2 kv~v~G~~~~GKTtli~~l~~~~   24 (164)
T smart00175        2 KIILIGDSGVGKSSLLSRFTDGK   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            47899999999999999998664

Rab GTPases are implicated in vesicle trafficking.

>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional

Probab=95.09  E-value=0.034  Score=46.60  Aligned_cols=27  Identities=22%  Similarity=0.434  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||.+.+......
T Consensus        30 Ge~~~i~G~nGsGKSTLl~~i~G~~~p   56 (262)
T PRK09984         30 GEMVALLGPSGSGKSTLLRHLSGLITG   56 (262)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCCC
Confidence            358999999999999999999977653

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=95.08  E-value=0.019  Score=43.09  Aligned_cols=25  Identities=20%  Similarity=0.200  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..|+++|.+|+|||||...+.....
T Consensus         2 ~ki~~~G~~~~GKstl~~~l~~~~~   26 (161)
T TIGR00231         2 IKIVIVGDPNVGKSTLLNRLLGNKF   26 (161)
T ss_pred             eEEEEECCCCCCHHHHHHHHhCCCC
Confidence            3689999999999999999987763

This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

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

Probab=95.08  E-value=0.033  Score=43.83  Aligned_cols=27  Identities=33%  Similarity=0.556  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|.|||||.+.+......
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~~~   51 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLLKP   51 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987654

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=95.07  E-value=0.031  Score=46.66  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|+|||||++.+......
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~i~G~~~~   57 (257)
T PRK10619         31 GDVISIIGSSGSGKSTFLRCINFLEKP   57 (257)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            458999999999999999999987653

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

Probab=95.06  E-value=0.61  Score=41.87  Aligned_cols=61  Identities=21%  Similarity=0.241  Sum_probs=42.5

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHh
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKL  168 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l  168 (276)
                      +..+..+-+-|.|-+|.|||.+...++.+......--.++++...+-.....++..|...+
T Consensus       170 le~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~~  230 (529)
T KOG2227|consen  170 LELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIFSSL  230 (529)
T ss_pred             hhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHHHHH
Confidence            4446678899999999999999999988876532112446666555455666666666555

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=95.06  E-value=0.034  Score=43.62  Aligned_cols=27  Identities=22%  Similarity=0.410  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|+|||||++.+......
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~~~   54 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDLKP   54 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCCC
Confidence            358999999999999999999987654

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=95.06  E-value=0.025  Score=41.14  Aligned_cols=25  Identities=40%  Similarity=0.679  Sum_probs=22.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      |.+.|.||+||||++..+......+
T Consensus         2 i~~~GkgG~GKTt~a~~la~~l~~~   26 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEK   26 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            7899999999999999998887654

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

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

Probab=95.06  E-value=0.03  Score=45.50  Aligned_cols=55  Identities=24%  Similarity=0.303  Sum_probs=39.9

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  163 (276)
                      .+.+.+-+.|.||+|+||||-+..+.+..-...+-+.+.=++.|..-.+.-+-..
T Consensus        44 ~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~   98 (333)
T KOG0991|consen   44 KEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNK   98 (333)
T ss_pred             HcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHH
Confidence            4567888999999999999988888887765544466666777766555444333

>cd04124 RabL2 RabL2 subfamily

Probab=95.06  E-value=0.02  Score=43.99  Aligned_cols=23  Identities=22%  Similarity=0.300  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||+..+.+..
T Consensus         2 ki~vvG~~~vGKTsli~~~~~~~   24 (161)
T cd04124           2 KIILLGDSAVGKSKLVERFLMDG   24 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999998877653

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. 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-b

>cd01864 Rab19 Rab19 subfamily

Probab=95.05  E-value=0.023  Score=43.67  Aligned_cols=24  Identities=17%  Similarity=0.278  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ...|.++|.+|+|||||...+...
T Consensus         3 ~~kv~vvG~~~~GKTsli~~l~~~   26 (165)
T cd01864           3 LFKIILIGDSNVGKTCVVQRFKSG   26 (165)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhhC
Confidence            357899999999999999998654

Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. 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-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=95.05  E-value=0.031  Score=46.04  Aligned_cols=27  Identities=22%  Similarity=0.389  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|.|..|.|||||++.+......
T Consensus        47 Ge~~~i~G~NGsGKSTLl~~i~Gl~~p   73 (236)
T cd03267          47 GEIVGFIGPNGAGKTTTLKILSGLLQP   73 (236)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCcCC
Confidence            358999999999999999999987643

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.05  E-value=0.091  Score=40.99  Aligned_cols=24  Identities=25%  Similarity=0.336  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +++.|.|.+|+|||++|..+....
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~~   25 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQS   25 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHHc
Confidence            468999999999999999998764

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.05  E-value=0.044  Score=49.64  Aligned_cols=30  Identities=20%  Similarity=0.417  Sum_probs=24.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccCCCCC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSDKLFD  144 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~  144 (276)
                      -+.|.|++|+|||+||+.+.........|.
T Consensus        41 hVLL~GpPGTGKT~LAraLa~~~~~~~~F~   70 (498)
T PRK13531         41 SVFLLGPPGIAKSLIARRLKFAFQNARAFE   70 (498)
T ss_pred             CEEEECCCChhHHHHHHHHHHHhcccCcce
Confidence            588999999999999999998765433444

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=95.04  E-value=0.037  Score=45.19  Aligned_cols=26  Identities=35%  Similarity=0.581  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|+.|.|||||++.+.....
T Consensus        33 Ge~~~l~G~nGsGKSTLlk~l~G~~~   58 (226)
T cd03234          33 GQVMAILGSSGSGKTTLLDAISGRVE   58 (226)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCccC
Confidence            45899999999999999999988765

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>COG1084 Predicted GTPase [General function prediction only]

Probab=95.04  E-value=1.3  Score=37.93  Aligned_cols=27  Identities=22%  Similarity=0.470  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+.+.|.|.|+|.+|||||.+.+....
T Consensus       166 p~~pTivVaG~PNVGKSSlv~~lT~Ak  192 (346)
T COG1084         166 PDLPTIVVAGYPNVGKSSLVRKLTTAK  192 (346)
T ss_pred             CCCCeEEEecCCCCcHHHHHHHHhcCC
Confidence            478999999999999999999987664

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=95.04  E-value=0.031  Score=51.36  Aligned_cols=33  Identities=24%  Similarity=0.433  Sum_probs=27.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      .+++.+.|++|+||||.++.+++...    |+.+-|.
T Consensus        45 ~~iLlLtGP~G~GKtttv~~La~elg----~~v~Ew~   77 (519)
T PF03215_consen   45 KRILLLTGPSGCGKTTTVKVLAKELG----FEVQEWI   77 (519)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHhC----CeeEEec
Confidence            56899999999999999999998874    5556665

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.04  E-value=0.031  Score=44.05  Aligned_cols=27  Identities=33%  Similarity=0.421  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|..|.|||||.+.+......
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~~~~   52 (182)
T cd03215          26 GEIVGIAGLVGNGQTELAEALFGLRPP   52 (182)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999987654

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.03  E-value=0.15  Score=44.09  Aligned_cols=117  Identities=23%  Similarity=0.185  Sum_probs=64.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc---------------------CCCCCeEEEEEecC----------cCCHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS---------------------DKLFDQVVFVEVSQ----------NQDIRKIQ  161 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~---------------------~~~f~~~~wv~~~~----------~~~~~~l~  161 (276)
                      .+-+.++|+.|+|||++|..+....--                     ..|.|.. ++.-.+          ...++++ 
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~-~~~p~~~~~~~g~~~~~I~id~i-   98 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFY-EITPLSDEPENGRKLLQIKIDAV-   98 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEE-EEecccccccccccCCCcCHHHH-
Confidence            456889999999999999998777521                     1233322 332211          1233333 


Q ss_pred             HHHHHHhCCCccc------------ccchhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKFHE------------ESESGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~~~------------~~~~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +.+.+.+......            .-+......+   .+....++.+|++|.+.. +..........+.+.+++.++..
T Consensus        99 R~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~  178 (325)
T PRK08699         99 REIIDNVYLTSVRGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEAL  178 (325)
T ss_pred             HHHHHHHhhCcccCCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHH
Confidence            3454444332111            0111111222   223345677888887754 43322333457889999999988


Q ss_pred             HHHHHh
Q 041612          226 SLFKKM  231 (276)
Q Consensus       226 ~Lf~~~  231 (276)
                      +.+...
T Consensus       179 ~~L~~~  184 (325)
T PRK08699        179 AYLRER  184 (325)
T ss_pred             HHHHhc
Confidence            877654

>PF13479 AAA_24: AAA domain

Probab=95.03  E-value=0.015  Score=47.10  Aligned_cols=20  Identities=45%  Similarity=0.575  Sum_probs=18.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEI  133 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v  133 (276)
                      -.+.|+|.+|+||||+|..+
T Consensus         4 ~~~lIyG~~G~GKTt~a~~~   23 (213)
T PF13479_consen    4 IKILIYGPPGSGKTTLAASL   23 (213)
T ss_pred             eEEEEECCCCCCHHHHHHhC
Confidence            46899999999999999886

>cd04136 Rap_like Rap-like subfamily

Probab=95.02  E-value=0.023  Score=43.47  Aligned_cols=23  Identities=26%  Similarity=0.599  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||||+..+.+..
T Consensus         3 ki~i~G~~~vGKTsl~~~~~~~~   25 (163)
T cd04136           3 KVVVLGSGGVGKSALTVQFVQGI   25 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58899999999999998877543

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>cd00876 Ras Ras family

Probab=95.02  E-value=0.02  Score=43.45  Aligned_cols=21  Identities=24%  Similarity=0.627  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHh
Q 041612          116 LGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~  136 (276)
                      |.|+|.+|+|||||...+.+.
T Consensus         2 i~i~G~~~~GKTsli~~l~~~   22 (160)
T cd00876           2 VVVLGAGGVGKSAITIQFVKG   22 (160)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998765

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=95.01  E-value=0.02  Score=49.67  Aligned_cols=27  Identities=30%  Similarity=0.391  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++.|++|+|||||-+.|..-....
T Consensus        32 ef~~lLGPSGcGKTTlLR~IAGfe~p~   58 (352)
T COG3842          32 EFVTLLGPSGCGKTTLLRMIAGFEQPS   58 (352)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCCCC
Confidence            479999999999999999998776554

---

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	276
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	7e-34
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-27
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	5e-24
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	5e-09

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  127 bits (321), Expect = 7e-34
 Identities = 31/282 (10%), Positives = 81/282 (28%), Gaps = 39/282 (13%)

Query: 30  SKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKGEEIEENVENWLARANNVIEAADNFT 89
             +  N Q+  ++      +    E  +        +    + +      NV +    + 
Sbjct: 73  DFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYI 132

Query: 90  KDEATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIAR--KVKSDKLFDQVV 147
           ++             L  + D D   L ++G  G GK+++A +            +D +V
Sbjct: 133 REYHVDRVI----KKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIV 188

Query: 148 FVEVSQN---------QDIRKIQEEIGDKLGLKFHEESESGRANSLFTHG---------- 188
           +++ S            DI  + +   D L     E   S     +  +           
Sbjct: 189 WLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFV 248

Query: 189 --------------HKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGD 234
                             + L+T R  ++ +    +     +  L  +E +   +     
Sbjct: 249 FDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMP 308

Query: 235 YIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWKD 276
                + + +     +  +G P +++   ++   K   +   
Sbjct: 309 MPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQ 350

>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 =  108 bits (271), Expect = 7e-27
 Identities = 58/310 (18%), Positives = 95/310 (30%), Gaps = 81/310 (26%)

Query: 40  KSEVDNL---KSERVRTEHQVDEAKRKGEEI-EENVE-------NWLA-------RANNV 81
           K E+D++   K     T         K EE+ ++ VE        +L        R  ++
Sbjct: 48  KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSM 107

Query: 82  IEAADNFTKDEATTNKRCF-KGNI----------LSALEDPDVNMLGIYGMGGIGKTMLA 130
           +       +D    + + F K N+           + LE      + I G+ G GKT +A
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVA 167

Query: 131 EEIARKVKSDKLFDQVVF-------------VEVSQN--QDIRKIQEEIGDKL-GLKFHE 174
            ++    K     D  +F             +E+ Q     I        D    +K   
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227

Query: 175 ESESGRANSLFTH-GHK--------------------GCKVLLTARSQ---DVLSGKMDS 210
            S       L     ++                     CK+LLT R +   D LS    +
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTT 287

Query: 211 RP--NFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRN 268
               +     L  +E  SL  K           Q + R+V       P  +  IA ++R+
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLD-----CRPQDLPREV---LTTNPRRLSIIAESIRD 339

Query: 269 --KRLFEWKD 276
                  WK 
Sbjct: 340 GLATWDNWKH 349

>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 = 44.8 bits (105), Expect = 2e-05
 Identities = 38/258 (14%), Positives = 73/258 (28%), Gaps = 98/258 (37%)

Query: 92  EATTNKRCFKGNILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVV---- 147
           E   ++  +K +ILS  ED  V+      +         +++ + + S +  D ++    
Sbjct: 10  ETGEHQYQYK-DILSVFEDAFVDNFDCKDV---------QDMPKSILSKEEIDHIIMSKD 59

Query: 148 ----------------------FVEVSQNQD----IRKIQEEIGDKLGLKFHEESESGR- 180
                                 FVE     +    +  I+ E      +      +  R 
Sbjct: 60  AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119

Query: 181 --ANSLFT----------------------------HGHKGC-KVLLTARSQDVL-SGKM 208
              N +F                              G  G  K  +     DV  S K+
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL---DVCLSYKV 176

Query: 209 DSRPNF-----SIGVLNEEEA-----WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVS 258
             + +F     ++   N  E        L  ++  ++   S+  S           + + 
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS----------NIKLR 226

Query: 259 IVTIARALRNKRLFEWKD 276
           I +I   LR  RL + K 
Sbjct: 227 IHSIQAELR--RLLKSKP 242

>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 =   99 bits (249), Expect = 5e-24
 Identities = 39/213 (18%), Positives = 69/213 (32%), Gaps = 42/213 (19%)

Query: 101 KGNILSAL--EDPDVNMLGIYGMGGIGKTMLAEEIAR--KVKSDKLFDQVVFVEVSQNQD 156
              I   L     +   + I+GM G GK++LA E  R   +        V +V V +   
Sbjct: 133 VNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDK 192

Query: 157 IRKI-----------------------QEEIGDKLGLKFHEESESGRA---------NSL 184
              +                        EE  D+L  +     +  R+         + +
Sbjct: 193 SGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRL--RILMLRKHPRSLLILDDVWDSWV 250

Query: 185 FTHGHKGCKVLLTARSQDVLSGKMDSRPN-FSIGVLNEEEAWSLFKKMAGDYIEDSEFQS 243
                  C++LLT R + V    M  +        L +E+   +         + ++   
Sbjct: 251 LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM--KKADLPE 308

Query: 244 IARDVAKECAGLPVSIVTIARALRNKRLFEWKD 276
            A  + KEC G P+ +  I   LR+     W+ 
Sbjct: 309 QAHSIIKECKGSPLVVSLIGALLRDFP-NRWEY 340

>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 = 56.0 bits (135), Expect = 5e-09
 Identities = 37/191 (19%), Positives = 64/191 (33%), Gaps = 37/191 (19%)

Query: 114 NMLGIYGMGGIGKTMLAEEIARKVK--SDKLFDQVVFVEVSQ------------------ 153
             + IYGM G GK++LA E  R            V +V + +                  
Sbjct: 148 GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLD 207

Query: 154 -----NQDIRKIQEEIGDKLGLKFHEESESG--------RANSLFTHGHKGCKVLLTARS 200
                +Q +    EE  D+L +    +                L    +  C++LLT R 
Sbjct: 208 QEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDN-QCQILLTTRD 266

Query: 201 QDVLSGKMDSRPNFSI-GVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI 259
           + V    M  +    +   L  E+   +        ++  +  + A  + KEC G P+ +
Sbjct: 267 KSVTDSVMGPKHVVPVESGLGREKGLEILSLFVN--MKKEDLPAEAHSIIKECKGSPLVV 324

Query: 260 VTIARALRNKR 270
             I   LR+  
Sbjct: 325 SLIGALLRDFP 335

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	276
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.95
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.87
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.86
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.82
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.37
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.83
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.82
2fna_A	357	Conserved hypothetical protein; structural genomic	98.8
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.73
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.72
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.62
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.53
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.5
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.41
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.34
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.18
3bos_A	242	Putative DNA replication factor; P-loop containing	98.04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.03
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.0
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.98
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.94
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.91
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.88
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.84
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.84
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.82
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.81
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.75
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.73
3pvs_A	447	Replication-associated recombination protein A; ma	97.72
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.72
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.69
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.67
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.67
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.66
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.61
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.53
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.51
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.5
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.49
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.48
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.45
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.44
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.43
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.32
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.3
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.3
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.28
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.25
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.24
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.24
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.21
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.17
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.11
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.09
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.06
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.02
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.95
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.92
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.91
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.89
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.89
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.78
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.76
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.76
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.75
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.75
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.74
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.72
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.71
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.71
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.71
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.69
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.68
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.67
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	96.63
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.62
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.62
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.6
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.59
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.58
2xxa_A	433	Signal recognition particle protein; protein trans	96.57
2og2_A	359	Putative signal recognition particle receptor; nuc	96.57
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.56
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.55
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.55
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.54
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.53
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.52
1via_A	175	Shikimate kinase; structural genomics, transferase	96.52
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.51
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.5
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.49
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.49
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.47
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.46
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.45
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.45
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.44
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.44
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.44
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.44
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.43
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.43
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.43
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.42
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.42
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.42
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.41
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	96.41
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.41
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.39
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.39
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.39
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.39
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.38
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.38
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.38
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.38
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.37
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.36
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.36
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.36
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.36
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.36
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.36
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.33
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.32
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.3
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.3
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.29
2hf9_A	226	Probable hydrogenase nickel incorporation protein	96.28
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.28
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.28
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.27
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.27
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.27
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.26
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.26
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	96.25
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.25
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	96.24
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	96.23
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.23
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.22
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	96.21
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	96.18
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	96.17
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.16
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.16
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.14
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.13
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.12
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.12
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.11
3fwy_A	314	Light-independent protochlorophyllide reductase I	96.1
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.1
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.09
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	96.09
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	96.09
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	96.08
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	96.07
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.06
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.06
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.04
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	96.03
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.03
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.99
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.97
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.96
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.96
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.96
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	95.95
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.93
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.92
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.9
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.9
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.9
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	95.89
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.89
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.89
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.89
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	95.88
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	95.88
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.87
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.86
2qgz_A	308	Helicase loader, putative primosome component; str	95.85
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.85
3io5_A	333	Recombination and repair protein; storage dimer, i	95.83
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.82
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.81
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.79
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	95.78
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.78
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.78
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.78
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.77
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.75
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.75
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	95.74
1b0u_A	262	Histidine permease; ABC transporter, transport pro	95.73
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.73
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.72
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.72
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.69
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	95.69
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	95.67
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	95.67
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.65
1ji0_A	240	ABC transporter; ATP binding protein, structural g	95.65
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	95.65
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.64
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	95.64
1g6h_A	257	High-affinity branched-chain amino acid transport	95.63
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	95.63
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	95.63
2z43_A	324	DNA repair and recombination protein RADA; archaea	95.63
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.61
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	95.61
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	95.59
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.58
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.57
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	95.57
3co5_A	143	Putative two-component system transcriptional RES	95.56
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	95.55
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	95.54
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	95.54
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	95.54
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.51
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	95.51
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	95.51
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	95.5
1sgw_A	214	Putative ABC transporter; structural genomics, P p	95.5
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.5
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.49
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	95.47
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.47
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	95.47
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.46
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.44
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	95.43
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	95.43
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.43
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.41
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.4
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	95.4
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	95.39
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	95.39
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.39
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	95.39
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.35
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.34
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.34
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	95.33
2wji_A	165	Ferrous iron transport protein B homolog; membrane	95.31
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.3
2ghi_A	260	Transport protein; multidrug resistance protein, M	95.29
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	95.27
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	95.26
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	95.25
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	95.24
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.23
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.23
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	95.2
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	95.2
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	95.18
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	95.15
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.13
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.13
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	95.1
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	95.09
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	95.07
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.05
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.05
2ged_A	193	SR-beta, signal recognition particle receptor beta	95.04
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	95.04
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	95.04
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.03
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	95.03
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	95.02
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.0
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	94.99
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	94.98
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	94.97
3end_A	307	Light-independent protochlorophyllide reductase ir	94.97
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	94.97
1nrj_B	218	SR-beta, signal recognition particle receptor beta	94.95
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	94.95
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	94.95
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.93
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.93
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	94.92
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	94.91
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	94.9
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	94.9
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	94.89
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.88
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	94.88
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	94.88
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.84
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	94.84
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	94.83
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	94.81
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	94.81
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.79
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	94.79
2r44_A	331	Uncharacterized protein; putative ATPase, structur	94.79
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.78
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.77
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	94.76
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	94.76
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	94.76
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	94.75
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	94.74
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	94.74
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.73
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	94.72
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	94.71
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.68
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.67
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.67
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	94.67
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	94.67
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	94.66
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	94.66
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	94.65
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	94.64
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	94.64
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	94.63
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	94.63
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	94.62
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	94.62
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	94.61
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.6
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	94.59
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	94.59
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	94.58
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	94.57
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	94.56
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	94.55
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	94.55
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	94.53
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	94.53
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	94.51
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	94.51
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.51
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	94.49
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	94.48
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	94.45
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.44
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	94.43
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	94.42
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	94.42
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.41
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.39
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	94.37
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	94.36
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	94.35
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	94.34
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	94.33
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.32
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	94.31
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	94.3
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	94.3
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	94.28
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	94.28
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	94.27
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	94.27
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	94.26
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	94.26
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	94.25
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	94.25
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	94.24
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	94.24
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	94.22
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	94.22
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	94.22
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.21
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	94.21
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	94.2
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.18
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	94.18
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	94.18
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.17
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	94.15
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	94.15
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	94.15
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	94.13
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	94.13
2fh5_B	214	SR-beta, signal recognition particle receptor beta	94.12
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	94.12
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	94.11
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.11
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	94.09
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	94.06
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.04
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	94.03
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	94.02
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	94.02
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	94.02
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	94.02
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	94.0
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	93.98
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.98
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	93.96
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	93.95
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	93.95
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	93.94
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	93.93
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	93.93
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.91
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	93.89
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	93.88
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	93.88
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	93.88
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	93.86
3llu_A	196	RAS-related GTP-binding protein C; structural geno	93.85
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	93.83
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.82
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	93.81
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	93.79
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.78
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.76
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	93.73
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	93.72
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	93.71
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	93.71
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.7
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	93.7
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	93.7
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	93.7
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	93.64
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	93.62
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	93.59
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.59
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	93.58
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.57
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	93.56
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	93.55
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	93.54
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	93.5
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	93.49
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.48
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	93.48
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	93.47
3cwq_A	209	Para family chromosome partitioning protein; alpha	93.45
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	93.44
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.44
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	93.42
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.41
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	93.4
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.39
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	93.39
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.38
3ice_A	422	Transcription termination factor RHO; transcriptio	93.36
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.35
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.33
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	93.33
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	93.33
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	93.32
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.31
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	93.3
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	93.29
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	93.29
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	93.27
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	93.25
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	93.24
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	93.24
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	93.23
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	93.22
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	93.17
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	93.14
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	93.13
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	93.11
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	93.06
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	93.01
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	93.0
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.0
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	92.97
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	92.87
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	92.86
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	92.86
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	92.86
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	92.85
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	92.83
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	92.83
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	92.77
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	92.76
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	92.57
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	92.53
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	92.53
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	92.52
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.49
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	92.44
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.42
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	92.4
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	92.32
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	92.28
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	92.28
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	92.25

>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=99.95  E-value=1.8e-28  Score=224.80  Aligned_cols=167  Identities=13%  Similarity=0.167  Sum_probs=130.6

Q ss_pred             HHHHhhcCC---CccEEEEEcCCCCcHHHHHHHHHH--hcccCCCCCeEEEEEecCcC--CHHHHHHHHHHHhCCCcc--
Q 041612          103 NILSALEDP---DVNMLGIYGMGGIGKTMLAEEIAR--KVKSDKLFDQVVFVEVSQNQ--DIRKIQEEIGDKLGLKFH--  173 (276)
Q Consensus       103 ~l~~~L~~~---~~~vi~I~G~gGiGKTtLa~~v~~--~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~~~l~~~~~--  173 (276)
                      +|.++|..+   +.++|+|+||||+||||||+.+|+  +...+.+|+.++|+++++.+  +...++..|+.+++....  
T Consensus       139 ~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l~~~~~~~  218 (549)
T 2a5y_B          139 RVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLL  218 (549)
T ss_dssp             HHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCT
T ss_pred             HHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHHhcCcccc
Confidence            777777543   689999999999999999999998  56667789999999999986  789999999999986521  


Q ss_pred             ---cccc---hhhhhhcc-------c----------------cCCCCcEEEEEeccccccccCCCCCCceeCCCCCHHHH
Q 041612          174 ---EESE---SGRANSLF-------T----------------HGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       174 ---~~~~---~~~~~~l~-------~----------------~~~~gs~IivTTR~~~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                         ....   ......+.       +                ...+||+||||||+..++.........|+|++|++++|
T Consensus       219 ~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~~~~~~~gs~ilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea  298 (549)
T 2a5y_B          219 NFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDEC  298 (549)
T ss_dssp             TCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHH
T ss_pred             cccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhhcccccCCCEEEEEcCCHHHHHHcCCCCeEEECCCCCHHHH
Confidence               0000   00001110       0                12379999999999999765322446799999999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHhCC
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK  269 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~~~  269 (276)
                      |+||.+.++....++++.+++.+|+++|+|+|||++++|++|+.+
T Consensus       299 ~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~  343 (549)
T 2a5y_B          299 YDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK  343 (549)
T ss_dssp             HHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS
T ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccc
Confidence            999999998544457888899999999999999999999998744

>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=99.87  E-value=4.4e-22  Score=197.82  Aligned_cols=165  Identities=21%  Similarity=0.328  Sum_probs=121.8

Q ss_pred             HHHHhhc--CCCccEEEEEcCCCCcHHHHHHHHHHhccc-CC-CCCeEEEEEecCcCC--HHHHHHHHHHHhCCCcccc-
Q 041612          103 NILSALE--DPDVNMLGIYGMGGIGKTMLAEEIARKVKS-DK-LFDQVVFVEVSQNQD--IRKIQEEIGDKLGLKFHEE-  175 (276)
Q Consensus       103 ~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~-~f~~~~wv~~~~~~~--~~~l~~~i~~~l~~~~~~~-  175 (276)
                      +|.+.|.  +++.++|+|+||||+||||||+++|++... .. .|+.++|+++++..+  ....+..++..+....... 
T Consensus       135 ~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  214 (1249)
T 3sfz_A          135 AIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQ  214 (1249)
T ss_dssp             HHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCS
T ss_pred             HHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHHHHHhhhhccccc
Confidence            6777764  457899999999999999999999988643 33 357888999998543  3444666777665432110 


Q ss_pred             ----cchhhhhhcc-----------------------ccCCCCcEEEEEeccccccccCCCCCCceeCCC-CCHHHHHHH
Q 041612          176 ----SESGRANSLF-----------------------THGHKGCKVLLTARSQDVLSGKMDSRPNFSIGV-LNEEEAWSL  227 (276)
Q Consensus       176 ----~~~~~~~~l~-----------------------~~~~~gs~IivTTR~~~va~~~~~~~~~~~l~~-L~~~ea~~L  227 (276)
                          ........+.                       ....+||+||||||++.++.........+.+.+ |++++|++|
T Consensus       215 ~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~~~~~~ilvTtR~~~~~~~~~~~~~~~~~~~~l~~~~a~~l  294 (1249)
T 3sfz_A          215 RLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEI  294 (1249)
T ss_dssp             SCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTTCSSCEEEEEESSTTTTTTCCSCBCCEECCSSCCHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhhcCCCEEEEEcCCHHHHHhhcCCceEEEecCCCCHHHHHHH
Confidence                1111111111                       045789999999999999755566777899996 999999999


Q ss_pred             HHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHhCC
Q 041612          228 FKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK  269 (276)
Q Consensus       228 f~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~~~  269 (276)
                      |...++..  .+++.+.+.+|+++|+|+||||+++|++|+.+
T Consensus       295 ~~~~~~~~--~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~  334 (1249)
T 3sfz_A          295 LSLFVNMK--KEDLPAEAHSIIKECKGSPLVVSLIGALLRDF  334 (1249)
T ss_dssp             HHHHHTSC--STTCCTHHHHHHHHTTTCHHHHHHHHHHHHHS
T ss_pred             HHHhhCCC--hhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcC
Confidence            99988632  23445578999999999999999999999943

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.86  E-value=9.4e-23  Score=193.21  Aligned_cols=164  Identities=22%  Similarity=0.279  Sum_probs=115.6

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCe-EEEEEecCcCCHHHHHHHHHHHhCCC---ccccc-
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQ-VVFVEVSQNQDIRKIQEEIGDKLGLK---FHEES-  176 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~-~~wv~~~~~~~~~~l~~~i~~~l~~~---~~~~~-  176 (276)
                      +|.++|.. ++.++|+|+||||+||||||+.+|++.+.+.+|+. ++|+++++.++...++..|...++..   ..... 
T Consensus       139 eL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i~~~~~~~~d  218 (1221)
T 1vt4_I          139 KLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD  218 (1221)
T ss_dssp             HHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHHCSSSTTTSC
T ss_pred             HHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhcCcccccccc
Confidence            66666654 56899999999999999999999988766666986 99999999999888877776643211   10000 


Q ss_pred             -------c----hhhhhhcc-----c----------------cCCCCcEEEEEeccccccccCCCCCCceeCC------C
Q 041612          177 -------E----SGRANSLF-----T----------------HGHKGCKVLLTARSQDVLSGKMDSRPNFSIG------V  218 (276)
Q Consensus       177 -------~----~~~~~~l~-----~----------------~~~~gs~IivTTR~~~va~~~~~~~~~~~l~------~  218 (276)
                             .    ...+..+.     +                ...+||+||||||++.++.. +.....|.++      +
T Consensus       219 ~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~pGSRILVTTRd~~Va~~-l~g~~vy~LeL~d~dL~  297 (1221)
T 1vt4_I          219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF-LSAATTTHISLDHHSMT  297 (1221)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHHSSCCEEEECSCSHHHHH-HHHHSSCEEEECSSSSC
T ss_pred             cccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhCCCeEEEEeccChHHHHh-cCCCeEEEecCccccCC
Confidence                   0    00111110     0                23489999999999998642 2222356666      9


Q ss_pred             CCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHhCC--CccccC
Q 041612          219 LNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNK--RLFEWK  275 (276)
Q Consensus       219 L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~~~--~~~~W~  275 (276)
                      |+++|||+||.+.....  ..   ++..++   |+|+||||.++|++|+.+  +.++|+
T Consensus       298 LS~eEA~eLF~~~~g~~--~e---eL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~  348 (1221)
T 1vt4_I          298 LTPDEVKSLLLKYLDCR--PQ---DLPREV---LTTNPRRLSIIAESIRDGLATWDNWK  348 (1221)
T ss_dssp             CCHHHHHHHHHHHHCCC--TT---THHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHH
T ss_pred             cCHHHHHHHHHHHcCCC--HH---HHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHh
Confidence            99999999999986432  11   223333   999999999999999933  667774

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.82  E-value=6.1e-20  Score=169.76  Aligned_cols=161  Identities=24%  Similarity=0.386  Sum_probs=110.8

Q ss_pred             HHHHhhc--CCCccEEEEEcCCCCcHHHHHHHHHHhccc-CCCC-CeEEEEEecCcCCHHHHHHH---HHHHhCCCc---
Q 041612          103 NILSALE--DPDVNMLGIYGMGGIGKTMLAEEIARKVKS-DKLF-DQVVFVEVSQNQDIRKIQEE---IGDKLGLKF---  172 (276)
Q Consensus       103 ~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~f-~~~~wv~~~~~~~~~~l~~~---i~~~l~~~~---  172 (276)
                      +|...|.  .++.++|+|+|+||+||||||..++++... ..+| +.++|++++.. +...++..   ++..++...   
T Consensus       135 ~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~~l~~~l~~~~~~~  213 (591)
T 1z6t_A          135 AIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFS  213 (591)
T ss_dssp             HHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHHHHHHHHCSSCCSC
T ss_pred             HHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHHHHHHHhccccccc
Confidence            6666665  356889999999999999999999987643 4458 58999999876 33333333   344444210   


Q ss_pred             --ccccchhhhhhc-----------------------cccCCCCcEEEEEeccccccccCCCCCCceeC---CCCCHHHH
Q 041612          173 --HEESESGRANSL-----------------------FTHGHKGCKVLLTARSQDVLSGKMDSRPNFSI---GVLNEEEA  224 (276)
Q Consensus       173 --~~~~~~~~~~~l-----------------------~~~~~~gs~IivTTR~~~va~~~~~~~~~~~l---~~L~~~ea  224 (276)
                        ...........+                       .....+||+||||||+..++....  ...+.+   ++|+.+|+
T Consensus       214 ~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l~~~~~ilvTsR~~~~~~~~~--~~~~~v~~l~~L~~~ea  291 (591)
T 1z6t_A          214 QRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVM--GPKYVVPVESSLGKEKG  291 (591)
T ss_dssp             SSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTTCSSCEEEEEESCGGGGTTCC--SCEEEEECCSSCCHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHhcCCCeEEEECCCcHHHHhcC--CCceEeecCCCCCHHHH
Confidence              000000000000                       014578999999999998865322  233443   68999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHhC
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRN  268 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~~  268 (276)
                      ++||...++..  .....+.+.+|+++|+|+|||+..+|++|+.
T Consensus       292 ~~L~~~~~~~~--~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~  333 (591)
T 1z6t_A          292 LEILSLFVNMK--KADLPEQAHSIIKECKGSPLVVSLIGALLRD  333 (591)
T ss_dssp             HHHHHHHHTSC--GGGSCTHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCC--cccccHHHHHHHHHhCCCcHHHHHHHHHHhc
Confidence            99999998732  2223456889999999999999999999983

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.37  E-value=6.9e-13  Score=95.62  Aligned_cols=79  Identities=6%  Similarity=0.109  Sum_probs=66.8

Q ss_pred             HHHHHHHhhhHHHHhhhcccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHHHHh
Q 041612            8 IVVEVVKCMVPPAYRRICYLRKSKYTSNLQNLKSEVDNLKSERVRTEHQVDEAKRKG-EEIEENVENWLARANNVIEAAD   86 (276)
Q Consensus         8 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~i~~~~~~a~~~~-~~~~~~~~~wl~~l~~~~~~~e   86 (276)
                      +++.++++|.+.+.+++..+         .+++++++.|++.|..|++++.+|+.+. ...++.++.|+.++++++||+|
T Consensus         2 ~v~~ll~KL~~ll~~E~~l~---------~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~E   72 (115)
T 3qfl_A            2 AISNLIPKLGELLTEEFKLH---------KGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIE   72 (115)
T ss_dssp             TTCSHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHH---------hchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHH
Confidence            35667888999999988877         4667777788899999999999999874 2358899999999999999999


Q ss_pred             hhhhhhhhh
Q 041612           87 NFTKDEATT   95 (276)
Q Consensus        87 d~ld~~~~~   95 (276)
                      |++|+|.+.
T Consensus        73 D~iD~f~~~   81 (115)
T 3qfl_A           73 DVVDKFLVQ   81 (115)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999765

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.83  E-value=8.1e-08  Score=82.26  Aligned_cols=76  Identities=12%  Similarity=0.142  Sum_probs=52.1

Q ss_pred             CCcEEEEEeccccccc------c----CC-CCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHH
Q 041612          190 KGCKVLLTARSQDVLS------G----KM-DSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       190 ~gs~IivTTR~~~va~------~----~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      ++.++|+|++......      .    .. .....+.+.+|+.+|+.+++........... ..+....++..|+|+|++
T Consensus       163 ~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~-~~~~~~~i~~~tgG~P~~  241 (350)
T 2qen_A          163 PNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV-PENEIEEAVELLDGIPGW  241 (350)
T ss_dssp             TTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHHTTCHHH
T ss_pred             CCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHhCCCHHH
Confidence            5788999988654211      0    11 1123789999999999999987643111111 124578899999999999


Q ss_pred             HHHHHHHH
Q 041612          259 IVTIARAL  266 (276)
Q Consensus       259 i~~i~~~L  266 (276)
                      +..++..+
T Consensus       242 l~~~~~~~  249 (350)
T 2qen_A          242 LVVFGVEY  249 (350)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99988754

>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=98.82  E-value=7.1e-08  Score=76.92  Aligned_cols=161  Identities=13%  Similarity=0.115  Sum_probs=93.3

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCC-----Ccc----
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGL-----KFH----  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~-----~~~----  173 (276)
                      .+..++.....+.+.|+|++|+|||+||+.+++.......-...+.++.+.......+...+......     ...    
T Consensus        28 ~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vli  107 (226)
T 2chg_A           28 RLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIF  107 (226)
T ss_dssp             HHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHHTSCCSTTCSCEEEE
T ss_pred             HHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHHHHHhcccCCCccCceEEE
Confidence            55555555555569999999999999999999876433111223444444444444443333322211     100    


Q ss_pred             --cc--cchh---hhhhccccCCCCcEEEEEecccccc-ccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhHHH
Q 041612          174 --EE--SESG---RANSLFTHGHKGCKVLLTARSQDVL-SGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQS  243 (276)
Q Consensus       174 --~~--~~~~---~~~~l~~~~~~gs~IivTTR~~~va-~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~~~  243 (276)
                        +.  ....   .+..+......++++|+||+..... .........+.+.+++.++..+++.+.+.  ....+   .+
T Consensus       108 iDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~---~~  184 (226)
T 2chg_A          108 LDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKIT---ED  184 (226)
T ss_dssp             EETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBC---HH
T ss_pred             EeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHHHHHcCCCCC---HH
Confidence              00  0001   1112222455678899988765421 11112223789999999999999988764  21222   24


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHH
Q 041612          244 IARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       244 ~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      ....+++.++|.|..+..+...+
T Consensus       185 ~~~~l~~~~~g~~r~l~~~l~~~  207 (226)
T 2chg_A          185 GLEALIYISGGDFRKAINALQGA  207 (226)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHH
Confidence            56778899999999765554443

>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=98.80  E-value=6.3e-08  Score=83.10  Aligned_cols=74  Identities=14%  Similarity=0.197  Sum_probs=51.6

Q ss_pred             CCcEEEEEecccccccc----------CCCC-CCceeCCCCCHHHHHHHHHHhhCC-CCCChhHHHHHHHHHHHcCCCcH
Q 041612          190 KGCKVLLTARSQDVLSG----------KMDS-RPNFSIGVLNEEEAWSLFKKMAGD-YIEDSEFQSIARDVAKECAGLPV  257 (276)
Q Consensus       190 ~gs~IivTTR~~~va~~----------~~~~-~~~~~l~~L~~~ea~~Lf~~~~~~-~~~~~~~~~~~~~i~~~c~G~PL  257 (276)
                      ++.++|+|++.......          ..+. ...+.+.+|+.+++.+++...+.. .......    ..|+..|+|+|+
T Consensus       169 ~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~----~~i~~~t~G~P~  244 (357)
T 2fna_A          169 KRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY----EVVYEKIGGIPG  244 (357)
T ss_dssp             TTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH----HHHHHHHCSCHH
T ss_pred             CCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH----HHHHHHhCCCHH
Confidence            47889999987642110          1111 247899999999999999876421 1111221    689999999999


Q ss_pred             HHHHHHHHHh
Q 041612          258 SIVTIARALR  267 (276)
Q Consensus       258 ai~~i~~~L~  267 (276)
                      ++..++..+.
T Consensus       245 ~l~~~~~~~~  254 (357)
T 2fna_A          245 WLTYFGFIYL  254 (357)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHc
Confidence            9999987764

>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=98.73  E-value=1.3e-07  Score=83.06  Aligned_cols=150  Identities=15%  Similarity=0.152  Sum_probs=90.1

Q ss_pred             CccEEEE--EcCCCCcHHHHHHHHHHhcccC---CCCC-eEEEEEecCcCCHHHHHHHHHHHhCCCcccc----------
Q 041612          112 DVNMLGI--YGMGGIGKTMLAEEIARKVKSD---KLFD-QVVFVEVSQNQDIRKIQEEIGDKLGLKFHEE----------  175 (276)
Q Consensus       112 ~~~vi~I--~G~gGiGKTtLa~~v~~~~~~~---~~f~-~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~----------  175 (276)
                      ..+.+.|  +|++|+|||+|++.+++.....   ..|+ ..+|++.....+...++..++.+++......          
T Consensus        49 ~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~  128 (412)
T 1w5s_A           49 SDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKA  128 (412)
T ss_dssp             CCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHH
T ss_pred             CCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHH
Confidence            4556777  9999999999999999886542   0123 3577776666677777777777665431100          


Q ss_pred             ----------------cch-----------hhhhhccc---cC---C--CCcEEEEEecccccccc--------CCCCCC
Q 041612          176 ----------------SES-----------GRANSLFT---HG---H--KGCKVLLTARSQDVLSG--------KMDSRP  212 (276)
Q Consensus       176 ----------------~~~-----------~~~~~l~~---~~---~--~gs~IivTTR~~~va~~--------~~~~~~  212 (276)
                                      ++.           ..+..+..   ..   .  ....||+||+...+...        ......
T Consensus       129 l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~  208 (412)
T 1w5s_A          129 LVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGF  208 (412)
T ss_dssp             HHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSE
T ss_pred             HHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCC
Confidence                            000           00100111   11   2  34458888875542110        011122


Q ss_pred             ceeCCCCCHHHHHHHHHHhhC---C-CCCChhHHHHHHHHHHHcC------CCcHHHHHHHH
Q 041612          213 NFSIGVLNEEEAWSLFKKMAG---D-YIEDSEFQSIARDVAKECA------GLPVSIVTIAR  264 (276)
Q Consensus       213 ~~~l~~L~~~ea~~Lf~~~~~---~-~~~~~~~~~~~~~i~~~c~------G~PLai~~i~~  264 (276)
                      .+.+++|+.++.+++|...+.   . ...+   .+....|++.|+      |.|..+..+..
T Consensus       209 ~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~---~~~~~~i~~~~~~~~~~~G~p~~~~~l~~  267 (412)
T 1w5s_A          209 KLHLPAYKSRELYTILEQRAELGLRDTVWE---PRHLELISDVYGEDKGGDGSARRAIVALK  267 (412)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHBCTTSCC---HHHHHHHHHHHCGGGTSCCCHHHHHHHHH
T ss_pred             eeeeCCCCHHHHHHHHHHHHHhcCCCCCCC---hHHHHHHHHHHHHhccCCCcHHHHHHHHH
Confidence            389999999999999976542   2 1122   345778888898      99976555543

>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=98.72  E-value=2.6e-07  Score=74.49  Aligned_cols=163  Identities=13%  Similarity=0.133  Sum_probs=93.9

Q ss_pred             HHHHhhcCC-CccEEEEEcCCCCcHHHHHHHHHHhcccCCCC-------------------CeEEEEEecCcCCHHHHHH
Q 041612          103 NILSALEDP-DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLF-------------------DQVVFVEVSQNQDIRKIQE  162 (276)
Q Consensus       103 ~l~~~L~~~-~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f-------------------~~~~wv~~~~~~~~~~l~~  162 (276)
                      .+...+... ..+.+.|+|++|+|||||++.+++.......+                   ...+.+..... .......
T Consensus        34 ~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  112 (250)
T 1njg_A           34 ALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASR-TKVEDTR  112 (250)
T ss_dssp             HHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEEETTCG-GGHHHHH
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEecCccc-ccHHHHH
Confidence            344444333 24589999999999999999998876543111                   11222222221 2233344


Q ss_pred             HHHHHhCCCc----------ccc--cchhhhhhcc---ccCCCCcEEEEEeccccccc-cCCCCCCceeCCCCCHHHHHH
Q 041612          163 EIGDKLGLKF----------HEE--SESGRANSLF---THGHKGCKVLLTARSQDVLS-GKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       163 ~i~~~l~~~~----------~~~--~~~~~~~~l~---~~~~~gs~IivTTR~~~va~-~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .++..+....          ++.  ........+.   .....+..+|+||+...... ........+.+++++.++..+
T Consensus       113 ~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~  192 (250)
T 1njg_A          113 DLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRH  192 (250)
T ss_dssp             HHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHH
T ss_pred             HHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHH
Confidence            5555543211          000  0111111222   24456788899887654221 112224578999999999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          227 LFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       227 Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ++...+...... -..+....|++.|+|.|..+..+...+.
T Consensus       193 ~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~~~~~~~~~~~~  232 (250)
T 1njg_A          193 QLEHILNEEHIA-HEPRALQLLARAAEGSLRDALSLTDQAI  232 (250)
T ss_dssp             HHHHHHHHTTCC-BCHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            998877421111 1124577899999999999888766543

>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=98.62  E-value=2.3e-07  Score=80.46  Aligned_cols=149  Identities=16%  Similarity=0.133  Sum_probs=83.4

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCC-CCeEEEEEecCcCCHHHHHHHHHHHhCCCccc--------------
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL-FDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHE--------------  174 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~--------------  174 (276)
                      ....+.+.|+|++|+|||||++.+++....... -...+|++.....+...++..++..++.....              
T Consensus        42 ~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~  121 (386)
T 2qby_A           42 EEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVK  121 (386)
T ss_dssp             TCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHH
T ss_pred             CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHH
Confidence            345678999999999999999999988754310 12456776554444444444433333221100              


Q ss_pred             ------------ccc---------hhhhhhccc-c---CCCCcEEEEEeccccccccCC-----CC-CCceeCCCCCHHH
Q 041612          175 ------------ESE---------SGRANSLFT-H---GHKGCKVLLTARSQDVLSGKM-----DS-RPNFSIGVLNEEE  223 (276)
Q Consensus       175 ------------~~~---------~~~~~~l~~-~---~~~gs~IivTTR~~~va~~~~-----~~-~~~~~l~~L~~~e  223 (276)
                                  .++         ......+.. .   ...+..+|+||+.........     .. ...+.+++++.++
T Consensus       122 ~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~  201 (386)
T 2qby_A          122 AVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEE  201 (386)
T ss_dssp             HHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHH
T ss_pred             HHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHH
Confidence                        000         011111111 1   344567788887664322111     11 1478999999999


Q ss_pred             HHHHHHHhhC----CCCCChhHHHHHHHHHHHcC---CCcHHHHH
Q 041612          224 AWSLFKKMAG----DYIEDSEFQSIARDVAKECA---GLPVSIVT  261 (276)
Q Consensus       224 a~~Lf~~~~~----~~~~~~~~~~~~~~i~~~c~---G~PLai~~  261 (276)
                      ..++|...+.    ....++   +....++..++   |.|..+..
T Consensus       202 ~~~il~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~G~~r~~~~  243 (386)
T 2qby_A          202 LEDILTKRAQMAFKPGVLPD---NVIKLCAALAAREHGDARRALD  243 (386)
T ss_dssp             HHHHHHHHHHHHBCSSCSCH---HHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHhhccCCCCCH---HHHHHHHHHHHHhcCCHHHHHH
Confidence            9999987653    122233   34556666666   99884443

>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=98.53  E-value=5.8e-07  Score=76.08  Aligned_cols=158  Identities=15%  Similarity=0.179  Sum_probs=90.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhC---CCc----ccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLG---LKF----HEE  175 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~---~~~----~~~  175 (276)
                      .+..++..+..+.+.++|++|+|||++|+.+++...........++++.+.......+ +.++..+.   ...    ...
T Consensus        32 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~~~~~~~~~~~~~~v  110 (323)
T 1sxj_B           32 RLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVV-RNQIKHFAQKKLHLPPGKHKI  110 (323)
T ss_dssp             HHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHH-HTHHHHHHHBCCCCCTTCCEE
T ss_pred             HHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHH-HHHHHHHHhccccCCCCCceE
Confidence            5566666665555999999999999999999988643211112444444443343333 33333221   110    100


Q ss_pred             ---cch-----hhh---hhccccCCCCcEEEEEeccccc-cccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhH
Q 041612          176 ---SES-----GRA---NSLFTHGHKGCKVLLTARSQDV-LSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEF  241 (276)
Q Consensus       176 ---~~~-----~~~---~~l~~~~~~gs~IivTTR~~~v-a~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~  241 (276)
                         ++.     ...   .........++.+|+||....- ..........+.+.+++.++..+++...+.  ....+   
T Consensus       111 iiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~---  187 (323)
T 1sxj_B          111 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYT---  187 (323)
T ss_dssp             EEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBC---
T ss_pred             EEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHcCCCCC---
Confidence               111     111   1222245567888888866432 111122234799999999999999988764  11222   


Q ss_pred             HHHHHHHHHHcCCCcH-HHHHHHH
Q 041612          242 QSIARDVAKECAGLPV-SIVTIAR  264 (276)
Q Consensus       242 ~~~~~~i~~~c~G~PL-ai~~i~~  264 (276)
                      .+....+++.|+|.|. |+..+..
T Consensus       188 ~~~~~~l~~~~~G~~r~a~~~l~~  211 (323)
T 1sxj_B          188 NDGLEAIIFTAEGDMRQAINNLQS  211 (323)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHH
Confidence            2456789999999995 4454443

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.50  E-value=5.5e-07  Score=78.21  Aligned_cols=152  Identities=15%  Similarity=0.124  Sum_probs=89.6

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcccC-----CC-CCeEEEEEecCcC-CHHHHHHHHHHHh-------------
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD-----KL-FDQVVFVEVSQNQ-DIRKIQEEIGDKL-------------  168 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-----~~-f~~~~wv~~~~~~-~~~~l~~~i~~~l-------------  168 (276)
                      .....+.+.|+|++|+|||+||+.+++.....     +. ....+|++..... +...++..++..+             
T Consensus        41 ~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  120 (384)
T 2qby_B           41 KNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLG  120 (384)
T ss_dssp             TTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTH
T ss_pred             cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHH
Confidence            34556789999999999999999999876332     11 2356777766655 6666665655544             


Q ss_pred             ----------CCCc-----ccccc------hhh-hhhccccCCCCcEEEEEeccccccccC-----CCCCCceeCCCCCH
Q 041612          169 ----------GLKF-----HEESE------SGR-ANSLFTHGHKGCKVLLTARSQDVLSGK-----MDSRPNFSIGVLNE  221 (276)
Q Consensus       169 ----------~~~~-----~~~~~------~~~-~~~l~~~~~~gs~IivTTR~~~va~~~-----~~~~~~~~l~~L~~  221 (276)
                                ....     ++...      ... ...+.... .+..||+||+........     ......+.+++++.
T Consensus       121 ~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~  199 (384)
T 2qby_B          121 EYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDA  199 (384)
T ss_dssp             HHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCH
T ss_pred             HHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCH
Confidence                      1100     00000      001 11112222 678899998875321110     11123799999999


Q ss_pred             HHHHHHHHHhhC----CCCCChhHHHHHHHHHHHcC---CCcH-HHHHHHH
Q 041612          222 EEAWSLFKKMAG----DYIEDSEFQSIARDVAKECA---GLPV-SIVTIAR  264 (276)
Q Consensus       222 ~ea~~Lf~~~~~----~~~~~~~~~~~~~~i~~~c~---G~PL-ai~~i~~  264 (276)
                      ++..++|...+.    ....++   +....+++.|+   |.|. |+..+-.
T Consensus       200 ~~~~~il~~~~~~~~~~~~~~~---~~~~~i~~~~~~~~G~~r~a~~~l~~  247 (384)
T 2qby_B          200 EQLKFILSKYAEYGLIKGTYDD---EILSYIAAISAKEHGDARKAVNLLFR  247 (384)
T ss_dssp             HHHHHHHHHHHHHTSCTTSCCS---HHHHHHHHHHHTTCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccCCcCH---HHHHHHHHHHHhccCCHHHHHHHHHH
Confidence            999999998752    122333   34556777777   8877 4444433

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.41  E-value=4.5e-06  Score=72.47  Aligned_cols=145  Identities=13%  Similarity=0.174  Sum_probs=89.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCccccc-----------------
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHEES-----------------  176 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~-----------------  176 (276)
                      +.+.|+|++|+|||||++.+++...... -...+|++.+...+...++..++..++.......                 
T Consensus        45 ~~~li~G~~G~GKTtl~~~l~~~~~~~~-~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~  123 (389)
T 1fnn_A           45 PRATLLGRPGTGKTVTLRKLWELYKDKT-TARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRER  123 (389)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTTSC-CCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHhhhc-CeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhc
Confidence            3899999999999999999998876541 1245677766666777777777776654221100                 


Q ss_pred             ---------c-----hhhhhhccc---c-CC---CCcEEEEEeccccccccCCC------CCCceeCCCCCHHHHHHHHH
Q 041612          177 ---------E-----SGRANSLFT---H-GH---KGCKVLLTARSQDVLSGKMD------SRPNFSIGVLNEEEAWSLFK  229 (276)
Q Consensus       177 ---------~-----~~~~~~l~~---~-~~---~gs~IivTTR~~~va~~~~~------~~~~~~l~~L~~~ea~~Lf~  229 (276)
                               +     ......+..   . ..   .+..||++|+..........      ....+.+++++.++..+++.
T Consensus       124 ~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~  203 (389)
T 1fnn_A          124 DLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILL  203 (389)
T ss_dssp             TCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHH
T ss_pred             CCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHH
Confidence                     0     000011111   1 11   46788888876643221110      11368999999999999998


Q ss_pred             HhhCC----CCCChhHHHHHHHHHHHc---------CCCcHHHHHH
Q 041612          230 KMAGD----YIEDSEFQSIARDVAKEC---------AGLPVSIVTI  262 (276)
Q Consensus       230 ~~~~~----~~~~~~~~~~~~~i~~~c---------~G~PLai~~i  262 (276)
                      ..+..    ...+   .+....++..+         .|.|..+..+
T Consensus       204 ~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~  246 (389)
T 1fnn_A          204 DRAKAGLAEGSYS---EDILQMIADITGAQTPLDTNRGDARLAIDI  246 (389)
T ss_dssp             HHHHHHBCTTSSC---HHHHHHHHHHHSBSSTTCTTSCCHHHHHHH
T ss_pred             HHHHhhcCCCCCC---HHHHHHHHHHHhhcccCCCCCCcHHHHHHH
Confidence            87531    1222   34567888888         7887554444

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.34  E-value=3.5e-06  Score=72.95  Aligned_cols=144  Identities=13%  Similarity=0.157  Sum_probs=82.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHHHHHHHHHHHhCCCccc------------
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHE------------  174 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~------------  174 (276)
                      ...+.+.|+|++|+|||+||+.+++.....    +.-...+|++.....+...++..++.+++.....            
T Consensus        42 ~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l  121 (387)
T 2v1u_A           42 EKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERL  121 (387)
T ss_dssp             CCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHH
T ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHH
Confidence            456789999999999999999999887432    0012456777666556555555555444321100            


Q ss_pred             --------------ccch----------hhhhhccccC-----CCCcEEEEEecccccccc----C-CCCC-CceeCCCC
Q 041612          175 --------------ESES----------GRANSLFTHG-----HKGCKVLLTARSQDVLSG----K-MDSR-PNFSIGVL  219 (276)
Q Consensus       175 --------------~~~~----------~~~~~l~~~~-----~~gs~IivTTR~~~va~~----~-~~~~-~~~~l~~L  219 (276)
                                    .++.          .....+....     ..+..+|.||+.......    . .... ..+.++++
T Consensus       122 ~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l  201 (387)
T 2v1u_A          122 VKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPY  201 (387)
T ss_dssp             HHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCC
T ss_pred             HHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCC
Confidence                          0000          0111111111     456678888876532111    0 1112 36889999


Q ss_pred             CHHHHHHHHHHhhC----CCCCChhHHHHHHHHHHHcC---CCcH
Q 041612          220 NEEEAWSLFKKMAG----DYIEDSEFQSIARDVAKECA---GLPV  257 (276)
Q Consensus       220 ~~~ea~~Lf~~~~~----~~~~~~~~~~~~~~i~~~c~---G~PL  257 (276)
                      +.++..+++...+.    ....+++   ....+++.++   |.|-
T Consensus       202 ~~~~~~~il~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~G~~r  243 (387)
T 2v1u_A          202 TAPQLRDILETRAEEAFNPGVLDPD---VVPLCAALAAREHGDAR  243 (387)
T ss_dssp             CHHHHHHHHHHHHHHHBCTTTBCSS---HHHHHHHHHHSSSCCHH
T ss_pred             CHHHHHHHHHHHHHhhccCCCCCHH---HHHHHHHHHHHhccCHH
Confidence            99999999987753    1222333   3556777777   9994

>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=98.18  E-value=4.6e-06  Score=70.63  Aligned_cols=163  Identities=13%  Similarity=0.102  Sum_probs=88.5

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHH---HHHHHHHHHhCCC--cccc--
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIR---KIQEEIGDKLGLK--FHEE--  175 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~---~l~~~i~~~l~~~--~~~~--  175 (276)
                      .+..++.....+.+.++|++|+|||++|+.+++.......-...+.++.+......   ..+..........  ....  
T Consensus        36 ~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vli  115 (327)
T 1iqp_A           36 RLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIF  115 (327)
T ss_dssp             HHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEE
T ss_pred             HHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHHHHHHHHHHHhhCCcCCCCCeEEE
Confidence            45555555555569999999999999999999886432100123333333221111   1222222111110  0000  


Q ss_pred             -cc-----hhh---hhhccccCCCCcEEEEEecccccc-ccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHH
Q 041612          176 -SE-----SGR---ANSLFTHGHKGCKVLLTARSQDVL-SGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIA  245 (276)
Q Consensus       176 -~~-----~~~---~~~l~~~~~~gs~IivTTR~~~va-~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~  245 (276)
                       ++     ...   +.........++++|+||....-. .........+.+.+++.++...++...+...... --.+..
T Consensus       116 iDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~~-~~~~~~  194 (327)
T 1iqp_A          116 LDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE-LTEEGL  194 (327)
T ss_dssp             EETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE-ECHHHH
T ss_pred             EeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcCCC-CCHHHH
Confidence             01     111   111222455678889888765321 1111112368899999999999998876422111 113456


Q ss_pred             HHHHHHcCCCcHHHHHHHHHH
Q 041612          246 RDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       246 ~~i~~~c~G~PLai~~i~~~L  266 (276)
                      ..|+..++|.|..+..+...+
T Consensus       195 ~~l~~~~~g~~r~~~~~l~~~  215 (327)
T 1iqp_A          195 QAILYIAEGDMRRAINILQAA  215 (327)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHHHHHH
Confidence            788899999998766554443

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.04  E-value=7.2e-05  Score=60.09  Aligned_cols=152  Identities=11%  Similarity=0.160  Sum_probs=82.8

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC----cccc---c
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK----FHEE---S  176 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~----~~~~---~  176 (276)
                      +..+......+.+.|+|++|+|||+||+.+.+.....  .....|++.+...+.   ...++..+...    .++.   .
T Consensus        43 l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~~vliiDe~~~~~  117 (242)
T 3bos_A           43 LKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL--ERRSFYIPLGIHASI---STALLEGLEQFDLICIDDVDAVA  117 (242)
T ss_dssp             HHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEEGGGGGGS---CGGGGTTGGGSSEEEEETGGGGT
T ss_pred             HHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEHHHHHHH---HHHHHHhccCCCEEEEecccccc
Confidence            3333334456789999999999999999999887654  334566665432211   00111111110    0000   0


Q ss_pred             chh-hhhhccc----cCCCCc-EEEEEeccccccccCC--------CCCCceeCCCCCHHHHHHHHHHhhC--CCCCChh
Q 041612          177 ESG-RANSLFT----HGHKGC-KVLLTARSQDVLSGKM--------DSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSE  240 (276)
Q Consensus       177 ~~~-~~~~l~~----~~~~gs-~IivTTR~~~va~~~~--------~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~  240 (276)
                      ... ....+..    ....+. ++|+||+...-.....        .....+.+++++.++..+++...+.  ....+  
T Consensus       118 ~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~--  195 (242)
T 3bos_A          118 GHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLP--  195 (242)
T ss_dssp             TCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCC--
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCC--
Confidence            000 0111111    112222 5888886542100000        1115789999999999999988764  21222  


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHH
Q 041612          241 FQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                       .+....+++.++|.+-.+..+.
T Consensus       196 -~~~~~~l~~~~~g~~r~l~~~l  217 (242)
T 3bos_A          196 -EDVGRFLLNRMARDLRTLFDVL  217 (242)
T ss_dssp             -HHHHHHHHHHTTTCHHHHHHHH
T ss_pred             -HHHHHHHHHHccCCHHHHHHHH
Confidence             3456788899999887766543

>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=3.4e-05  Score=64.98  Aligned_cols=161  Identities=12%  Similarity=0.116  Sum_probs=88.8

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcC---CHHHHHHHHHHHhCCC-c-cc--
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQ---DIRKIQEEIGDKLGLK-F-HE--  174 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~---~~~~l~~~i~~~l~~~-~-~~--  174 (276)
                      .+...+..+..+.+.++|++|+|||++|+.+.+...... +. ..+.++.+...   ........+....... . ..  
T Consensus        28 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl  106 (319)
T 2chq_A           28 RLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-WRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKII  106 (319)
T ss_dssp             HHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTC-HHHHCEEEETTSTTCTTTSSHHHHHHHHSCCSSSCCCEEE
T ss_pred             HHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCc-ccCCeEEEeCccccChHHHHHHHHHHHhcCCCCCCCceEE
Confidence            555555555555599999999999999999998863221 11 22334433322   2233333333222111 0 00  


Q ss_pred             ----c--cchhh---hhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHH
Q 041612          175 ----E--SESGR---ANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSI  244 (276)
Q Consensus       175 ----~--~~~~~---~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  244 (276)
                          .  -....   +..+......++++|+||.... +..........+.+.+++.++...++...+...... -..+.
T Consensus       107 iiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~-i~~~~  185 (319)
T 2chq_A          107 FLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK-ITEDG  185 (319)
T ss_dssp             EEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCCC-BCHHH
T ss_pred             EEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHH
Confidence                0  01111   1222224456778888876543 211111223478999999999999998776422111 11235


Q ss_pred             HHHHHHHcCCCcHHHHHHHHH
Q 041612          245 ARDVAKECAGLPVSIVTIARA  265 (276)
Q Consensus       245 ~~~i~~~c~G~PLai~~i~~~  265 (276)
                      ...++..++|.|..+..+...
T Consensus       186 l~~l~~~~~G~~r~~~~~l~~  206 (319)
T 2chq_A          186 LEALIYISGGDFRKAINALQG  206 (319)
T ss_dssp             HHHHHHTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHH
Confidence            677888999998866544433

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.00  E-value=8.7e-05  Score=64.48  Aligned_cols=145  Identities=15%  Similarity=0.159  Sum_probs=78.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-----HHHHHHHHHHHhCCC------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-----IRKIQEEIGDKLGLK------  171 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-----~~~l~~~i~~~l~~~------  171 (276)
                      ++...+.-..++=+.++|++|+|||.||+.+.+.....     .+.++.+.-.+     .+..++.++......      
T Consensus       172 e~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~-----f~~v~~s~l~sk~vGese~~vr~lF~~Ar~~aP~IIF  246 (405)
T 4b4t_J          172 ELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK-----FIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIF  246 (405)
T ss_dssp             HHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE-----EEEEEGGGGSCSSTTHHHHHHHHHHHHHHHTCSEEEE
T ss_pred             HHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC-----ceEEEhHHhhccccchHHHHHHHHHHHHHHhCCceEe
Confidence            33444444556789999999999999999999987643     23444433221     233444443322110      


Q ss_pred             ----------cccc--cchh----hhhhccc-----cCCCCcEEEEEecccccccc----CCCCCCceeCCCCCHHHHHH
Q 041612          172 ----------FHEE--SESG----RANSLFT-----HGHKGCKVLLTARSQDVLSG----KMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       172 ----------~~~~--~~~~----~~~~l~~-----~~~~gs~IivTTR~~~va~~----~~~~~~~~~l~~L~~~ea~~  226 (276)
                                ....  ....    ....+..     ....+--||.||-..+....    .-..+..+.++..+.++-.+
T Consensus       247 iDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~  326 (405)
T 4b4t_J          247 MDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAE  326 (405)
T ss_dssp             EESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHH
T ss_pred             eecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHH
Confidence                      0000  0000    1111111     23334445666654443221    12345678888889888889


Q ss_pred             HHHHhhCCCC--CChhHHHHHHHHHHHcCCCc
Q 041612          227 LFKKMAGDYI--EDSEFQSIARDVAKECAGLP  256 (276)
Q Consensus       227 Lf~~~~~~~~--~~~~~~~~~~~i~~~c~G~P  256 (276)
                      +|+.+.....  .+.+    ...+++.+.|+-
T Consensus       327 Il~~~~~~~~l~~dvd----l~~lA~~t~G~S  354 (405)
T 4b4t_J          327 ILRIHSRKMNLTRGIN----LRKVAEKMNGCS  354 (405)
T ss_dssp             HHHHHHTTSBCCSSCC----HHHHHHHCCSCC
T ss_pred             HHHHHhcCCCCCccCC----HHHHHHHCCCCC
Confidence            9987775222  2223    345777777754

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=97.98  E-value=5.7e-05  Score=63.87  Aligned_cols=149  Identities=13%  Similarity=0.084  Sum_probs=83.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCc----ccc--cchhhhhhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKF----HEE--SESGRANSLFT  186 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~----~~~--~~~~~~~~l~~  186 (276)
                      .+.+.|+|++|+|||+||+.+.+.....     ..+++.+.......+...+...+....    ++.  -.......+..
T Consensus        38 ~~~vll~G~~GtGKT~la~~i~~~~~~~-----~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~  112 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLAHVIAHELGVN-----LRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYP  112 (324)
T ss_dssp             CCCCEEECCTTCCCHHHHHHHHHHHTCC-----EEEECTTTCCSHHHHHHHHTTTCCTTCEEEETTTTSCCHHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhCCC-----EEEEeccccCChHHHHHHHHHhccCCCEEEEECCcccccchHHHHHH
Confidence            4578999999999999999999876422     234444444344444333322121110    111  11111111111


Q ss_pred             ---c------------------CCCCcEEEEEecccc-ccccCCC-CCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHH
Q 041612          187 ---H------------------GHKGCKVLLTARSQD-VLSGKMD-SRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQS  243 (276)
Q Consensus       187 ---~------------------~~~gs~IivTTR~~~-va~~~~~-~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~  243 (276)
                         .                  ..+...+|.||.... +...... ....+.+.+++.++...++...+...... -..+
T Consensus       113 ~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~-~~~~  191 (324)
T 1hqc_A          113 AMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR-ITEE  191 (324)
T ss_dssp             HHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCC-CCHH
T ss_pred             HHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCC-CCHH
Confidence               0                  112356676665443 2221222 22478999999999999998876421111 1134


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          244 IARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       244 ~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ....++..+.|.|-.+..+...+.
T Consensus       192 ~~~~l~~~~~G~~r~l~~~l~~~~  215 (324)
T 1hqc_A          192 AALEIGRRSRGTMRVAKRLFRRVR  215 (324)
T ss_dssp             HHHHHHHHSCSCHHHHHHHHHHHT
T ss_pred             HHHHHHHHccCCHHHHHHHHHHHH
Confidence            577899999999988877666553

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=97.94  E-value=0.00058  Score=55.65  Aligned_cols=147  Identities=17%  Similarity=0.164  Sum_probs=75.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-----HHHHHHHHHHHhCCC------ccccc----
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-----IRKIQEEIGDKLGLK------FHEES----  176 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-----~~~l~~~i~~~l~~~------~~~~~----  176 (276)
                      ..+-+.|+|++|+|||++|+.+.+.....     .+.++.+...+     ....+..++......      .++..    
T Consensus        38 ~~~~vll~G~~GtGKT~la~~la~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~  112 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLLAKAVATEAQVP-----FLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGK  112 (262)
T ss_dssp             CCCEEEEESCTTSSHHHHHHHHHHHHTCC-----EEEEETTTTSSSSTTHHHHHHHHHHHHHHHTCSEEEEEECC-----
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCCC-----EEEechHHHHhhccChhHHHHHHHHHHHHhcCCeEEEEeCcchhhc
Confidence            34668899999999999999999876432     23333332111     122222333222100      00000    


Q ss_pred             -------------chhhhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHhhCC
Q 041612          177 -------------ESGRANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKMAGD  234 (276)
Q Consensus       177 -------------~~~~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~  234 (276)
                                   .......+..     ....+..||.||........ ..   .....+.++..+.++-.++|...+..
T Consensus       113 ~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~  192 (262)
T 2qz4_A          113 KRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKS  192 (262)
T ss_dssp             --------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHH
T ss_pred             cccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHh
Confidence                         0001111111     12334556666654432111 11   22356789999999999999887642


Q ss_pred             CCCChhHHHHHHHHHHHcCCCcH-HHHHHH
Q 041612          235 YIEDSEFQSIARDVAKECAGLPV-SIVTIA  263 (276)
Q Consensus       235 ~~~~~~~~~~~~~i~~~c~G~PL-ai~~i~  263 (276)
                      .............++..+.|++- .+..+.
T Consensus       193 ~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~  222 (262)
T 2qz4_A          193 LKLTQSSTFYSQRLAELTPGFSGADIANIC  222 (262)
T ss_dssp             TTCCBTHHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCCCcchhhHHHHHHHHCCCCCHHHHHHHH
Confidence            22222222234678888988865 454443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.91  E-value=0.00018  Score=63.27  Aligned_cols=34  Identities=26%  Similarity=0.311  Sum_probs=27.8

Q ss_pred             HhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          106 SALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       106 ~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+.-..++=|.++|++|+|||.||+.+.+....
T Consensus       208 ~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~  241 (434)
T 4b4t_M          208 KDMGIRAPKGALMYGPPGTGKTLLARACAAQTNA  241 (434)
T ss_dssp             HHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             HhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCC
Confidence            3334455778999999999999999999998754

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.88  E-value=0.00026  Score=61.89  Aligned_cols=141  Identities=15%  Similarity=0.164  Sum_probs=74.0

Q ss_pred             HhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCCC---------
Q 041612          106 SALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGLK---------  171 (276)
Q Consensus       106 ~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~~---------  171 (276)
                      ..+.-.-++=|.++|++|+|||.||+.+.+.....  |   +.++.+.-.     ..+..++.++......         
T Consensus       209 ~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~--f---i~v~~s~l~sk~vGesek~ir~lF~~Ar~~aP~IIfiDE  283 (437)
T 4b4t_I          209 EEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSAT--F---LRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDE  283 (437)
T ss_dssp             HHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCE--E---EEEESGGGCCSSSSHHHHHHHHHHHHHHHTCSEEEEEEE
T ss_pred             HhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCC--E---EEEEHHHhhhccCchHHHHHHHHHHHHHhcCCcEEEEeh
Confidence            33344456789999999999999999999987643  2   333333221     2234444443322110         


Q ss_pred             -------c--ccccch----hhhhhccc-----cCCCCcEEEEEecccccccc-CCC---CCCceeCCCCCHHHHHHHHH
Q 041612          172 -------F--HEESES----GRANSLFT-----HGHKGCKVLLTARSQDVLSG-KMD---SRPNFSIGVLNEEEAWSLFK  229 (276)
Q Consensus       172 -------~--~~~~~~----~~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~~---~~~~~~l~~L~~~ea~~Lf~  229 (276)
                             -  ......    .....+..     ....+.-||.||-..+.... ...   .+..+.++..+.++-.++|+
T Consensus       284 iDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~  363 (437)
T 4b4t_I          284 IDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILG  363 (437)
T ss_dssp             ESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHH
Confidence                   0  000000    01111111     23334456666655444322 222   22357788888888888998


Q ss_pred             HhhCCC--CCChhHHHHHHHHHHHcCCC
Q 041612          230 KMAGDY--IEDSEFQSIARDVAKECAGL  255 (276)
Q Consensus       230 ~~~~~~--~~~~~~~~~~~~i~~~c~G~  255 (276)
                      .+....  ..+.++    ..+++.+.|+
T Consensus       364 ~~l~~~~l~~dvdl----~~LA~~T~Gf  387 (437)
T 4b4t_I          364 IHTSKMNLSEDVNL----ETLVTTKDDL  387 (437)
T ss_dssp             HHHTTSCBCSCCCH----HHHHHHCCSC
T ss_pred             HHhcCCCCCCcCCH----HHHHHhCCCC
Confidence            777522  222233    4566777765

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.84  E-value=0.00016  Score=59.91  Aligned_cols=146  Identities=18%  Similarity=0.193  Sum_probs=76.0

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCCCc------cccc
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGLKF------HEES  176 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~~~------~~~~  176 (276)
                      +.-...+-+.|+|++|+|||+||+.+++.....     .+.++.+.-.     ........+........      ++..
T Consensus        46 ~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~-----~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid  120 (285)
T 3h4m_A           46 VGIEPPKGILLYGPPGTGKTLLAKAVATETNAT-----FIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEID  120 (285)
T ss_dssp             HCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCE-----EEEEEGGGGCCCSTTHHHHHHHHHHHHHHHTCSEEEEEETTH
T ss_pred             cCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehHHHHHhccchHHHHHHHHHHHHHHcCCeEEEEECHH
Confidence            333445679999999999999999999876432     2233322211     12233333333221110      0000


Q ss_pred             -------------ch---hhhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHh
Q 041612          177 -------------ES---GRANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKM  231 (276)
Q Consensus       177 -------------~~---~~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~  231 (276)
                                   ..   .....+..     ....+..||.||........ ..   .....+.++.++.++..++|...
T Consensus       121 ~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~  200 (285)
T 3h4m_A          121 AIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIH  200 (285)
T ss_dssp             HHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHH
T ss_pred             HhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHH
Confidence                         00   01111111     23345667777765433221 11   22336889999999999999888


Q ss_pred             hCCCC--CChhHHHHHHHHHHHcCCC-cHHHHHH
Q 041612          232 AGDYI--EDSEFQSIARDVAKECAGL-PVSIVTI  262 (276)
Q Consensus       232 ~~~~~--~~~~~~~~~~~i~~~c~G~-PLai~~i  262 (276)
                      +....  ....    ...++..+.|. |-.+..+
T Consensus       201 ~~~~~~~~~~~----~~~l~~~~~g~~~~~i~~l  230 (285)
T 3h4m_A          201 TRKMNLAEDVN----LEEIAKMTEGCVGAELKAI  230 (285)
T ss_dssp             HTTSCBCTTCC----HHHHHHHCTTCCHHHHHHH
T ss_pred             HhcCCCCCcCC----HHHHHHHcCCCCHHHHHHH
Confidence            75222  2222    34577777764 4344433

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.84  E-value=0.00022  Score=62.85  Aligned_cols=145  Identities=21%  Similarity=0.255  Sum_probs=75.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-----HHHHHHHHHHHhCCC------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-----IRKIQEEIGDKLGLK------  171 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-----~~~l~~~i~~~l~~~------  171 (276)
                      ++...+.-..++=|.++|++|+|||.||+.+.+.....     .+.++.+.-.+     ....++.+.......      
T Consensus       205 ~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~-----~~~v~~s~l~sk~~Gese~~ir~~F~~A~~~~P~Iif  279 (437)
T 4b4t_L          205 EIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGAN-----FIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIF  279 (437)
T ss_dssp             HHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGTCCSSSSHHHHHHHHHHHHHHHSCSEEEE
T ss_pred             HHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehhhhccccchHHHHHHHHHHHHHHhcCCceee
Confidence            33333444557889999999999999999999987643     23344333221     233334443322100      


Q ss_pred             ----------c-cc-ccchh----hhhhccc-----cCCCCcEEEEEecccccccc-CCC---CCCceeCCCCCHHHHHH
Q 041612          172 ----------F-HE-ESESG----RANSLFT-----HGHKGCKVLLTARSQDVLSG-KMD---SRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       172 ----------~-~~-~~~~~----~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~~---~~~~~~l~~L~~~ea~~  226 (276)
                                - .. .....    ....+..     ....+..||.||-....... ...   ....+.++..+.++-.+
T Consensus       280 iDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~  359 (437)
T 4b4t_L          280 MDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLE  359 (437)
T ss_dssp             EECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHH
T ss_pred             eecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHH
Confidence                      0 00 00000    0111111     23334567777755544322 222   23467788888888888


Q ss_pred             HHHHhhCC--CCCChhHHHHHHHHHHHcCCCc
Q 041612          227 LFKKMAGD--YIEDSEFQSIARDVAKECAGLP  256 (276)
Q Consensus       227 Lf~~~~~~--~~~~~~~~~~~~~i~~~c~G~P  256 (276)
                      +|+.+...  ...+.++    ..+++.+.|+-
T Consensus       360 Il~~~~~~~~~~~d~dl----~~lA~~t~G~s  387 (437)
T 4b4t_L          360 IFKIHTAKVKKTGEFDF----EAAVKMSDGFN  387 (437)
T ss_dssp             HHHHHHHTSCBCSCCCH----HHHHHTCCSCC
T ss_pred             HHHHHhcCCCCCcccCH----HHHHHhCCCCC
Confidence            88877642  1222233    45667777653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.82  E-value=0.00098  Score=56.24  Aligned_cols=66  Identities=11%  Similarity=0.148  Sum_probs=45.0

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCC---C-C-eEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL---F-D-QVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---f-~-~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      |...+.....+.+.|+|++|+|||++++.+++.......   . . ..++++.....+...++..|++++.
T Consensus        36 L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~  106 (318)
T 3te6_A           36 IYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAIS  106 (318)
T ss_dssp             HHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHS
T ss_pred             HHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhc
Confidence            333444566778999999999999999999998864311   1 1 3455555566677777777877774

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.81  E-value=7.4e-05  Score=65.89  Aligned_cols=145  Identities=14%  Similarity=0.168  Sum_probs=76.3

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCCC------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGLK------  171 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~~------  171 (276)
                      ++...+.-..++=|.++|++|+|||.||+.+.+.....     .+.++.+.-.     ..+..++.++......      
T Consensus       233 e~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~-----fi~vs~s~L~sk~vGesek~ir~lF~~Ar~~aP~IIf  307 (467)
T 4b4t_H          233 ERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDAT-----FIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIF  307 (467)
T ss_dssp             HHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGGCCCSSSHHHHHHHHHHHHHHHTCSEEEE
T ss_pred             HHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCC-----eEEEEhHHhhcccCCHHHHHHHHHHHHHHhcCCceEe
Confidence            33344444567889999999999999999999987643     2334333221     1233444443322110      


Q ss_pred             ----------cc-cc-cchhh----hhhccc-----cCCCCcEEEEEecccccccc-C---CCCCCceeCCCCCHHHHHH
Q 041612          172 ----------FH-EE-SESGR----ANSLFT-----HGHKGCKVLLTARSQDVLSG-K---MDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       172 ----------~~-~~-~~~~~----~~~l~~-----~~~~gs~IivTTR~~~va~~-~---~~~~~~~~l~~L~~~ea~~  226 (276)
                                .. .. .....    ...+..     ....+.-||.||-....... .   -.....+.++..+.++-.+
T Consensus       308 iDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~  387 (467)
T 4b4t_H          308 FDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRAN  387 (467)
T ss_dssp             EECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHH
T ss_pred             ecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHH
Confidence                      00 00 00000    011111     22233345556644433221 1   1345578888888888889


Q ss_pred             HHHHhhCCCC--CChhHHHHHHHHHHHcCCCc
Q 041612          227 LFKKMAGDYI--EDSEFQSIARDVAKECAGLP  256 (276)
Q Consensus       227 Lf~~~~~~~~--~~~~~~~~~~~i~~~c~G~P  256 (276)
                      +|+.++....  .+-++    ..|++.+.|+-
T Consensus       388 Ilk~~l~~~~l~~dvdl----~~LA~~T~GfS  415 (467)
T 4b4t_H          388 IFRIHSKSMSVERGIRW----ELISRLCPNST  415 (467)
T ss_dssp             HHHHHHTTSCBCSSCCH----HHHHHHCCSCC
T ss_pred             HHHHHhcCCCCCCCCCH----HHHHHHCCCCC
Confidence            9988775222  22233    45777777763

>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=97.75  E-value=0.00011  Score=65.12  Aligned_cols=143  Identities=18%  Similarity=0.187  Sum_probs=77.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH--------HHHHhC-CC----cccc---c
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE--------IGDKLG-LK----FHEE---S  176 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~--------i~~~l~-~~----~~~~---~  176 (276)
                      ...+.|+|++|+||||||+.+.+.......-...++++...-  ...+...        +...+. ..    .++.   .
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~  207 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKF--LNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLI  207 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHH--HHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGS
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH--HHHHHHHHHcccHHHHHHHhcCCCCEEEEeCccccc
Confidence            678999999999999999999988754310123455543321  1112111        112222 11    0000   0


Q ss_pred             ch-hhhhhccc----cCCCCcEEEEEecccccc-----cc---CCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhH
Q 041612          177 ES-GRANSLFT----HGHKGCKVLLTARSQDVL-----SG---KMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEF  241 (276)
Q Consensus       177 ~~-~~~~~l~~----~~~~gs~IivTTR~~~va-----~~---~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~  241 (276)
                      .. .....+..    ....|..||+||.+..-.     ..   .+.....+.+++++.++...++.+.+.  ....+++ 
T Consensus       208 ~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e-  286 (440)
T 2z4s_A          208 GKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEE-  286 (440)
T ss_dssp             SCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTT-
T ss_pred             CChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHH-
Confidence            00 11111211    235678899998764221     00   012234688999999999999988764  2222222 


Q ss_pred             HHHHHHHHHHcCCCcHHHH
Q 041612          242 QSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       242 ~~~~~~i~~~c~G~PLai~  260 (276)
                        ....|+..+.|.+-.+.
T Consensus       287 --~l~~la~~~~gn~R~l~  303 (440)
T 2z4s_A          287 --VLNFVAENVDDNLRRLR  303 (440)
T ss_dssp             --HHHHHHHHCCSCHHHHH
T ss_pred             --HHHHHHHhcCCCHHHHH
Confidence              35567778888775444

>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=97.73  E-value=0.00015  Score=61.86  Aligned_cols=158  Identities=13%  Similarity=0.182  Sum_probs=85.3

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcCCHHHHHHHHHH--HhC----------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQDIRKIQEEIGD--KLG----------  169 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~--~l~----------  169 (276)
                      .+...+.....+.+.++|++|+||||+|+.+.+.......+. ....++.+.......+...+..  ...          
T Consensus        48 ~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (353)
T 1sxj_D           48 VLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLE  127 (353)
T ss_dssp             HHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHH
T ss_pred             HHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHHHHHHHHhhhcccccchhhcc
Confidence            666666666555599999999999999999988754210011 1233333332233322221111  110          


Q ss_pred             ---CCcccc---cc-----hhh---hhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCC
Q 041612          170 ---LKFHEE---SE-----SGR---ANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGD  234 (276)
Q Consensus       170 ---~~~~~~---~~-----~~~---~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~  234 (276)
                         ......   ++     ...   +...........++|++|.... +..........+.+.+++.++....+...+..
T Consensus       128 ~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~  207 (353)
T 1sxj_D          128 NYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQ  207 (353)
T ss_dssp             HSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHT
T ss_pred             cCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHHHHHHHHHH
Confidence               000000   00     011   1111223445677887775442 21111111236889999999999999887642


Q ss_pred             --CCCChhHHHHHHHHHHHcCCCcHHHHHHH
Q 041612          235 --YIEDSEFQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       235 --~~~~~~~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                        ...+   .+....|++.++|.|-.+..+.
T Consensus       208 ~~~~i~---~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          208 ENVKCD---DGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             TTCCCC---HHHHHHHHHHTSSCHHHHHHHH
T ss_pred             hCCCCC---HHHHHHHHHHcCCCHHHHHHHH
Confidence              1122   3457789999999998755443

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.72  E-value=8.7e-05  Score=65.87  Aligned_cols=157  Identities=17%  Similarity=0.212  Sum_probs=80.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHH---HHHHHHHh--CCC-----
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKI---QEEIGDKL--GLK-----  171 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l---~~~i~~~l--~~~-----  171 (276)
                      .+...+.....+.+.|+|++|+||||||+.+.+.....  |     +.++. ......+   +.......  +..     
T Consensus        40 ~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~~~--f-----~~l~a~~~~~~~ir~~~~~a~~~~~~~~~~iLfI  112 (447)
T 3pvs_A           40 PLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYANAD--V-----ERISAVTSGVKEIREAIERARQNRNAGRRTILFV  112 (447)
T ss_dssp             HHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTTCE--E-----EEEETTTCCHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhCCC--e-----EEEEeccCCHHHHHHHHHHHHHhhhcCCCcEEEE
Confidence            45555556667789999999999999999999887432  2     22222 2223322   22221111  110     


Q ss_pred             -cccccchhhhhhccccC-CCCcEEEE-Eecccc--ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCC------CCChh
Q 041612          172 -FHEESESGRANSLFTHG-HKGCKVLL-TARSQD--VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDY------IEDSE  240 (276)
Q Consensus       172 -~~~~~~~~~~~~l~~~~-~~gs~Iiv-TTR~~~--va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~------~~~~~  240 (276)
                       ..+.-+......+.... .....+|. ||.+..  +..........+.+++++.++...++.+.+...      ....-
T Consensus       113 DEI~~l~~~~q~~LL~~le~~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i  192 (447)
T 3pvs_A          113 DEVHRFNKSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVL  192 (447)
T ss_dssp             ETTTCC------CCHHHHHTTSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEEC
T ss_pred             eChhhhCHHHHHHHHHHHhcCceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcC
Confidence             00001111111222211 12233333 455543  211122333478899999999999998876420      11111


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHH
Q 041612          241 FQSIARDVAKECAGLPVSIVTIARAL  266 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~PLai~~i~~~L  266 (276)
                      ..+....++..++|.+-.+.-+-..+
T Consensus       193 ~~~al~~L~~~~~Gd~R~lln~Le~a  218 (447)
T 3pvs_A          193 PDETRRAIAELVNGDARRALNTLEMM  218 (447)
T ss_dssp             CHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            23456778888888877665544433

>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=97.72  E-value=0.00035  Score=60.12  Aligned_cols=148  Identities=13%  Similarity=0.190  Sum_probs=82.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCC-------------------CeEEEEEecCcCCHHHHHHHHHHHhCCCc-
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLF-------------------DQVVFVEVSQNQDIRKIQEEIGDKLGLKF-  172 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f-------------------~~~~wv~~~~~~~~~~l~~~i~~~l~~~~-  172 (276)
                      .+.+.|+|++|+|||++|+.+.+.......+                   ...+.+......... ..+.+.+.+.... 
T Consensus        38 ~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~  116 (373)
T 1jr3_A           38 HHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVE-DTRDLLDNVQYAPA  116 (373)
T ss_dssp             CSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCSSCEEEETTCSCCSS-CHHHHHHHTTSCCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCCceEEecccccCCHH-HHHHHHHHHhhccc
Confidence            4578999999999999999998876432111                   012333322211111 1223333332110 


Q ss_pred             ---------ccc--cchhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhC--CC
Q 041612          173 ---------HEE--SESGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DY  235 (276)
Q Consensus       173 ---------~~~--~~~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~  235 (276)
                               ++.  -+......+   ......+..+|++|.... +..........+.+.+++.++...++...+.  ..
T Consensus       117 ~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~  196 (373)
T 1jr3_A          117 RGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI  196 (373)
T ss_dssp             SSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCC
Confidence                     000  011111112   224455677777776443 2111122235789999999999999987763  11


Q ss_pred             CCChhHHHHHHHHHHHcCCCcHHHHHHHH
Q 041612          236 IEDSEFQSIARDVAKECAGLPVSIVTIAR  264 (276)
Q Consensus       236 ~~~~~~~~~~~~i~~~c~G~PLai~~i~~  264 (276)
                      ..+   .+....|+..++|.|..+..+..
T Consensus       197 ~~~---~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          197 AHE---PRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             CBC---HHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             CCC---HHHHHHHHHHCCCCHHHHHHHHH
Confidence            122   23467899999999998776543

>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=97.69  E-value=0.00012  Score=62.67  Aligned_cols=78  Identities=8%  Similarity=0.105  Sum_probs=49.1

Q ss_pred             cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhHHHHHHHHHHHcCCCcHHHHHHH
Q 041612          187 HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQSIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       187 ~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~~~~~~~i~~~c~G~PLai~~i~  263 (276)
                      ....++.+|++|.+.. +..........+++++++.++....+...+.  ....+  ..+....|++.++|.+-.+..+.
T Consensus       160 ~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          160 KYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLE--TKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             HSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEEC--CSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCC--cHHHHHHHHHHcCCCHHHHHHHH
Confidence            3445778888887643 2222122235789999999999999988764  11111  02346678889999887665554


Q ss_pred             HHH
Q 041612          264 RAL  266 (276)
Q Consensus       264 ~~L  266 (276)
                      ..+
T Consensus       238 ~~~  240 (354)
T 1sxj_E          238 ESM  240 (354)
T ss_dssp             THH
T ss_pred             HHH
Confidence            433

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.67  E-value=0.00087  Score=57.06  Aligned_cols=151  Identities=15%  Similarity=0.167  Sum_probs=87.3

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC--------------------CCCeEEEEEec---CcCCHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK--------------------LFDQVVFVEVS---QNQDIR  158 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~~~---~~~~~~  158 (276)
                      .+...+..+. .+.+.++|++|+|||++|+.+........                    |++ ..++...   ......
T Consensus        13 ~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~~~~~i~   91 (334)
T 1a5t_A           13 KLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAPEKGKNTLGVD   91 (334)
T ss_dssp             HHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECCCTTCSSBCHH
T ss_pred             HHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccccCCCCCHH
Confidence            3444444444 45799999999999999999988764321                    233 2344432   233444


Q ss_pred             HHHHHHHHHhCCCccc----c---cc-----hhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHH
Q 041612          159 KIQEEIGDKLGLKFHE----E---SE-----SGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEE  222 (276)
Q Consensus       159 ~l~~~i~~~l~~~~~~----~---~~-----~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~  222 (276)
                      .+ +.+.+.+......    .   ++     ....+.+   .+....++.+|++|.+.. +..........+++.+++++
T Consensus        92 ~i-r~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~  170 (334)
T 1a5t_A           92 AV-REVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQ  170 (334)
T ss_dssp             HH-HHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHH
T ss_pred             HH-HHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHH
Confidence            43 4555555432110    0   11     1111122   224445677777776653 33222233457899999999


Q ss_pred             HHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHH
Q 041612          223 EAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT  261 (276)
Q Consensus       223 ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~  261 (276)
                      +..+.+.+..   ..+   .+....++..++|.|..+..
T Consensus       171 ~~~~~L~~~~---~~~---~~~~~~l~~~s~G~~r~a~~  203 (334)
T 1a5t_A          171 YAVTWLSREV---TMS---QDALLAALRLSAGSPGAALA  203 (334)
T ss_dssp             HHHHHHHHHC---CCC---HHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHhc---CCC---HHHHHHHHHHcCCCHHHHHH
Confidence            9999988875   111   23456788899999876543

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.67  E-value=0.00065  Score=59.68  Aligned_cols=34  Identities=29%  Similarity=0.398  Sum_probs=27.6

Q ss_pred             HhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          106 SALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       106 ~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+.-..++=+.++|++|+|||.||+.+.+....
T Consensus       199 ~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~  232 (428)
T 4b4t_K          199 EQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKA  232 (428)
T ss_dssp             HHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTC
T ss_pred             HhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3334455677999999999999999999998754

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.66  E-value=0.0013  Score=55.70  Aligned_cols=146  Identities=17%  Similarity=0.175  Sum_probs=74.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCCCc------cccc-----
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGLKF------HEES-----  176 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~~~------~~~~-----  176 (276)
                      .+-+.++|++|+|||+||+.+.+.....    ..+.++.+.-.     .....++.+........      ++..     
T Consensus        45 ~~~iLL~GppGtGKT~la~ala~~~~~~----~~~~i~~~~l~~~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~  120 (322)
T 1xwi_A           45 WRGILLFGPPGTGKSYLAKAVATEANNS----TFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGS  120 (322)
T ss_dssp             CSEEEEESSSSSCHHHHHHHHHHHTTSC----EEEEEECCSSCCSSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCC
T ss_pred             CceEEEECCCCccHHHHHHHHHHHcCCC----cEEEEEhHHHHhhhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccc
Confidence            4679999999999999999999886221    12233332211     12334444433221100      0000     


Q ss_pred             ----chh----hhhhccc----c--CCCCcEEEEEecccccccc--CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChh
Q 041612          177 ----ESG----RANSLFT----H--GHKGCKVLLTARSQDVLSG--KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSE  240 (276)
Q Consensus       177 ----~~~----~~~~l~~----~--~~~gs~IivTTR~~~va~~--~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  240 (276)
                          ...    ....+..    .  ...+..||.||........  .......+.++..+.++-.++|..++......- 
T Consensus       121 ~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-  199 (322)
T 1xwi_A          121 RSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSL-  199 (322)
T ss_dssp             SSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCC-
T ss_pred             cccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCC-
Confidence                000    0111111    1  2334445555643322111  012334678888999999999988775322111 


Q ss_pred             HHHHHHHHHHHcCCC-cHHHHHHH
Q 041612          241 FQSIARDVAKECAGL-PVSIVTIA  263 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~-PLai~~i~  263 (276)
                      .......|++.+.|+ +-.+..+.
T Consensus       200 ~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          200 TEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             CHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            123466788999887 43354443

>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=97.61  E-value=0.00087  Score=60.61  Aligned_cols=143  Identities=13%  Similarity=0.127  Sum_probs=76.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHh-CC-----------------Cccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKL-GL-----------------KFHE  174 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l-~~-----------------~~~~  174 (276)
                      .+.+.|+|++|+|||++|+.+.+...    + ..+.++.+...+...+ ...+... ..                 ....
T Consensus        77 ~~~lLL~GppGtGKTtla~~la~~l~----~-~~i~in~s~~~~~~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (516)
T 1sxj_A           77 FRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQNASDVRSKTLL-NAGVKNALDNMSVVGYFKHNEEAQNLNGKHF  150 (516)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEECTTSCCCHHHH-HHTGGGGTTBCCSTTTTTC----CCSSTTSE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC----C-CEEEEeCCCcchHHHH-HHHHHHHhccccHHHHHhhhhhhhhccCCCe
Confidence            47899999999999999999998873    2 2344444444343322 2222211 00                 0000


Q ss_pred             c---cchhh--------hhhccc-cCCCCcEEEEEecccc--ccccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCC
Q 041612          175 E---SESGR--------ANSLFT-HGHKGCKVLLTARSQD--VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIED  238 (276)
Q Consensus       175 ~---~~~~~--------~~~l~~-~~~~gs~IivTTR~~~--va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~  238 (276)
                      .   ++.+.        ...+.. ....+..||+++.+..  ...........+.+++++.++..+++...+.  ....+
T Consensus       151 vliIDEid~l~~~~~~~l~~L~~~l~~~~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~  230 (516)
T 1sxj_A          151 VIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD  230 (516)
T ss_dssp             EEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             EEEEECCCccchhhHHHHHHHHHHHHhcCCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCC
Confidence            0   00000        011111 1123345666654432  1112223344689999999999998887764  22222


Q ss_pred             hhHHHHHHHHHHHcCC-CcHHHHHHHH
Q 041612          239 SEFQSIARDVAKECAG-LPVSIVTIAR  264 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G-~PLai~~i~~  264 (276)
                      ++   ....|++.++| ++-++..+..
T Consensus       231 ~~---~l~~la~~s~GdiR~~i~~L~~  254 (516)
T 1sxj_A          231 PN---VIDRLIQTTRGDIRQVINLLST  254 (516)
T ss_dssp             TT---HHHHHHHHTTTCHHHHHHHHTH
T ss_pred             HH---HHHHHHHHcCCcHHHHHHHHHH
Confidence            22   36678889988 5555655543

>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=97.53  E-value=0.00096  Score=56.85  Aligned_cols=153  Identities=14%  Similarity=0.185  Sum_probs=80.8

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcCCHHHHHHHHHHHh--CCCc---ccc-
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQDIRKIQEEIGDKL--GLKF---HEE-  175 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l--~~~~---~~~-  175 (276)
                      .|...+..+..+.+.++|++|+||||+|+.+.+...... +. ...-++.+.......+...+....  ....   ... 
T Consensus        36 ~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~-~~~~~~~~~~~~~~~~~~ir~~i~~~~~~~~~~~~~~~vi  114 (340)
T 1sxj_C           36 TVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKN-YSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLI  114 (340)
T ss_dssp             HHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTS-HHHHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEE
T ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-ccceEEEEcCcccccHHHHHHHHHHHHhhcccCCCCceEE
Confidence            444445555554589999999999999999998865331 11 223333333333433332221111  1111   000 


Q ss_pred             --cch-----h---hhhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhHH
Q 041612          176 --SES-----G---RANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQ  242 (276)
Q Consensus       176 --~~~-----~---~~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~~  242 (276)
                        ++.     .   .+.+........+++|++|.... +..........+.+.+++.++..+.+...+.  ....+   .
T Consensus       115 iiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~~i~---~  191 (340)
T 1sxj_C          115 ILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLS---P  191 (340)
T ss_dssp             EETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBC---H
T ss_pred             EEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcCCCCC---H
Confidence              110     0   11112224445667777765432 2111112233678999999999888877663  11122   2


Q ss_pred             HHHHHHHHHcCCCcHHH
Q 041612          243 SIARDVAKECAGLPVSI  259 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai  259 (276)
                      +....++..++|-+--+
T Consensus       192 ~~~~~i~~~s~G~~r~~  208 (340)
T 1sxj_C          192 NAEKALIELSNGDMRRV  208 (340)
T ss_dssp             HHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHcCCCHHHH
Confidence            34667888888877644

>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=97.51  E-value=0.0024  Score=54.83  Aligned_cols=148  Identities=9%  Similarity=0.055  Sum_probs=76.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-----HHHHHHHHHHHhCCCccc---ccch-----
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-----IRKIQEEIGDKLGLKFHE---ESES-----  178 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-----~~~l~~~i~~~l~~~~~~---~~~~-----  178 (276)
                      ..+-+.|+|++|+|||+||+.+.+....     ..+.++.+.-.+     .....+.+..........   .++.     
T Consensus       116 ~~~~vLl~GppGtGKT~la~aia~~~~~-----~~~~i~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~  190 (357)
T 3d8b_A          116 PPKGILLFGPPGTGKTLIGKCIASQSGA-----TFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLS  190 (357)
T ss_dssp             CCSEEEEESSTTSSHHHHHHHHHHHTTC-----EEEEEEGGGGCCSSTTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTB
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHcCC-----eEEEEehHHhhccccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhc
Confidence            4568999999999999999999887632     233444433221     233333333322110000   0000     


Q ss_pred             -----------hhhhhccc-------cCCCCcEEEEEeccccccc-c-CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCC
Q 041612          179 -----------GRANSLFT-------HGHKGCKVLLTARSQDVLS-G-KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIED  238 (276)
Q Consensus       179 -----------~~~~~l~~-------~~~~gs~IivTTR~~~va~-~-~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  238 (276)
                                 .....+..       ....+..||.||....... . .......+.+...+.++..+++...+......
T Consensus       191 ~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~  270 (357)
T 3d8b_A          191 QRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCC  270 (357)
T ss_dssp             C------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBC
T ss_pred             cCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCC
Confidence                       00111111       1123445555664432211 1 11223467888899999999888776421111


Q ss_pred             hhHHHHHHHHHHHcCC-CcHHHHHHHHH
Q 041612          239 SEFQSIARDVAKECAG-LPVSIVTIARA  265 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G-~PLai~~i~~~  265 (276)
                       -..+....|++.+.| .|-.+..+...
T Consensus       271 -l~~~~l~~la~~t~G~s~~dl~~l~~~  297 (357)
T 3d8b_A          271 -LSEEEIEQIVQQSDAFSGADMTQLCRE  297 (357)
T ss_dssp             -CCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             -ccHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence             012346778888888 45556655443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.50  E-value=0.00073  Score=58.07  Aligned_cols=47  Identities=4%  Similarity=-0.043  Sum_probs=32.6

Q ss_pred             ceeCCCCCHHHHHHHHHHhhCC--CCCChhHHHHHHHHHHHcC-CCcHHHHHH
Q 041612          213 NFSIGVLNEEEAWSLFKKMAGD--YIEDSEFQSIARDVAKECA-GLPVSIVTI  262 (276)
Q Consensus       213 ~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~~~~~~i~~~c~-G~PLai~~i  262 (276)
                      .+.+++++.++...++...+..  ...+   .+....|++.+. |.|-.+..+
T Consensus       253 ~i~~~~~~~~e~~~il~~~~~~~~~~~~---~~~l~~l~~~~~~G~~r~~~~l  302 (368)
T 3uk6_A          253 IVSTTPYSEKDTKQILRIRCEEEDVEMS---EDAYTVLTRIGLETSLRYAIQL  302 (368)
T ss_dssp             EEEECCCCHHHHHHHHHHHHHHTTCCBC---HHHHHHHHHHHHHSCHHHHHHH
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHhcCCCHHHHHHH
Confidence            4789999999999999877642  2222   345677888887 766654433

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.49  E-value=0.002  Score=54.68  Aligned_cols=146  Identities=15%  Similarity=0.168  Sum_probs=76.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC----ccc--ccchhhhhhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK----FHE--ESESGRANSLF  185 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~----~~~--~~~~~~~~~l~  185 (276)
                      ..+.+.|+|++|+|||+||+.+.+.....  |   +.++.+.......+ ..++......    .++  .-.......+.
T Consensus        54 ~~~~vll~G~~GtGKT~la~~ia~~~~~~--~---~~~~~~~~~~~~~~-~~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll  127 (338)
T 3pfi_A           54 CLDHILFSGPAGLGKTTLANIISYEMSAN--I---KTTAAPMIEKSGDL-AAILTNLSEGDILFIDEIHRLSPAIEEVLY  127 (338)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHTTCC--E---EEEEGGGCCSHHHH-HHHHHTCCTTCEEEEETGGGCCHHHHHHHH
T ss_pred             CCCeEEEECcCCCCHHHHHHHHHHHhCCC--e---EEecchhccchhHH-HHHHHhccCCCEEEEechhhcCHHHHHHHH
Confidence            45578999999999999999998775432  2   22332222222222 2222222111    000  00111111111


Q ss_pred             c---c------------------CCCCcEEEEEeccccccc-c-CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHH
Q 041612          186 T---H------------------GHKGCKVLLTARSQDVLS-G-KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ  242 (276)
Q Consensus       186 ~---~------------------~~~gs~IivTTR~~~va~-~-~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~  242 (276)
                      .   .                  ..++..+|.+|....... . .......+.+++++.++...++...+..... .-..
T Consensus       128 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~-~~~~  206 (338)
T 3pfi_A          128 PAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNK-TCEE  206 (338)
T ss_dssp             HHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-EECH
T ss_pred             HHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCC-CCCH
Confidence            1   0                  111345666665433211 1 1122357999999999999999877642111 1123


Q ss_pred             HHHHHHHHHcCCCcHHHHHHHH
Q 041612          243 SIARDVAKECAGLPVSIVTIAR  264 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai~~i~~  264 (276)
                      +....++..+.|.|-.+..+..
T Consensus       207 ~~~~~l~~~~~G~~r~l~~~l~  228 (338)
T 3pfi_A          207 KAALEIAKRSRSTPRIALRLLK  228 (338)
T ss_dssp             HHHHHHHHTTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHH
Confidence            4567788889999855544433

>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=97.48  E-value=0.00059  Score=57.78  Aligned_cols=145  Identities=17%  Similarity=0.148  Sum_probs=74.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-----CCHHHHHHHHHHHhCCCc------cccc-----
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-----QDIRKIQEEIGDKLGLKF------HEES-----  176 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-----~~~~~l~~~i~~~l~~~~------~~~~-----  176 (276)
                      .+-+.++|++|+|||+||+.+++.....     .+.++.+.-     ......+..+........      ++..     
T Consensus        51 ~~~vLl~GppGtGKT~la~aia~~~~~~-----~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~  125 (322)
T 3eie_A           51 TSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGT  125 (322)
T ss_dssp             CCEEEEECSSSSCHHHHHHHHHHHHTCE-----EEEEEHHHHHTTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHCCC-----EEEEchHHHhhcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhcc
Confidence            4579999999999999999999876432     233332211     122333334433221100      0000     


Q ss_pred             --------chhhhhhccc------cCCCCcEEEEEecccccccc--CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChh
Q 041612          177 --------ESGRANSLFT------HGHKGCKVLLTARSQDVLSG--KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSE  240 (276)
Q Consensus       177 --------~~~~~~~l~~------~~~~gs~IivTTR~~~va~~--~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  240 (276)
                              .......+..      ....+..||.||........  .......+.++..+.++-.++|...+......-.
T Consensus       126 ~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~  205 (322)
T 3eie_A          126 RGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLT  205 (322)
T ss_dssp             ------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCC
T ss_pred             CCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCC
Confidence                    0000111111      13344555556654432211  0122346778889999999999988763221111


Q ss_pred             HHHHHHHHHHHcCCC-cHHHHHHH
Q 041612          241 FQSIARDVAKECAGL-PVSIVTIA  263 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~-PLai~~i~  263 (276)
                       ......|++.+.|+ +-.+..+.
T Consensus       206 -~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          206 -KEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             -HHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             -HHHHHHHHHHcCCCCHHHHHHHH
Confidence             22456788888874 43444333

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.45  E-value=0.0025  Score=53.01  Aligned_cols=146  Identities=15%  Similarity=0.132  Sum_probs=74.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCCCc------cccc-----
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGLKF------HEES-----  176 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~~~------~~~~-----  176 (276)
                      .+.+.|+|++|+|||++|+.+.+.....     .+.++.+...     ......+.+........      ++..     
T Consensus        54 ~~~vll~Gp~GtGKT~la~~la~~~~~~-----~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~  128 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLARAVATECSAT-----FLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSE  128 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHHHHHHHTTCE-----EEEEESTTTSSSSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBC
T ss_pred             CCeEEEECcCCCCHHHHHHHHHHHhCCC-----eEEeeHHHHhhcccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccc
Confidence            4678999999999999999999876422     2333333211     23333444333221100      0000     


Q ss_pred             --------chhhhhhccc----c----CCCCcEEEEEecccccccc-C-CCCCCceeCCCCCHHHHHHHHHHhhCCCCCC
Q 041612          177 --------ESGRANSLFT----H----GHKGCKVLLTARSQDVLSG-K-MDSRPNFSIGVLNEEEAWSLFKKMAGDYIED  238 (276)
Q Consensus       177 --------~~~~~~~l~~----~----~~~gs~IivTTR~~~va~~-~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  238 (276)
                              .......+..    .    ...+..||.||........ . ......+.+...+.++...++...+......
T Consensus       129 ~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~  208 (297)
T 3b9p_A          129 RSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSP  208 (297)
T ss_dssp             C-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCC
T ss_pred             cccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCC
Confidence                    0000011111    1    1134456666665432111 0 1123457777888888888887776421111


Q ss_pred             hhHHHHHHHHHHHcCCCcH-HHHHHHH
Q 041612          239 SEFQSIARDVAKECAGLPV-SIVTIAR  264 (276)
Q Consensus       239 ~~~~~~~~~i~~~c~G~PL-ai~~i~~  264 (276)
                      - ..+....+++.+.|.+- ++..+..
T Consensus       209 ~-~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          209 L-DTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             S-CHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             C-CHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            0 12346678889999886 5544443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.44  E-value=0.00064  Score=56.91  Aligned_cols=122  Identities=15%  Similarity=0.117  Sum_probs=64.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC--eEEEEEecCcC-----CHHHHHHHHHHHhCCCc---cccc-----
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD--QVVFVEVSQNQ-----DIRKIQEEIGDKLGLKF---HEES-----  176 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~--~~~wv~~~~~~-----~~~~l~~~i~~~l~~~~---~~~~-----  176 (276)
                      ....+.|+|++|+|||+||+.+.+.........  ..+.++.+.-.     ....-...++.......   ++..     
T Consensus        66 ~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~~~~vl~iDEid~l~~~  145 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAMGGVLFIDEAYYLYRP  145 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTCCSSTTCHHHHHHHHHHHHTTSEEEEETGGGSCCC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhhhhcccccHHHHHHHHHhcCCCEEEEEChhhhccC
Confidence            345799999999999999999888775543222  23333322211     12222233333332110   0000     


Q ss_pred             ------chhhhhhcc---ccCCCCcEEEEEecccccc------ccC-CCCCCceeCCCCCHHHHHHHHHHhhC
Q 041612          177 ------ESGRANSLF---THGHKGCKVLLTARSQDVL------SGK-MDSRPNFSIGVLNEEEAWSLFKKMAG  233 (276)
Q Consensus       177 ------~~~~~~~l~---~~~~~gs~IivTTR~~~va------~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~  233 (276)
                            .......+.   .....+..||.||......      ... ......+.+++++.++...++...+.
T Consensus       146 ~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~  218 (309)
T 3syl_A          146 DNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLD  218 (309)
T ss_dssp             C---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHH
T ss_pred             CCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHH
Confidence                  111112222   2444566777877543210      000 11225788999999999999988764

>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=97.43  E-value=0.0014  Score=53.94  Aligned_cols=29  Identities=28%  Similarity=0.245  Sum_probs=24.9

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+.+.|+|++|+|||+||+.+.+...
T Consensus        61 ~~~~~~vLl~G~~GtGKT~la~~ia~~~~   89 (272)
T 1d2n_A           61 RTPLVSVLLEGPPHSGKTALAAKIAEESN   89 (272)
T ss_dssp             SCSEEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            44567899999999999999999998753

>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=97.32  E-value=0.0011  Score=56.98  Aligned_cols=144  Identities=17%  Similarity=0.165  Sum_probs=72.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc-----CCHHHHHHHHHHHh---CCC---cccccc----
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN-----QDIRKIQEEIGDKL---GLK---FHEESE----  177 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~-----~~~~~l~~~i~~~l---~~~---~~~~~~----  177 (276)
                      .+-+.|+|++|+|||+||+.+.+.....     .+.++.+.-     ......++.++...   ...   .++...    
T Consensus        84 ~~~iLL~GppGtGKT~la~ala~~~~~~-----~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~  158 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGT  158 (355)
T ss_dssp             CCCEEEECSTTSCHHHHHHHHHHHHTCE-----EEEEEHHHHHSCC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC-
T ss_pred             CceEEEECCCCCcHHHHHHHHHHHhCCC-----EEEeeHHHHhhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccc
Confidence            3568899999999999999999887432     222322211     01223333333322   110   000000    


Q ss_pred             ---------hhhhhhccc------cCCCCcEEEEEecccccccc--CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChh
Q 041612          178 ---------SGRANSLFT------HGHKGCKVLLTARSQDVLSG--KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSE  240 (276)
Q Consensus       178 ---------~~~~~~l~~------~~~~gs~IivTTR~~~va~~--~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  240 (276)
                               ......+..      ....+..||.||........  .......+.+...+.++-.++|..++......-.
T Consensus       159 r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~  238 (355)
T 2qp9_X          159 RGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLT  238 (355)
T ss_dssp             -----CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCC
T ss_pred             CCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCC
Confidence                     000111111      12334555556654422111  1123356788899999999999888763221111


Q ss_pred             HHHHHHHHHHHcCCC-cHHHHHH
Q 041612          241 FQSIARDVAKECAGL-PVSIVTI  262 (276)
Q Consensus       241 ~~~~~~~i~~~c~G~-PLai~~i  262 (276)
                       ......|++.+.|+ |-.|..+
T Consensus       239 -~~~l~~la~~t~G~sg~dl~~l  260 (355)
T 2qp9_X          239 -KEDYRTLGAMTEGYSGSDIAVV  260 (355)
T ss_dssp             -HHHHHHHHHHTTTCCHHHHHHH
T ss_pred             -HHHHHHHHHHcCCCCHHHHHHH
Confidence             22356788899885 4334433

>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=97.30  E-value=0.0028  Score=52.98  Aligned_cols=28  Identities=36%  Similarity=0.502  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+.+.|+|++|+|||+||+.+.+...
T Consensus        47 ~~~~~vLL~Gp~GtGKT~la~ala~~~~   74 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLLAKAIANECQ   74 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             CCCceEEEECCCCcCHHHHHHHHHHHhC
Confidence            3456799999999999999999998764

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.30  E-value=0.0061  Score=52.87  Aligned_cols=146  Identities=16%  Similarity=0.163  Sum_probs=73.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCC---C--c-cccc-----
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGL---K--F-HEES-----  176 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~---~--~-~~~~-----  176 (276)
                      .+-+.|+|++|+|||+||+.+.+.....     .+.++.+.-.     .....+..++.....   .  . ++..     
T Consensus       148 ~~~vLL~GppGtGKT~la~aia~~~~~~-----~~~v~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~  222 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAKAVAAESNAT-----FFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCE  222 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHHHHHHHTTCE-----EEEECSCCC-------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhcCc-----EEEeeHHHhhccccchHHHHHHHHHHHHHhcCCeEEEEECchhhccc
Confidence            4689999999999999999998775322     2333322211     112223333322211   0  0 0000     


Q ss_pred             --------chhhhhhccc-------cCCCCcEEEEEeccccccc-cC-CCCCCceeCCCCCHHHHHHHHHHhhCCCCCCh
Q 041612          177 --------ESGRANSLFT-------HGHKGCKVLLTARSQDVLS-GK-MDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDS  239 (276)
Q Consensus       177 --------~~~~~~~l~~-------~~~~gs~IivTTR~~~va~-~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~  239 (276)
                              .......+..       .......||.||....-.. .. ......+.+...+.++...++...+...... 
T Consensus       223 ~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~-  301 (389)
T 3vfd_A          223 RREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSP-  301 (389)
T ss_dssp             ------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCC-
T ss_pred             CCCccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCC-
Confidence                    0000011111       1123345555664432211 11 1223467888999999999998887522111 


Q ss_pred             hHHHHHHHHHHHcCCCcH-HHHHHHH
Q 041612          240 EFQSIARDVAKECAGLPV-SIVTIAR  264 (276)
Q Consensus       240 ~~~~~~~~i~~~c~G~PL-ai~~i~~  264 (276)
                      -..+....+++.+.|..- ++..+..
T Consensus       302 l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          302 LTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             SCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            112346788899988655 5555544

>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=97.28  E-value=0.00034  Score=59.19  Aligned_cols=136  Identities=12%  Similarity=0.141  Sum_probs=70.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHH--------HHHhCCC----ccccc--ch
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEI--------GDKLGLK----FHEES--ES  178 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i--------~~~l~~~----~~~~~--~~  178 (276)
                      ...+.|+|++|+||||||+.+.+.....  -...++++....  ...+...+        .......    .++..  ..
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~--~~~~~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~~  112 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKR--GYRVIYSSADDF--AQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSG  112 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHT--TCCEEEEEHHHH--HHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTT
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHC--CCEEEEEEHHHH--HHHHHHHHHcCcHHHHHHHhcCCCEEEEcCcccccC
Confidence            4679999999999999999999887543  123445543321  11111111        1111100    00100  00


Q ss_pred             --hhhhhccc----cCCCCcEEEEEecccccc-----cc---CCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhHH
Q 041612          179 --GRANSLFT----HGHKGCKVLLTARSQDVL-----SG---KMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQ  242 (276)
Q Consensus       179 --~~~~~l~~----~~~~gs~IivTTR~~~va-----~~---~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~~  242 (276)
                        .....+..    ....+..||+||.+..-.     ..   .......+.+++ +.++...++...+.  ....+   .
T Consensus       113 ~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~---~  188 (324)
T 1l8q_A          113 KERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELR---K  188 (324)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCC---H
T ss_pred             ChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCC---H
Confidence              01111111    233466788888654221     00   011224588999 99999999988764  22222   2


Q ss_pred             HHHHHHHHHcCCCcH
Q 041612          243 SIARDVAKECAGLPV  257 (276)
Q Consensus       243 ~~~~~i~~~c~G~PL  257 (276)
                      +....|+..+ |.+-
T Consensus       189 ~~l~~l~~~~-g~~r  202 (324)
T 1l8q_A          189 EVIDYLLENT-KNVR  202 (324)
T ss_dssp             HHHHHHHHHC-SSHH
T ss_pred             HHHHHHHHhC-CCHH
Confidence            3455667777 5543

>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=97.25  E-value=0.0032  Score=55.74  Aligned_cols=67  Identities=13%  Similarity=0.149  Sum_probs=39.0

Q ss_pred             CCCcEEEEEecccccccc--CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCc
Q 041612          189 HKGCKVLLTARSQDVLSG--KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLP  256 (276)
Q Consensus       189 ~~gs~IivTTR~~~va~~--~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~P  256 (276)
                      ..+..||.||........  .......+.+...+.++-..+|..++....... .......|++.+.|+.
T Consensus       269 ~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~s  337 (444)
T 2zan_A          269 NDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSL-TEADFQELGRKTDGYS  337 (444)
T ss_dssp             CSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEEC-CHHHHHHHHHHTTTCC
T ss_pred             CCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCC
Confidence            345566666654432211  112334677888888888899988875322110 1233567888898853

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.24  E-value=0.00029  Score=54.13  Aligned_cols=37  Identities=24%  Similarity=0.407  Sum_probs=30.2

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+...+.....+.+.|+|++|+|||+||+.+++....
T Consensus        33 ~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           33 RTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             HHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            5666666666678899999999999999999988643

>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=97.24  E-value=0.011  Score=52.57  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++-+.|+|++|+|||+||+.+.+...
T Consensus        49 p~gvLL~GppGtGKT~Laraia~~~~   74 (476)
T 2ce7_A           49 PKGILLVGPPGTGKTLLARAVAGEAN   74 (476)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            34588999999999999999998764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.21  E-value=0.0077  Score=48.91  Aligned_cols=26  Identities=38%  Similarity=0.456  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+-+.|+|++|+||||||+.+.+...
T Consensus        45 ~~~vll~G~~GtGKT~la~~la~~~~   70 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLAKAIAGEAK   70 (257)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEECcCCCCHHHHHHHHHHHcC
Confidence            34588999999999999999998764

>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=97.17  E-value=0.0023  Score=60.50  Aligned_cols=138  Identities=14%  Similarity=0.171  Sum_probs=73.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC----cC-CHHHHHHHHHHHhCCCccc-----------
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ----NQ-DIRKIQEEIGDKLGLKFHE-----------  174 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~----~~-~~~~l~~~i~~~l~~~~~~-----------  174 (276)
                      ..++-|.++|++|+|||+||+.+.+.....     .+.++.+.    .. ..+..++.+++......+.           
T Consensus       236 ~~p~GILL~GPPGTGKT~LAraiA~elg~~-----~~~v~~~~l~sk~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~  310 (806)
T 3cf2_A          236 KPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIA  310 (806)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHTTTTCE-----EEEEEHHHHHSSCTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTC
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHhCCe-----EEEEEhHHhhcccchHHHHHHHHHHHHHHHcCCeEEEEehhcccc
Confidence            346789999999999999999999876532     24444322    11 2344455555443221100           


Q ss_pred             ----cc----chhhhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHhhCCC--
Q 041612          175 ----ES----ESGRANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKMAGDY--  235 (276)
Q Consensus       175 ----~~----~~~~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~--  235 (276)
                          ..    .......+..     ....+--||.||...+.... ..   ...+.+.+...+.++-.++|+.+....  
T Consensus       311 ~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~  390 (806)
T 3cf2_A          311 PKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKL  390 (806)
T ss_dssp             CTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEE
T ss_pred             cccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCC
Confidence                00    0001111111     12223334445544332222 12   233468888888888888998776522  


Q ss_pred             CCChhHHHHHHHHHHHcCCCcH
Q 041612          236 IEDSEFQSIARDVAKECAGLPV  257 (276)
Q Consensus       236 ~~~~~~~~~~~~i~~~c~G~PL  257 (276)
                      ..+.+    ...++.++.|+--
T Consensus       391 ~~dvd----l~~lA~~T~Gfsg  408 (806)
T 3cf2_A          391 ADDVD----LEQVANETHGHVG  408 (806)
T ss_dssp             CTTCC----HHHHHHHCCSCCH
T ss_pred             CcccC----HHHHHHhcCCCCH
Confidence            12223    3457788887753

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.11  E-value=0.00038  Score=53.34  Aligned_cols=37  Identities=27%  Similarity=0.337  Sum_probs=29.8

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+...+.....+.+.|+|++|+|||+||+.+.+....
T Consensus        33 ~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           33 RAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             HHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            5555666666677899999999999999999988643

>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=97.09  E-value=0.0035  Score=52.60  Aligned_cols=126  Identities=20%  Similarity=0.160  Sum_probs=73.2

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc-c-CCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCcc----cc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK-S-DKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFH----EE  175 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~-~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~----~~  175 (276)
                      .|...+..+..+...++|++|+|||++|+.+.+... . ..+.+. .+++.++ ......+ +.+.+.+.....    ..
T Consensus         8 ~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~-~~l~~~~~~~~id~i-r~li~~~~~~p~~~~~kv   85 (305)
T 2gno_A            8 TLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDI-RTIKDFLNYSPELYTRKY   85 (305)
T ss_dssp             HHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHH-HHHHHHHTSCCSSSSSEE
T ss_pred             HHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCE-EEEcCCcCCCCHHHH-HHHHHHHhhccccCCceE
Confidence            344445555577899999999999999999987531 1 123343 4455443 3444443 345554432211    00


Q ss_pred             ---c-----chhhhhhcc---ccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhh
Q 041612          176 ---S-----ESGRANSLF---THGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMA  232 (276)
Q Consensus       176 ---~-----~~~~~~~l~---~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  232 (276)
                         +     .....+.+.   +..++.+.+|++|.+.. +... .... .+++.++++++..+.+.+..
T Consensus        86 viIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~t-I~SR-~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           86 VIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPT-IKSR-VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             EEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHH-HHTT-SEEEECCCCHHHHHHHHHHH
T ss_pred             EEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHH-HHce-eEeCCCCCHHHHHHHHHHHh
Confidence               1     111122222   25556778888775543 3322 1222 89999999999999887775

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.06  E-value=0.00033  Score=53.88  Aligned_cols=26  Identities=31%  Similarity=0.349  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+.|+|++|+|||||++.+++...
T Consensus        38 g~~~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999999875

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.02  E-value=0.00053  Score=53.70  Aligned_cols=36  Identities=31%  Similarity=0.295  Sum_probs=28.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      +.+.|+|++|+|||+||+.+++....+  ...++|++.
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~--~~~~~~~~~   90 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKR--NVSSLIVYV   90 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTT--TCCEEEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEh
Confidence            689999999999999999999988654  334556654

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=96.95  E-value=0.014  Score=52.31  Aligned_cols=151  Identities=14%  Similarity=0.188  Sum_probs=75.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc----CC-HHHHHHHHHHHhCCCc-----
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN----QD-IRKIQEEIGDKLGLKF-----  172 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~----~~-~~~l~~~i~~~l~~~~-----  172 (276)
                      ++...+.....+-+.|+|++|+|||++|+.+.+....     ..+.++.+.-    .. ....+..++.......     
T Consensus       228 ~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~-----~fv~vn~~~l~~~~~g~~~~~~~~~f~~A~~~~p~iLf  302 (489)
T 3hu3_A          228 ALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA-----FFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIF  302 (489)
T ss_dssp             HHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSS-----EEEEEEHHHHHTSCTTHHHHHHHHHHHHHHHTCSEEEE
T ss_pred             HHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCC-----CEEEEEchHhhhhhcchhHHHHHHHHHHHHhcCCcEEE
Confidence            3334444445567999999999999999999887632     2233332211    11 1222222222211100     


Q ss_pred             -ccc-----------c--chhhhhhccc-----cCCCCcEEEEEecccc-ccccCC---CCCCceeCCCCCHHHHHHHHH
Q 041612          173 -HEE-----------S--ESGRANSLFT-----HGHKGCKVLLTARSQD-VLSGKM---DSRPNFSIGVLNEEEAWSLFK  229 (276)
Q Consensus       173 -~~~-----------~--~~~~~~~l~~-----~~~~gs~IivTTR~~~-va~~~~---~~~~~~~l~~L~~~ea~~Lf~  229 (276)
                       ++.           .  .......+..     .......||.||.... +-....   .....+.+...+.++-.++|.
T Consensus       303 LDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~  382 (489)
T 3hu3_A          303 IDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQ  382 (489)
T ss_dssp             EESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHH
T ss_pred             ecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHH
Confidence             000           0  0011111211     2233445555665442 211111   223368899999999999999


Q ss_pred             HhhCCCC--CChhHHHHHHHHHHHcCCC-cHHHHHH
Q 041612          230 KMAGDYI--EDSEFQSIARDVAKECAGL-PVSIVTI  262 (276)
Q Consensus       230 ~~~~~~~--~~~~~~~~~~~i~~~c~G~-PLai~~i  262 (276)
                      .++....  .+..    ...++..+.|+ +-.+..+
T Consensus       383 ~~~~~~~l~~~~~----l~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          383 IHTKNMKLADDVD----LEQVANETHGHVGADLAAL  414 (489)
T ss_dssp             HHTTTSCBCTTCC----HHHHHHTCTTCCHHHHHHH
T ss_pred             HHHhcCCCcchhh----HHHHHHHccCCcHHHHHHH
Confidence            8875222  2222    34577777775 4444444

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.92  E-value=0.00054  Score=51.97  Aligned_cols=20  Identities=35%  Similarity=0.532  Sum_probs=18.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEI  133 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v  133 (276)
                      ++|.|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            57999999999999999999

>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=96.91  E-value=0.00057  Score=51.85  Aligned_cols=25  Identities=16%  Similarity=0.268  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|++|+||||+++.+.....
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            5799999999999999999987754

>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=96.89  E-value=0.019  Score=48.54  Aligned_cols=59  Identities=22%  Similarity=0.284  Sum_probs=38.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~  171 (276)
                      ....+++|+|++|+||||+++.+........  ..+.+....- .....+-+......++.+
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~~~~--g~V~l~g~D~~r~~a~eql~~~~~~~gv~  186 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLKNHG--FSVVIAASDTFRAGAIEQLEEHAKRIGVK  186 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEECCSSTTHHHHHHHHHHHTTCE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcC--CEEEEEeecccccchHHHHHHHHHHcCce
Confidence            3467999999999999999999998876642  2344443321 123344445556666643

>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=96.89  E-value=0.00064  Score=51.98  Aligned_cols=25  Identities=16%  Similarity=0.234  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|++|+||||+++.+.....
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            5799999999999999999988764

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.78  E-value=0.00084  Score=51.30  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5799999999999999999987

>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=96.76  E-value=0.015  Score=51.08  Aligned_cols=29  Identities=28%  Similarity=0.252  Sum_probs=25.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+|.++|.+|+||||++..+......+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~  124 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKR  124 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            36799999999999999999998877654

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.76  E-value=0.00082  Score=51.12  Aligned_cols=25  Identities=20%  Similarity=0.412  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+|+|+|++|+||||+++.+.....
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999987754

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.75  E-value=0.00096  Score=52.21  Aligned_cols=27  Identities=33%  Similarity=0.444  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|.|+|++|+||||+++.+.....
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            346899999999999999999987763

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.75  E-value=0.00081  Score=52.70  Aligned_cols=25  Identities=28%  Similarity=0.470  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .++|.|.|++|+||||+|+.+....
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998775

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.74  E-value=0.00099  Score=52.18  Aligned_cols=27  Identities=26%  Similarity=0.439  Sum_probs=23.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....+++|+|++|+|||||++.+....
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            345689999999999999999998765

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.72  E-value=0.001  Score=51.27  Aligned_cols=25  Identities=20%  Similarity=0.418  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++++|+|++|+|||||++.+.....
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5899999999999999999987653

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.71  E-value=0.001  Score=51.21  Aligned_cols=26  Identities=27%  Similarity=0.473  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.|.|+|++|+||||+++.+.....
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999987764

>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=96.71  E-value=0.00099  Score=51.54  Aligned_cols=24  Identities=38%  Similarity=0.486  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ..+++|+|++|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999876

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.71  E-value=0.00099  Score=51.47  Aligned_cols=26  Identities=15%  Similarity=0.379  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ++|.|.|++|+||||+++.+......
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            47999999999999999999987764

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.69  E-value=0.0015  Score=51.57  Aligned_cols=29  Identities=24%  Similarity=0.517  Sum_probs=25.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +...+++|+|++|+|||||++.+......
T Consensus        20 ~~g~~v~I~G~sGsGKSTl~~~l~~~~~~   48 (208)
T 3c8u_A           20 PGRQLVALSGAPGSGKSTLSNPLAAALSA   48 (208)
T ss_dssp             CSCEEEEEECCTTSCTHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34569999999999999999999887764

>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=96.68  E-value=0.0011  Score=51.83  Aligned_cols=28  Identities=21%  Similarity=0.332  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+|+|+|++|+|||||++.+.....
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4457999999999999999999988775

>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=96.67  E-value=0.018  Score=50.68  Aligned_cols=29  Identities=28%  Similarity=0.421  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+.+|.++|.+|+||||++..+......+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~  127 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKR  127 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHC
Confidence            37899999999999999999998877654

>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=96.63  E-value=0.0013  Score=50.75  Aligned_cols=24  Identities=33%  Similarity=0.526  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++|+|++|+|||||++.+.....
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            689999999999999999987764

>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=96.62  E-value=0.0013  Score=50.82  Aligned_cols=26  Identities=15%  Similarity=0.367  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+|.|.|++|+||||+++.+......
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~   29 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRK   29 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            58999999999999999999887653

>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=96.62  E-value=0.0014  Score=50.70  Aligned_cols=25  Identities=24%  Similarity=0.375  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+|.|.|++|+||||+++.+....
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998766

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.60  E-value=0.0016  Score=54.41  Aligned_cols=28  Identities=36%  Similarity=0.479  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++.+.++|++|+|||+||+.+++....
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~~   62 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMGI   62 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4668889999999999999999998843

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.59  E-value=0.0013  Score=51.23  Aligned_cols=24  Identities=33%  Similarity=0.686  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|+|.|++|+||||+++.+.....
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            689999999999999999988764

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.57  E-value=0.036  Score=48.74  Aligned_cols=29  Identities=17%  Similarity=0.331  Sum_probs=25.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+++|.++|.+|+||||++..+......+
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            46799999999999999999998877654

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=96.57  E-value=0.011  Score=50.60  Aligned_cols=29  Identities=28%  Similarity=0.447  Sum_probs=25.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+++|+|+.|+||||+++.+.......
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~  184 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKNE  184 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhcccc
Confidence            35699999999999999999999887654

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.56  E-value=0.0018  Score=50.62  Aligned_cols=27  Identities=22%  Similarity=0.383  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....+|+|.|++|+||||+++.+....
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            456789999999999999999998765

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.55  E-value=0.0014  Score=51.20  Aligned_cols=24  Identities=29%  Similarity=0.458  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+++|+|++|+|||||++.+....
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhC
Confidence            589999999999999999998764

>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=96.55  E-value=0.0014  Score=50.19  Aligned_cols=26  Identities=35%  Similarity=0.503  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.|.|.|++|+||||+++.+.....
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999987653

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.54  E-value=0.0015  Score=51.32  Aligned_cols=25  Identities=24%  Similarity=0.456  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .++|.|+|++|+|||||++.+....
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhC
Confidence            4689999999999999999998876

>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=96.53  E-value=0.011  Score=49.66  Aligned_cols=150  Identities=13%  Similarity=0.157  Sum_probs=75.4

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHH---HHHhCCC-c-----
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEI---GDKLGLK-F-----  172 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i---~~~l~~~-~-----  172 (276)
                      .+..++.... .+.+.+.|++|+|||++|+.+.+....     ..+.++.+. .....+...+   ....... .     
T Consensus        37 ~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~-----~~~~i~~~~-~~~~~i~~~~~~~~~~~~~~~~~~vli  110 (324)
T 3u61_B           37 TFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNA-----DMMFVNGSD-CKIDFVRGPLTNFASAASFDGRQKVIV  110 (324)
T ss_dssp             HHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTE-----EEEEEETTT-CCHHHHHTHHHHHHHBCCCSSCEEEEE
T ss_pred             HHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCC-----CEEEEcccc-cCHHHHHHHHHHHHhhcccCCCCeEEE
Confidence            5555555544 456777888999999999999887732     234444433 2333332222   2211100 0     


Q ss_pred             -cccc--c-hhhhhhcc---ccCCCCcEEEEEecccccc-ccCCCCCCceeCCCCCHHHHHHHH-------HHhhC--CC
Q 041612          173 -HEES--E-SGRANSLF---THGHKGCKVLLTARSQDVL-SGKMDSRPNFSIGVLNEEEAWSLF-------KKMAG--DY  235 (276)
Q Consensus       173 -~~~~--~-~~~~~~l~---~~~~~gs~IivTTR~~~va-~~~~~~~~~~~l~~L~~~ea~~Lf-------~~~~~--~~  235 (276)
                       ++..  . ......+.   .....+.++|+||....-. .........+.+++++.++-.+++       ...+.  ..
T Consensus       111 iDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~  190 (324)
T 3u61_B          111 IDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGI  190 (324)
T ss_dssp             EESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             EECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence             0100  1 11111111   1334567888887654321 111111236889999988854332       22222  11


Q ss_pred             CCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          236 IEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       236 ~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      ..++  .+....+++.++|-+-.+.
T Consensus       191 ~~~~--~~~~~~l~~~~~gd~R~a~  213 (324)
T 3u61_B          191 AIAD--MKVVAALVKKNFPDFRKTI  213 (324)
T ss_dssp             CBSC--HHHHHHHHHHTCSCTTHHH
T ss_pred             CCCc--HHHHHHHHHhCCCCHHHHH
Confidence            1111  2456778888888765433

>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=96.52  E-value=0.0018  Score=51.13  Aligned_cols=27  Identities=19%  Similarity=0.337  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+++|+|++|+|||||++.+.....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            356899999999999999999988764

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.52  E-value=0.0014  Score=50.02  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|.|.|++|+||||+|+.+.....
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            4689999999999999999987754

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.51  E-value=0.0016  Score=50.29  Aligned_cols=25  Identities=24%  Similarity=0.239  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999988765

>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=96.50  E-value=0.0017  Score=49.45  Aligned_cols=25  Identities=28%  Similarity=0.566  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+++|+|++|+||||+++.+....
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999998764

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.49  E-value=0.0018  Score=50.21  Aligned_cols=26  Identities=31%  Similarity=0.393  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|.|.|++|+||||+++.+.....
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l~   34 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKYG   34 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999987653

>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=96.49  E-value=0.0022  Score=49.42  Aligned_cols=25  Identities=40%  Similarity=0.372  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ....|.|+|++|+||||+++.+...
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            3568999999999999999999876

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.47  E-value=0.0017  Score=53.03  Aligned_cols=25  Identities=36%  Similarity=0.349  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|++|+||||||+.+.....
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCC
Confidence            4789999999999999999987653

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.46  E-value=0.0018  Score=50.25  Aligned_cols=26  Identities=27%  Similarity=0.342  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|+|.|++|+||||+|+.+.....
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            36899999999999999999987753

>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=96.45  E-value=0.0016  Score=50.16  Aligned_cols=25  Identities=20%  Similarity=0.408  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|++|+||||+|+.+.....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            4699999999999999999987654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.45  E-value=0.0022  Score=50.21  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+++|+|++|+||||+++.+....
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            4589999999999999999998766

>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=96.44  E-value=0.0019  Score=51.42  Aligned_cols=24  Identities=29%  Similarity=0.480  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+|+|+|++|+||||+++.+....
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999987754

>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=96.44  E-value=0.0018  Score=49.99  Aligned_cols=22  Identities=27%  Similarity=0.481  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .+++|+|++|+|||||++.+..
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

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.44  E-value=0.0014  Score=50.09  Aligned_cols=22  Identities=23%  Similarity=0.448  Sum_probs=19.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      -.+++|+|++|+|||||++.++
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHc
Confidence            4589999999999999999643

>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=96.44  E-value=0.0019  Score=50.54  Aligned_cols=22  Identities=27%  Similarity=0.459  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .+|+|.|++|+||||+++.+..
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            4799999999999999999987

>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=96.43  E-value=0.002  Score=52.15  Aligned_cols=26  Identities=27%  Similarity=0.312  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|+|+|++|+|||||++.+.....
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            56999999999999999999996553

>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=96.43  E-value=0.0081  Score=48.08  Aligned_cols=57  Identities=12%  Similarity=0.248  Sum_probs=37.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEEEecCcCCHHHHHHHHHHHhCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFVEVSQNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  170 (276)
                      -.++.|+|++|+|||||++.+........    .-..++|++.....+...+. .++..++.
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~   84 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGL   84 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCC
Confidence            45899999999999999999988532210    12578888776654544432 33444443

>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=96.43  E-value=0.0018  Score=50.27  Aligned_cols=25  Identities=24%  Similarity=0.340  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      |.|.|+|++|+|||||++.+.....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            5688999999999999999987754

>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=96.42  E-value=0.0024  Score=49.85  Aligned_cols=27  Identities=26%  Similarity=0.260  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|.|.|++|+||||+|+.+.....
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999987663

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.42  E-value=0.002  Score=50.65  Aligned_cols=27  Identities=37%  Similarity=0.490  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+++|.|+.|+|||||++.+.....
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            446899999999999999999988754

>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=96.42  E-value=0.0022  Score=49.98  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=23.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +...+|+|.|+.|+||||+++.+...
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            34679999999999999999999875

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.41  E-value=0.0022  Score=50.36  Aligned_cols=27  Identities=19%  Similarity=0.314  Sum_probs=23.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+|.|.|++|+||||+++.+.......
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            589999999999999999999877543

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=96.41  E-value=0.0017  Score=50.78  Aligned_cols=24  Identities=21%  Similarity=0.346  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.++|+|++|+|||||++.+....
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            579999999999999999998765

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.41  E-value=0.0015  Score=50.01  Aligned_cols=26  Identities=27%  Similarity=0.378  Sum_probs=19.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|.|.|++|+||||+|+.+.....
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            46899999999999999999987654

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.39  E-value=0.0038  Score=46.10  Aligned_cols=26  Identities=19%  Similarity=0.252  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-|.|+|.+|+|||++|+.+++....
T Consensus        25 ~~vll~G~~GtGKt~lA~~i~~~~~~   50 (145)
T 3n70_A           25 IAVWLYGAPGTGRMTGARYLHQFGRN   50 (145)
T ss_dssp             SCEEEESSTTSSHHHHHHHHHHSSTT
T ss_pred             CCEEEECCCCCCHHHHHHHHHHhCCc
Confidence            35789999999999999999887543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.39  E-value=0.0016  Score=48.65  Aligned_cols=48  Identities=13%  Similarity=0.301  Sum_probs=32.5

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      .++..|..-.-..+.|+|.+|+|||||++.+++.....+ + ..++++..
T Consensus        26 ~~~~~l~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g-~-~~~~~~~~   73 (149)
T 2kjq_A           26 ELVYVLRHKHGQFIYVWGEEGAGKSHLLQAWVAQALEAG-K-NAAYIDAA   73 (149)
T ss_dssp             HHHHHCCCCCCSEEEEESSSTTTTCHHHHHHHHHHHTTT-C-CEEEEETT
T ss_pred             HHHHHHHhcCCCEEEEECCCCCCHHHHHHHHHHHHHhcC-C-cEEEEcHH
Confidence            333444332456899999999999999999998876431 1 24555543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.39  E-value=0.0021  Score=49.43  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|.+.|++|+||||+++.+....
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999998765

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.39  E-value=0.0022  Score=48.55  Aligned_cols=27  Identities=33%  Similarity=0.507  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|+|.|++|+||||+++.+.....
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHhC
Confidence            467899999999999999999988754

>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=96.38  E-value=0.0022  Score=52.44  Aligned_cols=26  Identities=19%  Similarity=0.565  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|.|.|++|+||||+|+.+.....
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999988743

>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=96.38  E-value=0.002  Score=48.89  Aligned_cols=25  Identities=28%  Similarity=0.421  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|++|+||||+|+.+.....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999987653

>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=96.38  E-value=0.0046  Score=48.75  Aligned_cols=44  Identities=23%  Similarity=0.232  Sum_probs=33.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~  161 (276)
                      -.++.|+|.+|+|||||+..+..  ..   -..++|++.....+...+.
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~--~~---~~~v~~i~~~~~~~~~~~~   63 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL--LS---GKKVAYVDTEGGFSPERLV   63 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH--HH---CSEEEEEESSCCCCHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--Hc---CCcEEEEECCCCCCHHHHH
Confidence            45899999999999999999988  21   2467888776655555443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.38  E-value=0.0026  Score=49.00  Aligned_cols=29  Identities=24%  Similarity=0.385  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+|.+.|++|+||||+++.+.......
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~~   40 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQKE   40 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            45689999999999999999999887643

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.37  E-value=0.0023  Score=50.90  Aligned_cols=27  Identities=22%  Similarity=0.373  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.++|.|.|++|+||+|.|+.+...+.
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~~~g   54 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQKFH   54 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            578999999999999999999998764

>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=96.36  E-value=0.0077  Score=47.74  Aligned_cols=44  Identities=25%  Similarity=0.360  Sum_probs=31.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC---C-CCCeEEEEEecCcCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD---K-LFDQVVFVEVSQNQD  156 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~-~f~~~~wv~~~~~~~  156 (276)
                      -.+++|+|++|+|||||++.+.......   . .-...+|++......
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~   72 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFR   72 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCC
Confidence            3589999999999999999998754331   0 124577776544333

>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=96.36  E-value=0.0077  Score=48.82  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=21.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|+|++|+|||||++.+.+...
T Consensus        52 ~ll~G~~G~GKTtl~~~i~~~~~   74 (254)
T 1ixz_A           52 VLLVGPPGVGKTHLARAVAGEAR   74 (254)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            89999999999999999998764

>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=96.36  E-value=0.0023  Score=49.38  Aligned_cols=26  Identities=27%  Similarity=0.332  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++|+|.|++|+||||+++.+.....
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999987653

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.36  E-value=0.0034  Score=52.16  Aligned_cols=27  Identities=26%  Similarity=0.261  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....+|.|.|++|+||||+++.+....
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            346789999999999999999998765

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.36  E-value=0.0023  Score=49.45  Aligned_cols=25  Identities=28%  Similarity=0.468  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|+|.|++|+||||+++.+.....
T Consensus         1 ~~I~l~G~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            1 MLIAFEGIDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3689999999999999999998764

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.36  E-value=0.0023  Score=48.27  Aligned_cols=24  Identities=17%  Similarity=0.304  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            689999999999999999988654

>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=96.33  E-value=0.043  Score=51.86  Aligned_cols=130  Identities=16%  Similarity=0.188  Sum_probs=69.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCC----CCeEEE-EEec-------CcCCHHHHHHHHHHHhCC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKL----FDQVVF-VEVS-------QNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----f~~~~w-v~~~-------~~~~~~~l~~~i~~~l~~  170 (276)
                      .++..|......-+.++|.+|+|||++|+.+.+.......    +...+| ++.+       .....+..++.+++.+..
T Consensus       197 ~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~  276 (758)
T 1r6b_X          197 RAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQ  276 (758)
T ss_dssp             HHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSS
T ss_pred             HHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHh
Confidence            6666666666677899999999999999999987643211    133333 2211       112345556666665543


Q ss_pred             Ccccc---c--------------chhhhhhccc-cCCCCcEEEEEeccccccc------cCCCCCCceeCCCCCHHHHHH
Q 041612          171 KFHEE---S--------------ESGRANSLFT-HGHKGCKVLLTARSQDVLS------GKMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       171 ~~~~~---~--------------~~~~~~~l~~-~~~~gs~IivTTR~~~va~------~~~~~~~~~~l~~L~~~ea~~  226 (276)
                      .....   +              .......+.. .......+|.+|.......      ........+.++.++.++..+
T Consensus       277 ~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~~~~~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~  356 (758)
T 1r6b_X          277 DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQ  356 (758)
T ss_dssp             SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHH
T ss_pred             cCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhCCCeEEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHH
Confidence            21100   0              1111111222 1223455666655432110      011112258899999999988


Q ss_pred             HHHHhh
Q 041612          227 LFKKMA  232 (276)
Q Consensus       227 Lf~~~~  232 (276)
                      ++....
T Consensus       357 il~~l~  362 (758)
T 1r6b_X          357 IINGLK  362 (758)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=96.32  E-value=0.016  Score=55.65  Aligned_cols=37  Identities=24%  Similarity=0.388  Sum_probs=29.6

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++..|.....+.+.++|.+|+|||+||+.+.+....
T Consensus       181 ~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~  217 (854)
T 1qvr_A          181 RVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVK  217 (854)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhc
Confidence            5566665555667899999999999999999988743

>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=96.30  E-value=0.0027  Score=49.70  Aligned_cols=27  Identities=15%  Similarity=0.372  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..++++|+|++|+|||||++.+.....
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            457899999999999999999987654

>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=96.30  E-value=0.0029  Score=48.23  Aligned_cols=29  Identities=24%  Similarity=0.313  Sum_probs=24.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..+++.|.|..|+|||||+..+......+
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~~~   31 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAVRE   31 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhHhc
Confidence            35789999999999999999999887644

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.29  E-value=0.0026  Score=50.75  Aligned_cols=25  Identities=24%  Similarity=0.298  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|.|++|+||||+++.+....
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998765

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=96.28  E-value=0.0029  Score=50.23  Aligned_cols=28  Identities=32%  Similarity=0.468  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .....|.|+|.+|+|||||+..+.....
T Consensus        36 ~~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           36 HGVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             TTCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            3467899999999999999999987754

>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=96.28  E-value=0.0075  Score=51.63  Aligned_cols=43  Identities=21%  Similarity=0.269  Sum_probs=33.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      -.++.|+|++|+|||||+..+.......  =..++|++....++.
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~--gg~VlyId~E~s~~~  103 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKM--GGVAAFIDAEHALDP  103 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEecccccch
Confidence            4699999999999999999998876543  234677776655554

>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=96.28  E-value=0.003  Score=49.68  Aligned_cols=29  Identities=10%  Similarity=0.226  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+|+|.|++|+||||+++.+.......
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~~   36 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALCAA   36 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            34689999999999999999999876543

>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=96.27  E-value=0.0029  Score=50.18  Aligned_cols=26  Identities=19%  Similarity=0.261  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|.|.|++|+||||+++.+.....
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999987653

>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=96.27  E-value=0.0028  Score=49.79  Aligned_cols=25  Identities=32%  Similarity=0.594  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+|+|+|++|+||||+++.+....
T Consensus        21 ~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            5689999999999999999998754

>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=96.27  E-value=0.0023  Score=54.46  Aligned_cols=49  Identities=16%  Similarity=0.158  Sum_probs=34.5

Q ss_pred             ceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHH
Q 041612          213 NFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTI  262 (276)
Q Consensus       213 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i  262 (276)
                      ...+++.+.++-.+++.+.+...... -..+.+..|+.+++|.|-.+.-+
T Consensus       174 ~~~Ld~~~~~~l~~iL~~~~~~~~~~-~~~~~~~~ia~~~~G~~R~a~~l  222 (334)
T 1in4_A          174 ILELDFYTVKELKEIIKRAASLMDVE-IEDAAAEMIAKRSRGTPRIAIRL  222 (334)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHTTCC-BCHHHHHHHHHTSTTCHHHHHHH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHhcCCChHHHHHH
Confidence            57899999999999998876311111 11345788999999999755443

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.26  E-value=0.0027  Score=50.44  Aligned_cols=27  Identities=30%  Similarity=0.208  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....|.|.|++|+||||+++.+.....
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346799999999999999999988764

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.26  E-value=0.0029  Score=49.65  Aligned_cols=27  Identities=15%  Similarity=0.240  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+|+|.|++|+||||+++.+......
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            468999999999999999999887654

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=96.25  E-value=0.0028  Score=50.06  Aligned_cols=24  Identities=33%  Similarity=0.482  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~   25 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYE   25 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999987653

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.25  E-value=0.0098  Score=49.03  Aligned_cols=23  Identities=35%  Similarity=0.489  Sum_probs=21.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.++|++|+|||||++.+.....
T Consensus        47 vlL~Gp~GtGKTtLakala~~~~   69 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVANESG   69 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHHHHcC
Confidence            99999999999999999998764

>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=96.24  E-value=0.0028  Score=49.83  Aligned_cols=25  Identities=12%  Similarity=0.329  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.+++|+|++|+|||||++.+..-.
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4589999999999999999998776

>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=96.23  E-value=0.0015  Score=51.42  Aligned_cols=25  Identities=28%  Similarity=0.567  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|+|.|++|+||||+++.+.....
T Consensus         1 ~~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            1 MLIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             CEEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            3789999999999999999987764

>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=96.23  E-value=0.0033  Score=52.36  Aligned_cols=29  Identities=17%  Similarity=0.148  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ....+|+|.|.+|+|||||++.+......
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            45679999999999999999998877654

>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=96.22  E-value=0.0026  Score=49.84  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .+|+|.|++|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>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=96.21  E-value=0.0031  Score=49.85  Aligned_cols=23  Identities=35%  Similarity=0.469  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|.|++|+||||+|+.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998765

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=96.18  E-value=0.0028  Score=50.44  Aligned_cols=25  Identities=28%  Similarity=0.464  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.+++|+|++|+|||||++.+....
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4589999999999999999998765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=96.17  E-value=0.011  Score=48.71  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=21.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcc
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|+|++|+|||||++.+.....
T Consensus        76 vll~Gp~GtGKTtl~~~i~~~~~   98 (278)
T 1iy2_A           76 VLLVGPPGVGKTHLARAVAGEAR   98 (278)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTT
T ss_pred             EEEECCCcChHHHHHHHHHHHcC
Confidence            89999999999999999998774

>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=96.16  E-value=0.0036  Score=48.80  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|.|++|+||||+++.+....
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998876

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.14  E-value=0.0036  Score=48.98  Aligned_cols=29  Identities=31%  Similarity=0.538  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ....+++|.|.+|+||||+++.+......
T Consensus        20 ~~~~~i~i~G~~GsGKstl~~~l~~~~~~   48 (201)
T 1rz3_A           20 AGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (201)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34579999999999999999999887644

>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=96.13  E-value=0.0037  Score=52.64  Aligned_cols=29  Identities=21%  Similarity=0.340  Sum_probs=25.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ....+++|.|.+|+|||||++.+......
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhccc
Confidence            34569999999999999999999887754

>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=96.12  E-value=0.0038  Score=50.51  Aligned_cols=26  Identities=15%  Similarity=0.125  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+.+|.|.|++|+||||+|+.+....
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998765

>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=96.12  E-value=0.0039  Score=50.69  Aligned_cols=28  Identities=18%  Similarity=0.334  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.+|+|.|++|+||||+|+.+.....
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3467899999999999999999987654

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.11  E-value=0.0039  Score=50.40  Aligned_cols=26  Identities=23%  Similarity=0.387  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...+|+|.|+.|+|||||++.+....
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999988754

>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=96.10  E-value=0.0035  Score=52.84  Aligned_cols=30  Identities=23%  Similarity=0.527  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++.++|+|.|-||+||||.+-.+.-.....
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~~   75 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSIL   75 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHHC
Confidence            568999999999999999998887776654

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=96.10  E-value=0.012  Score=48.97  Aligned_cols=52  Identities=12%  Similarity=0.210  Sum_probs=35.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcCCHHHHHHHHHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQDIRKIQEEIGDK  167 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~  167 (276)
                      .-.+++|.|.+|+|||||++.+.......  .. .+.|++...  +...+...+...
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~~~~--~G~~v~~~~~e~--~~~~~~~r~~~~   86 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAMLEE--SVEETAEDLIGL   86 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHHHHT--SCCCEEEEESSS--CHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHH--cCCeEEEEeCcC--CHHHHHHHHHHH
Confidence            34589999999999999999999887654  23 466665432  444554444433

>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=96.09  E-value=0.0064  Score=50.94  Aligned_cols=29  Identities=21%  Similarity=0.355  Sum_probs=25.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+++|+|++|+|||||++.+.......
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~~  129 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQNL  129 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            45799999999999999999999887754

>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=96.09  E-value=0.0039  Score=46.95  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+++|+|+.|.|||||.+.+....
T Consensus        34 e~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           34 IMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            589999999999999999998876

>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=96.09  E-value=0.0039  Score=49.63  Aligned_cols=26  Identities=15%  Similarity=0.234  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|++|+|||||.+.+.....
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            46899999999999999999988765

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=96.08  E-value=0.0031  Score=48.21  Aligned_cols=27  Identities=26%  Similarity=0.370  Sum_probs=23.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+++|+|.+|+|||||++.+.......
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~   29 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRER   29 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            589999999999999999998877654

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=96.07  E-value=0.0033  Score=49.72  Aligned_cols=27  Identities=30%  Similarity=0.438  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..++|+|+|.+|+|||||+..+.....
T Consensus        29 ~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           29 GTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            457999999999999999999988754

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.06  E-value=0.0039  Score=50.72  Aligned_cols=25  Identities=24%  Similarity=0.461  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+|+|.|+.|+||||+++.+....
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998554

>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=96.06  E-value=0.014  Score=48.68  Aligned_cols=28  Identities=21%  Similarity=0.307  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...+++++|.+|+||||++..+......
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~  131 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISML  131 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999999999888764

>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=96.04  E-value=0.0041  Score=49.01  Aligned_cols=25  Identities=28%  Similarity=0.364  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|+||+||+|.|+.+...+.
T Consensus         1 M~Iil~GpPGsGKgTqa~~La~~~g   25 (206)
T 3sr0_A            1 MILVFLGPPGAGKGTQAKRLAKEKG   25 (206)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            3688999999999999999998764

>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=96.03  E-value=0.12  Score=45.16  Aligned_cols=29  Identities=34%  Similarity=0.417  Sum_probs=25.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...++.++|.+|+||||++..+......+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~  125 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK  125 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            45789999999999999999999888654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.03  E-value=0.016  Score=48.81  Aligned_cols=51  Identities=18%  Similarity=0.171  Sum_probs=37.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK  167 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  167 (276)
                      -.++.|.|.+|+|||||+..+..+...++  ..++|++.-  .+..++...+...
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~  118 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVT  118 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHH
Confidence            45899999999999999999987765543  567777764  4566666555543

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.99  E-value=0.0033  Score=51.14  Aligned_cols=27  Identities=19%  Similarity=0.239  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|.|.|++|+||||+|+.+.....
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            457899999999999999999987754

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.97  E-value=0.0041  Score=49.31  Aligned_cols=26  Identities=27%  Similarity=0.258  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|.|.|++|+||||+++.+.....
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l~   30 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEYG   30 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35789999999999999999987763

>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=95.96  E-value=0.0045  Score=48.77  Aligned_cols=28  Identities=21%  Similarity=0.294  Sum_probs=24.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+|.|.|++|+||||+++.+.....
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3456899999999999999999988765

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.96  E-value=0.0052  Score=51.85  Aligned_cols=28  Identities=18%  Similarity=0.277  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+.+|+|.|.+|+|||||++.+.....
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3466999999999999999999887765

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.96  E-value=0.0039  Score=48.44  Aligned_cols=24  Identities=29%  Similarity=0.404  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +++|+|+.|+|||||.+.+.....
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            689999999999999999988764

>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=0.0054  Score=49.41  Aligned_cols=27  Identities=26%  Similarity=0.322  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl~~p   57 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCLDKP   57 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            458999999999999999999877654

>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=95.93  E-value=0.0048  Score=48.71  Aligned_cols=23  Identities=26%  Similarity=0.177  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|.|++|+||||+++.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998766

>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=95.92  E-value=0.013  Score=49.24  Aligned_cols=28  Identities=18%  Similarity=0.207  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+|+|.|..|+|||||++.+.....
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3456999999999999999999988764

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.90  E-value=0.057  Score=44.98  Aligned_cols=37  Identities=27%  Similarity=0.266  Sum_probs=28.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~  151 (276)
                      ..+++++|.+|+||||++..+......++  ..+.+++.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g--~~v~l~~~  134 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKG--FKVGLVGA  134 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTT--CCEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEec
Confidence            56999999999999999999988876542  23445544

>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=95.90  E-value=0.0053  Score=47.80  Aligned_cols=26  Identities=27%  Similarity=0.434  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.+|+|.|+.|+||||+++.+....
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHhc
Confidence            35689999999999999999988763

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.90  E-value=0.0051  Score=49.00  Aligned_cols=23  Identities=26%  Similarity=0.354  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|.|++|+||||+++.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68999999999999999998765

>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=95.89  E-value=0.024  Score=49.30  Aligned_cols=58  Identities=14%  Similarity=0.250  Sum_probs=38.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      -.++.|+|.+|+|||||+..++-.....    ..-..++|++....++...+ ..+++.++..
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~  239 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLD  239 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCC
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCC
Confidence            4699999999999999999876443221    01346888887666555544 3355666543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.89  E-value=0.0063  Score=48.27  Aligned_cols=47  Identities=21%  Similarity=0.290  Sum_probs=31.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  163 (276)
                      -.+++|+|.+|+|||||++.+.......  -..+.|++...  ....+...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~~--~~~v~~~~~~~--~~~~~~~~   69 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLRD--GDPCIYVTTEE--SRDSIIRQ   69 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHH--TCCEEEEESSS--CHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHC--CCeEEEEEccc--CHHHHHHH
Confidence            3589999999999999999998766533  13456665433  34444333

>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=95.89  E-value=0.0058  Score=48.31  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      ..+|+|.|+.|+||||+++.+..
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            46899999999999999999875

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=95.88  E-value=0.0081  Score=48.52  Aligned_cols=26  Identities=35%  Similarity=0.433  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||.+.+..-...
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~p   50 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVKP   50 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            78999999999999999999877653

>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=95.88  E-value=0.006  Score=48.89  Aligned_cols=27  Identities=22%  Similarity=0.194  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....|.|.|++|+||||+|+.+.....
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346899999999999999999988764

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.87  E-value=0.0054  Score=46.89  Aligned_cols=27  Identities=19%  Similarity=0.279  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+|+|.|+.|+||||+++.+......
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~   31 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVC   31 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            457899999999999999999887643

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.86  E-value=0.0057  Score=51.23  Aligned_cols=29  Identities=28%  Similarity=0.447  Sum_probs=25.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+++|+|+.|+||||+++.+.......
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~  127 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKNE  127 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            35699999999999999999999887654

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.85  E-value=0.0097  Score=49.93  Aligned_cols=37  Identities=24%  Similarity=0.368  Sum_probs=28.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc-cCCCCCeEEEEEe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK-SDKLFDQVVFVEV  151 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~f~~~~wv~~  151 (276)
                      ...+.|+|++|+|||+||..+++... .++  ..+.+++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g--~~v~~~~~  189 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKG--VSTTLLHF  189 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSC--CCEEEEEH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcC--CcEEEEEH
Confidence            46889999999999999999999876 442  23445543

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.85  E-value=0.006  Score=50.49  Aligned_cols=23  Identities=30%  Similarity=0.674  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      .+.+|+|.|++|+||||+|+.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            46789999999999999999988

>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=95.83  E-value=0.017  Score=48.45  Aligned_cols=54  Identities=9%  Similarity=-0.017  Sum_probs=38.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  173 (276)
                      ++.|+|.+|+|||||+.++......+..=..++|++.....+..     -+++++.+..
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d   83 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPE   83 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGG
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHH
Confidence            78999999999999999987776532112467888877776654     2567776543

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.82  E-value=0.007  Score=47.51  Aligned_cols=36  Identities=22%  Similarity=0.321  Sum_probs=26.6

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+..++.. +..+.+.++|++|+|||++|..+.+...
T Consensus        47 ~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           47 ALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             HHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            44444443 2234799999999999999999888764

>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=95.81  E-value=0.0061  Score=48.99  Aligned_cols=26  Identities=23%  Similarity=0.431  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+|+|.|++|+||||+++.+.....
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999987653

>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=95.79  E-value=0.011  Score=50.56  Aligned_cols=44  Identities=20%  Similarity=0.283  Sum_probs=33.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      .-.++.|+|.+|+|||||+..+.......  =..++|++.....+.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~--g~~vlyi~~E~~~~~  103 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA--GGIAAFIDAEHALDP  103 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCcCH
Confidence            35689999999999999999998776543  245778877655543

>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=95.78  E-value=0.006  Score=53.74  Aligned_cols=27  Identities=33%  Similarity=0.541  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|.|+|.+|+||||++..+.....
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l~  124 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYIQ  124 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            357999999999999999999887764

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.78  E-value=0.0036  Score=50.11  Aligned_cols=25  Identities=24%  Similarity=0.329  Sum_probs=16.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH-Hhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA-RKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~-~~~  137 (276)
                      -.+++|+|+.|+|||||++.+. ...
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3589999999999999999998 554

>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=95.78  E-value=0.011  Score=45.24  Aligned_cols=27  Identities=22%  Similarity=0.395  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++++|+|..|+|||||+..+......
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~   32 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCA   32 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccc
Confidence            578999999999999999999887654

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.78  E-value=0.0053  Score=49.92  Aligned_cols=25  Identities=32%  Similarity=0.461  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..|+|+|++|+||||+++.+.....
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4799999999999999999987654

>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=95.77  E-value=0.0063  Score=47.51  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|+|.|+.|+||||+++.+.....
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            899999999999999999987654

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.75  E-value=0.012  Score=49.27  Aligned_cols=29  Identities=21%  Similarity=0.352  Sum_probs=25.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...++.|+|.+|+||||++..+.......
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~  131 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDE  131 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhc
Confidence            45799999999999999999999887654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.75  E-value=0.01  Score=47.61  Aligned_cols=47  Identities=15%  Similarity=0.250  Sum_probs=32.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEE  163 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  163 (276)
                      -.++.|.|.+|+|||||+..+.......  =..++|++...  +...+.+.
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~~~--~~~v~~~~~e~--~~~~~~~~   69 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGLKM--GEPGIYVALEE--HPVQVRQN   69 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHHHT--TCCEEEEESSS--CHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccC--CHHHHHHH
Confidence            3589999999999999998887665433  24577776543  34444433

>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=95.74  E-value=0.024  Score=48.23  Aligned_cols=59  Identities=14%  Similarity=0.313  Sum_probs=41.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      .-.++.|+|.+|+|||+|+..+........    .-..++|++....++...+. .++..++.+
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~~  183 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNVD  183 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCCC
Confidence            346899999999999999999988743211    12468899888776766654 344555543

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=95.73  E-value=0.0072  Score=49.50  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl~~p   58 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFLEKP   58 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999876653

>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=0.053  Score=48.60  Aligned_cols=29  Identities=24%  Similarity=0.359  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+++|+|+|.+|+||||++..+......+
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~  128 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRK  128 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            46799999999999999999998776543

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.72  E-value=0.0099  Score=50.71  Aligned_cols=30  Identities=30%  Similarity=0.408  Sum_probs=24.6

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..+....|.|+|++|+||||+++.+.....
T Consensus        20 ~~g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           20 EDNYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             TTCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccCCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            344566799999999999999998887654

>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=95.72  E-value=0.1  Score=43.28  Aligned_cols=29  Identities=34%  Similarity=0.417  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ...+++++|.+|+||||++..+.......
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~  125 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK  125 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            45699999999999999999999887654

>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=95.69  E-value=0.0066  Score=53.26  Aligned_cols=26  Identities=19%  Similarity=0.308  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...+|.|+|++|+||||+|+.+....
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            46799999999999999999988755

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=95.69  E-value=0.0053  Score=48.45  Aligned_cols=23  Identities=35%  Similarity=0.304  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .+++|+|+.|+|||||.+.+...
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            47999999999999999999876

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=95.67  E-value=0.006  Score=48.72  Aligned_cols=27  Identities=22%  Similarity=0.249  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~Gl~~p   56 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGLLDAP   56 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999876653

>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=95.67  E-value=0.0079  Score=49.63  Aligned_cols=27  Identities=26%  Similarity=0.416  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~Gl~~p   60 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNGILKP   60 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCCCC
Confidence            358999999999999999999876643

>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=95.65  E-value=0.013  Score=50.12  Aligned_cols=44  Identities=20%  Similarity=0.318  Sum_probs=34.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      .-+++.|.|.+|+||||||..+.......  -..++|++.....+.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~--g~~vlyid~E~s~~~  105 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDP  105 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEeCCCCccH
Confidence            35689999999999999999988776544  236788887666553

>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=95.65  E-value=0.0083  Score=48.42  Aligned_cols=27  Identities=30%  Similarity=0.430  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p   58 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAGLVRA   58 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999877653

>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=95.65  E-value=0.0064  Score=49.68  Aligned_cols=27  Identities=30%  Similarity=0.388  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+-+.|+|++|+|||+||+.+++....
T Consensus        44 ~~~vll~G~~GtGKT~la~~la~~~~~   70 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLAKAVAGEAHV   70 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHHHHHHHHHTC
T ss_pred             CceEEEECCCCCcHHHHHHHHHHHhCC
Confidence            344789999999999999999987643

>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=95.64  E-value=0.02  Score=48.96  Aligned_cols=57  Identities=25%  Similarity=0.349  Sum_probs=36.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCC----CeEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLF----DQVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f----~~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      .-.++.|+|.+|+|||||+..+..........    ..++|++....+....+ ..+.+..+
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~  190 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRG  190 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcC
Confidence            45699999999999999999998876321001    24478876555433333 23444433

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=95.64  E-value=0.0079  Score=53.59  Aligned_cols=36  Identities=28%  Similarity=0.440  Sum_probs=28.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++..+......-+.++|++|+|||++|+.+.+...
T Consensus       191 ~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~  226 (468)
T 3pxg_A          191 RVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQII  226 (468)
T ss_dssp             HHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            556666555556778999999999999999998864

>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=95.63  E-value=0.0084  Score=48.94  Aligned_cols=27  Identities=30%  Similarity=0.332  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~Gl~~p   59 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITGFLKA   59 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999877653

>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=95.63  E-value=0.0085  Score=48.60  Aligned_cols=27  Identities=33%  Similarity=0.466  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p   61 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRFYIP   61 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999877654

>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=95.63  E-value=0.0084  Score=49.14  Aligned_cols=28  Identities=14%  Similarity=0.182  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+++|+|+.|+|||||.+.+..-...
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~~p   76 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLEDF   76 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCCCC
Confidence            3458999999999999999999877653

>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=95.63  E-value=0.028  Score=47.44  Aligned_cols=58  Identities=24%  Similarity=0.422  Sum_probs=41.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      -.++.|+|.+|+|||+|+..+........    .-..++|++....++...+. .++..++.+
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~  168 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLD  168 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCC
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCC
Confidence            46899999999999999999987643221    02468898888776666654 344555543

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.61  E-value=0.0075  Score=51.20  Aligned_cols=25  Identities=36%  Similarity=0.434  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+|+|.|+.|+||||||..+.....
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            4899999999999999999988754

>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=95.61  E-value=0.0087  Score=49.11  Aligned_cols=27  Identities=26%  Similarity=0.391  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl~~p   63 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGYLSP   63 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            358999999999999999999876654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=95.59  E-value=0.013  Score=48.79  Aligned_cols=37  Identities=22%  Similarity=0.370  Sum_probs=27.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      ..+.++|++|+|||++|+.+.+.....  -...+.++.+
T Consensus        48 ~~~ll~G~~GtGKt~la~~la~~~~~~--~~~~~~~~~~   84 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMT   84 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHHHHHHHHSC--GGGEEEEEGG
T ss_pred             eEEEEECCCCcCHHHHHHHHHHHHcCC--CcceEEeecc
Confidence            479999999999999999999887543  1233444444

>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=95.58  E-value=0.014  Score=46.80  Aligned_cols=28  Identities=21%  Similarity=0.324  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ....|.|.|++|+||||+++.+......
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3468999999999999999999988865

>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=95.57  E-value=0.0077  Score=50.12  Aligned_cols=23  Identities=30%  Similarity=0.414  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .+|.|.|++|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999874

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=95.57  E-value=0.0091  Score=49.16  Aligned_cols=27  Identities=19%  Similarity=0.287  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl~~p   71 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNLYQP   71 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999877653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.56  E-value=0.0024  Score=47.08  Aligned_cols=25  Identities=12%  Similarity=0.038  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .-|.|+|.+|+|||++|+.+.+...
T Consensus        28 ~~vll~G~~GtGKt~lA~~i~~~~~   52 (143)
T 3co5_A           28 SPVFLTGEAGSPFETVARYFHKNGT   52 (143)
T ss_dssp             SCEEEEEETTCCHHHHHGGGCCTTS
T ss_pred             CcEEEECCCCccHHHHHHHHHHhCC
Confidence            3478999999999999999876543

>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=95.55  E-value=0.0077  Score=48.97  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999985

>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=95.54  E-value=0.0095  Score=48.62  Aligned_cols=27  Identities=30%  Similarity=0.465  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl~~p   67 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTLIKP   67 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999877643

>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=95.54  E-value=0.0073  Score=48.68  Aligned_cols=27  Identities=19%  Similarity=0.355  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p   57 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAEMDK   57 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTCSEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999877654

>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=95.54  E-value=0.0083  Score=46.34  Aligned_cols=26  Identities=23%  Similarity=0.335  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...++|+|.+|+|||||.+.+.....
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~~~   54 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRNEF   54 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCCC
Confidence            45799999999999999999987654

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.51  E-value=0.0085  Score=50.50  Aligned_cols=25  Identities=28%  Similarity=0.279  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|+|+.|+||||||..+.....
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~   30 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALP   30 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            4899999999999999999987753

>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=95.51  E-value=0.0069  Score=48.55  Aligned_cols=27  Identities=30%  Similarity=0.398  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p   60 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGELEP   60 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCcC
Confidence            358999999999999999999887654

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=95.51  E-value=0.0089  Score=50.31  Aligned_cols=24  Identities=29%  Similarity=0.422  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .+++.|+|++|+|||+||.++...
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            356789999999999999999876

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=95.50  E-value=0.0091  Score=44.21  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|.++|.+|+|||||...+.+..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            568999999999999999998764

>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=95.50  E-value=0.0061  Score=48.32  Aligned_cols=26  Identities=38%  Similarity=0.583  Sum_probs=22.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||.+.+..-...
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl~~p   61 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTYLKP   61 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            48999999999999999999877653

>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=95.50  E-value=0.028  Score=47.31  Aligned_cols=59  Identities=14%  Similarity=0.296  Sum_probs=40.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc-----------C-CCC--CeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS-----------D-KLF--DQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~-----------~-~~f--~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      .-.++.|+|.+|+|||+||..+......           . +..  ..++|++....++...+.+ ++..++.+
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~  169 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGID  169 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCC
Confidence            3468999999999999999998876321           1 101  4688888887777766653 34555543

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=95.49  E-value=0.013  Score=47.73  Aligned_cols=26  Identities=23%  Similarity=0.309  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-+.|+|.+|+|||++|+.+.+....
T Consensus        30 ~~vll~G~~GtGKt~la~~i~~~~~~   55 (265)
T 2bjv_A           30 KPVLIIGERGTGKELIASRLHYLSSR   55 (265)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHTSTT
T ss_pred             CCEEEECCCCCcHHHHHHHHHHhcCc
Confidence            46789999999999999999987643

>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=95.47  E-value=0.0082  Score=49.30  Aligned_cols=24  Identities=29%  Similarity=0.468  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -.+++|+|+.|+|||||.+.+..-
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            358999999999999999999985

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.47  E-value=0.011  Score=48.38  Aligned_cols=27  Identities=15%  Similarity=0.308  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .-.+++|+|+.|+|||||.+.+.....
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCC
Confidence            346899999999999999999877654

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=95.47  E-value=0.01  Score=49.06  Aligned_cols=27  Identities=26%  Similarity=0.367  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~Gl~~p   73 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNAYEPA   73 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCC
Confidence            358999999999999999999877653

>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=95.46  E-value=0.008  Score=49.98  Aligned_cols=26  Identities=27%  Similarity=0.422  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..-+.++|++|+|||++|+.+.+...
T Consensus        50 ~~~vll~G~~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhC
Confidence            45688999999999999999998773

>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=95.44  E-value=0.016  Score=49.70  Aligned_cols=28  Identities=25%  Similarity=0.491  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+|+|+|.+|+|||||+..+.....
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~~l~  104 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGMHLI  104 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4577999999999999999999887654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=95.43  E-value=0.0093  Score=49.07  Aligned_cols=24  Identities=21%  Similarity=0.421  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++|+|..|+|||||.+.++....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~   27 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQV   27 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            589999999999999999988654

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=95.43  E-value=0.011  Score=48.53  Aligned_cols=27  Identities=26%  Similarity=0.309  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl~~p   59 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGLIEP   59 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCC
Confidence            358999999999999999999876543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.43  E-value=0.031  Score=52.89  Aligned_cols=24  Identities=33%  Similarity=0.452  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.++|++|+|||++|+.+.+...
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~  546 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIF  546 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            699999999999999999998863

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=95.41  E-value=0.015  Score=51.81  Aligned_cols=41  Identities=20%  Similarity=0.367  Sum_probs=30.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      ...+++|+|.+|+|||||++.+.......   ...+++.....+
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~---~G~V~l~g~D~~  332 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDTF  332 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEECCCTT
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhc---CCeEEEecCccc
Confidence            35699999999999999999999887654   334444433333

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.40  E-value=0.018  Score=48.62  Aligned_cols=30  Identities=23%  Similarity=0.325  Sum_probs=25.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ....+++|+|.+|+||||++..+.......
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~  132 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMANYYAEL  132 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            346799999999999999999998877654

>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=95.40  E-value=0.0078  Score=48.67  Aligned_cols=26  Identities=19%  Similarity=0.299  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|+.|+|||||.+.+..-..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   53 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERFYQ   53 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35899999999999999999987654

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=95.39  E-value=0.029  Score=44.36  Aligned_cols=28  Identities=21%  Similarity=0.317  Sum_probs=24.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~  141 (276)
                      ..|.+.|+.|+||||+++.+.......+
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~   31 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQLG   31 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            5799999999999999999999887653

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=95.39  E-value=0.011  Score=47.57  Aligned_cols=26  Identities=19%  Similarity=0.280  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.|.|.|..|+||||+++.+.....
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999998863

>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=95.39  E-value=0.0098  Score=49.79  Aligned_cols=27  Identities=30%  Similarity=0.480  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.-.+++|+|++|+|||||++.+..-.
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            344689999999999999999988654

>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=95.39  E-value=0.01  Score=46.03  Aligned_cols=25  Identities=24%  Similarity=0.392  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...++|+|.+|+|||||.+.+....
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcCC
Confidence            3578999999999999999998764

>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=95.35  E-value=0.011  Score=49.45  Aligned_cols=25  Identities=24%  Similarity=0.438  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .++|.|.|+.|+||||||..+....
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhC
Confidence            3589999999999999999998765

>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=95.34  E-value=0.032  Score=44.08  Aligned_cols=32  Identities=16%  Similarity=0.275  Sum_probs=26.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCe
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQ  145 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~  145 (276)
                      ...|.+.|+.|+||||+++.+.......+ +..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~-~~v   37 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRERG-IEV   37 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTTT-CCE
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHcC-CCc
Confidence            35899999999999999999998887552 444

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.34  E-value=0.0062  Score=50.68  Aligned_cols=27  Identities=11%  Similarity=0.348  Sum_probs=20.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +..+|+|.|..|+||||+|+.+.....
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999887543

>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=95.33  E-value=0.029  Score=45.14  Aligned_cols=31  Identities=19%  Similarity=0.433  Sum_probs=26.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD  144 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~  144 (276)
                      ...|.|.|++|+||||+++.+........ +.
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~~-~~   57 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQNG-ID   57 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHTT-CC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcC-CC
Confidence            46899999999999999999999887652 54

>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=95.31  E-value=0.01  Score=44.57  Aligned_cols=23  Identities=13%  Similarity=0.349  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ..|+|+|.+|+|||||...+.+.
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            47899999999999999999864

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.30  E-value=0.011  Score=50.10  Aligned_cols=26  Identities=27%  Similarity=0.452  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++|.|+|+.|+|||||+..+.....
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHCC
Confidence            35899999999999999999998764

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=95.29  E-value=0.0098  Score=48.63  Aligned_cols=26  Identities=23%  Similarity=0.284  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.+++|+|+.|+|||||.+.+..-..
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCC
Confidence            45899999999999999999987653

>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=95.27  E-value=0.0088  Score=48.60  Aligned_cols=25  Identities=28%  Similarity=0.462  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|+|+.|+|||||.+.+..-..
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            4899999999999999999987654

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=95.26  E-value=0.0092  Score=48.60  Aligned_cols=27  Identities=22%  Similarity=0.415  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p   57 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGIHRP   57 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            358999999999999999999877653

>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=95.25  E-value=0.011  Score=48.79  Aligned_cols=26  Identities=31%  Similarity=0.471  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -.++.|+|.+|+|||||+..+.....
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            35899999999999999999887554

>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=95.24  E-value=0.016  Score=49.68  Aligned_cols=27  Identities=33%  Similarity=0.332  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaGl~~p   56 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAGFEQP   56 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCCCC
Confidence            358999999999999999999887654

>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=95.23  E-value=0.013  Score=49.10  Aligned_cols=27  Identities=26%  Similarity=0.239  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..++|.|+|+.|+||||||..+.....
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~~   35 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKILP   35 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhCC
Confidence            356899999999999999999987753

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=95.23  E-value=0.011  Score=50.78  Aligned_cols=26  Identities=38%  Similarity=0.520  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.+.++|++|+|||++|+.+.+...
T Consensus        51 ~~~vll~GppGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           51 KSNILLIGPTGSGKTLLAETLARLLD   76 (363)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            45789999999999999999998873

>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=95.20  E-value=0.015  Score=47.10  Aligned_cols=26  Identities=31%  Similarity=0.452  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..++.+.|.||+||||++..+.....
T Consensus        14 ~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           14 SMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            56888899999999999999987765

>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=95.20  E-value=0.014  Score=44.80  Aligned_cols=28  Identities=11%  Similarity=0.338  Sum_probs=23.4

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .++...|+++|.+|+|||||...+.+..
T Consensus        20 ~~~~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 1svi_A           20 EGGLPEIALAGRSNVGKSSFINSLINRK   47 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHTC-
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3456789999999999999999998654

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=95.18  E-value=0.015  Score=46.62  Aligned_cols=26  Identities=27%  Similarity=0.355  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...+|+|.|+.|+||||+++.+....
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            35689999999999999999988754

>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=95.15  E-value=0.011  Score=49.42  Aligned_cols=28  Identities=21%  Similarity=0.265  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+++|+|+.|+|||||++.+..-...
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~gl~~p  106 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFRFYDI  106 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTTSSCC
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcCCCC
Confidence            3458999999999999999999876654

>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=95.13  E-value=0.025  Score=48.64  Aligned_cols=43  Identities=26%  Similarity=0.309  Sum_probs=33.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      -.++.|+|.+|+||||||..+.......  -..++|++.....+.
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~--g~~vlyi~~E~s~~~  116 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKA--GGTCAFIDAEHALDP  116 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHC--CCeEEEEECCCChhH
Confidence            4589999999999999999988776543  246788887665543

>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=0.016  Score=50.07  Aligned_cols=27  Identities=26%  Similarity=0.203  Sum_probs=23.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .....++|+|++|+|||||++.+....
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            445699999999999999999999754

>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=95.10  E-value=0.019  Score=43.71  Aligned_cols=26  Identities=23%  Similarity=0.364  Sum_probs=22.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +....|+++|.+|+|||||...+.+.
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhcC
Confidence            45678999999999999999998765

>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=95.09  E-value=0.0092  Score=45.66  Aligned_cols=22  Identities=36%  Similarity=0.499  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|+|+|.+|+|||||...+...
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            5899999999999999998763

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=95.07  E-value=0.014  Score=44.58  Aligned_cols=24  Identities=13%  Similarity=0.321  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ...|+++|.+|+|||||...+.+.
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            357999999999999999999874

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.05  E-value=0.013  Score=50.52  Aligned_cols=26  Identities=27%  Similarity=0.489  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+.++|++|+|||++|+.+.+...
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l~   97 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHLD   97 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhC
Confidence            35688999999999999999998773

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=95.05  E-value=0.015  Score=51.56  Aligned_cols=48  Identities=8%  Similarity=-0.080  Sum_probs=32.7

Q ss_pred             ceeCCCCCHHHHHHHHHHhhC--CCCCChhHHHHHHHHHHHc-CCCcHHHHHHH
Q 041612          213 NFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQSIARDVAKEC-AGLPVSIVTIA  263 (276)
Q Consensus       213 ~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~~~~~~~i~~~c-~G~PLai~~i~  263 (276)
                      .+++.+++.++..+++...+.  ....++   +....|+..+ .|.|..+..+.
T Consensus       360 ~~~~~~~~~~e~~~iL~~~~~~~~~~~~~---~~~~~i~~~a~~g~~r~a~~ll  410 (456)
T 2c9o_A          360 IIRTMLYTPQEMKQIIKIRAQTEGINISE---EALNHLGEIGTKTTLRYSVQLL  410 (456)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBCH---HHHHHHHHHHHHSCHHHHHHTH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHhCCCCCH---HHHHHHHHHccCCCHHHHHHHH
Confidence            478999999999999987763  222222   3456777777 78887655543

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=95.04  E-value=0.017  Score=44.26  Aligned_cols=26  Identities=23%  Similarity=0.115  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+++|.+|+|||||...+.+..
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34689999999999999999998764

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=95.04  E-value=0.03  Score=50.19  Aligned_cols=24  Identities=33%  Similarity=0.476  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -+.|+|++|+|||+||+.+.+...
T Consensus        66 GvLL~GppGtGKTtLaraIa~~~~   89 (499)
T 2dhr_A           66 GVLLVGPPGVGKTHLARAVAGEAR   89 (499)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            489999999999999999998764

>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=95.04  E-value=0.015  Score=44.07  Aligned_cols=33  Identities=21%  Similarity=0.256  Sum_probs=25.1

Q ss_pred             HHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          104 ILSALED-PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       104 l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +.+.+.. .....|+++|.+|+|||||...+.+.
T Consensus         8 ~~~~~~~~~~~~~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A            8 MFDKLWGSNKELRILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             HHGGGTTCSSCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             HHHHhcCCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            3333444 55678999999999999999988743

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.03  E-value=0.051  Score=46.11  Aligned_cols=51  Identities=14%  Similarity=0.083  Sum_probs=37.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK  167 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  167 (276)
                      -.++.|.|.+|+||||||..+.......  =..+.|++.  ..+..++...++..
T Consensus        46 G~LiiIaG~pG~GKTt~al~ia~~~a~~--g~~Vl~fSl--Ems~~ql~~Rlls~   96 (338)
T 4a1f_A           46 GSLVIIGARPSMGKTSLMMNMVLSALND--DRGVAVFSL--EMSAEQLALRALSD   96 (338)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHT--TCEEEEEES--SSCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEEeC--CCCHHHHHHHHHHH
Confidence            3589999999999999999998887653  245667665  45566666666543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=95.03  E-value=0.024  Score=42.69  Aligned_cols=27  Identities=26%  Similarity=0.274  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +....|+++|.+|+|||||...+.+..
T Consensus         6 ~~~~~i~v~G~~~~GKssl~~~l~~~~   32 (178)
T 2lkc_A            6 ERPPVVTIMGHVDHGKTTLLDAIRHSK   32 (178)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHTTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            345689999999999999999998654

>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=95.02  E-value=0.024  Score=46.31  Aligned_cols=34  Identities=29%  Similarity=0.346  Sum_probs=27.7

Q ss_pred             HHHHhhcCC-C-ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          103 NILSALEDP-D-VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       103 ~l~~~L~~~-~-~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -+..+|... . ...+.++|++|+|||.+|..+.+.
T Consensus        92 ~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            566677654 2 457999999999999999999885

>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=95.00  E-value=0.016  Score=42.92  Aligned_cols=23  Identities=30%  Similarity=0.580  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+....
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58999999999999999998764

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=94.99  E-value=0.037  Score=47.19  Aligned_cols=34  Identities=24%  Similarity=0.397  Sum_probs=27.4

Q ss_pred             HHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          105 LSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       105 ~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+.....+++.+.|.||+||||+|..+.....
T Consensus        10 ~~~l~~~~~~i~~~~gkGGvGKTt~a~~lA~~la   43 (348)
T 3io3_A           10 ESIVQHDSLKWIFVGGKGGVGKTTTSSSVAVQLA   43 (348)
T ss_dssp             HHHHTCTTCSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHhcCCCcEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            3445556678999999999999999999887766

>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=94.98  E-value=0.021  Score=49.00  Aligned_cols=28  Identities=21%  Similarity=0.379  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+++|+|+.|+|||||.+.+..-...
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~GL~~p   80 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNLLERP   80 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhcCCCC
Confidence            3458999999999999999999877654

>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=94.97  E-value=0.021  Score=49.31  Aligned_cols=27  Identities=26%  Similarity=0.240  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|++|+|||||.+.+..-...
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaGl~~p   55 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAGLETI   55 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEEcCCCchHHHHHHHHHcCCCC
Confidence            358999999999999999999887654

>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=94.97  E-value=0.021  Score=48.91  Aligned_cols=27  Identities=26%  Similarity=0.290  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~~p   55 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAGIYKP   55 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEEcCCCchHHHHHHHHHCCCCC
Confidence            358999999999999999999877653

>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=94.95  E-value=0.019  Score=45.11  Aligned_cols=27  Identities=22%  Similarity=0.116  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .....|.++|.+|+|||||...+.+..
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345689999999999999999998765

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=94.95  E-value=0.012  Score=48.15  Aligned_cols=25  Identities=32%  Similarity=0.343  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            3589999999999999999998765

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=94.95  E-value=0.022  Score=48.76  Aligned_cols=27  Identities=33%  Similarity=0.469  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaGl~~p   67 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAGLERP   67 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCC
Confidence            358999999999999999999877653

>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=94.93  E-value=0.014  Score=45.53  Aligned_cols=26  Identities=27%  Similarity=0.245  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -+.|.|.|++|+||||||..+.....
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~   59 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH   59 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC
Confidence            46789999999999999999987653

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.93  E-value=0.046  Score=42.59  Aligned_cols=26  Identities=19%  Similarity=0.388  Sum_probs=23.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .|+|-|..|+||||.++.+.+....+
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~   27 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKR   27 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            57899999999999999999988765

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=94.92  E-value=0.022  Score=48.87  Aligned_cols=27  Identities=30%  Similarity=0.386  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~~p   55 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAGIYKP   55 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCCCC
Confidence            458999999999999999999877653

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.91  E-value=0.022  Score=43.51  Aligned_cols=28  Identities=18%  Similarity=0.226  Sum_probs=23.4

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .......|+++|.+|+|||||...+.+.
T Consensus        12 ~~~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           12 FNHQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             HTTSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             cCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            3445568999999999999999999854

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=94.90  E-value=0.011  Score=47.26  Aligned_cols=25  Identities=24%  Similarity=0.165  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ...+|+|.|+.|+|||||++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            3468999999999999999998775

>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding, HYDR magnesium, metal-binding, nucleotide-binding, potassium, TR processing; HET: GDP FON; 3.20A {Nostoc SP}

Probab=94.90  E-value=0.042  Score=48.75  Aligned_cols=23  Identities=22%  Similarity=0.323  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+|+|.+|+|||||...+.+..
T Consensus       226 kV~ivG~~nvGKSSLln~L~~~~  248 (462)
T 3geh_A          226 KVAIVGRPNVGKSSLLNAWSQSD  248 (462)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHhCCC
Confidence            48999999999999999988764

>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=94.89  E-value=0.023  Score=49.00  Aligned_cols=27  Identities=26%  Similarity=0.261  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~~p   55 (372)
T 1g29_1           29 GEFMILLGPSGCGKTTTLRMIAGLEEP   55 (372)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCcHHHHHHHHHHcCCCC
Confidence            358999999999999999999877653

>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=94.88  E-value=0.018  Score=42.83  Aligned_cols=25  Identities=16%  Similarity=0.408  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|.++|.+|+|||||...+.+..
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            3468999999999999999998764

>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=94.88  E-value=0.016  Score=49.73  Aligned_cols=27  Identities=22%  Similarity=0.395  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...++|+|.+|+|||||++.+......
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~  196 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNT  196 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTC
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            458999999999999999999887654

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=94.88  E-value=0.04  Score=46.72  Aligned_cols=46  Identities=20%  Similarity=0.357  Sum_probs=32.3

Q ss_pred             hhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc
Q 041612          107 ALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN  154 (276)
Q Consensus       107 ~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~  154 (276)
                      .+.....+++.+.|.||+||||+|..+.......+  ..+.-++....
T Consensus        10 ~l~~~~~~i~~~sgkGGvGKTt~a~~lA~~la~~g--~~vllid~D~~   55 (334)
T 3iqw_A           10 ILDQRSLRWIFVGGKGGVGKTTTSCSLAIQLAKVR--RSVLLLSTDPA   55 (334)
T ss_dssp             HHHCTTCCEEEEECSTTSSHHHHHHHHHHHHTTSS--SCEEEEECCSS
T ss_pred             HhcCCCeEEEEEeCCCCccHHHHHHHHHHHHHhCC--CcEEEEECCCC
Confidence            34445577888899999999999999888776542  23445554433

>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=94.84  E-value=0.019  Score=43.74  Aligned_cols=25  Identities=24%  Similarity=0.379  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+.+|+|..|+|||||...++.-.
T Consensus        26 ~g~~~i~G~NGsGKStll~ai~~~l   50 (182)
T 3kta_A           26 KGFTAIVGANGSGKSNIGDAILFVL   50 (182)
T ss_dssp             SSEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHH
Confidence            3489999999999999999987654

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=94.84  E-value=0.037  Score=46.98  Aligned_cols=29  Identities=21%  Similarity=0.413  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ....+++|+|.+|+|||||.+.+......
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~~~   81 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLLTA   81 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhhhh
Confidence            34569999999999999999999876543

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=94.83  E-value=0.041  Score=43.82  Aligned_cols=31  Identities=23%  Similarity=0.392  Sum_probs=25.8

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .......|.+.|+.|+||||+++.+......
T Consensus        17 ~~~~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           17 QGPGSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             --CCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3345678999999999999999999988765

>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=94.81  E-value=0.024  Score=48.78  Aligned_cols=27  Identities=30%  Similarity=0.291  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaGl~~p   63 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAGLEEP   63 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCC
Confidence            458999999999999999999876643

>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=94.81  E-value=0.02  Score=48.91  Aligned_cols=27  Identities=33%  Similarity=0.304  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaGl~~p   52 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAGFHVP   52 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCccHHHHHHHHHcCCCC
Confidence            358999999999999999999877654

>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=94.79  E-value=0.0098  Score=48.55  Aligned_cols=27  Identities=15%  Similarity=0.239  Sum_probs=23.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .....|+|.|..|+||||+++.+....
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~~l   48 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQLC   48 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHhc
Confidence            356799999999999999999988765

>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=94.79  E-value=0.017  Score=43.68  Aligned_cols=24  Identities=25%  Similarity=0.255  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+|+|.+|+|||||...+....
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~~   28 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGRE   28 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999998754

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=94.79  E-value=0.014  Score=49.35  Aligned_cols=25  Identities=20%  Similarity=0.421  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .-+.++|++|+|||+||+.+.+...
T Consensus        47 ~~vll~G~pGtGKT~la~~la~~~~   71 (331)
T 2r44_A           47 GHILLEGVPGLAKTLSVNTLAKTMD   71 (331)
T ss_dssp             CCEEEESCCCHHHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHhC
Confidence            3688999999999999999988664

>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=94.78  E-value=0.018  Score=42.71  Aligned_cols=24  Identities=25%  Similarity=0.434  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+++|.+|+|||||...+.+..
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            468999999999999999998764

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.77  E-value=0.021  Score=44.02  Aligned_cols=26  Identities=23%  Similarity=0.009  Sum_probs=21.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++.|+|+.|+||||++..+..+...
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~   29 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKL   29 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            47889999999999999777766543

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=94.76  E-value=0.013  Score=52.66  Aligned_cols=25  Identities=20%  Similarity=0.355  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .-+.++|++|+|||+||+.+.+...
T Consensus        42 ~~VLL~GpPGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           42 ESVFLLGPPGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             CEEEEECCSSSSHHHHHHHGGGGBS
T ss_pred             CeeEeecCchHHHHHHHHHHHHHHh
Confidence            3688999999999999999998774

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=94.76  E-value=0.043  Score=43.94  Aligned_cols=41  Identities=29%  Similarity=0.490  Sum_probs=29.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI  157 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~  157 (276)
                      .|+|.|.||+||||+|..+.......+  ..+.-++.....+.
T Consensus         2 kI~vs~kGGvGKTt~a~~LA~~la~~g--~~VlliD~D~~~~l   42 (254)
T 3kjh_A            2 KLAVAGKGGVGKTTVAAGLIKIMASDY--DKIYAVDGDPDSCL   42 (254)
T ss_dssp             EEEEECSSSHHHHHHHHHHHHHHTTTC--SCEEEEEECTTSCH
T ss_pred             EEEEecCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCcCh
Confidence            467799999999999999998887653  34555555543443

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=94.76  E-value=0.017  Score=52.38  Aligned_cols=27  Identities=37%  Similarity=0.523  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+.++|++|+||||||+.+.....
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~~l~  133 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAKSLG  133 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456899999999999999999998874

>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=94.75  E-value=0.021  Score=43.96  Aligned_cols=33  Identities=15%  Similarity=0.202  Sum_probs=25.5

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +.+.+.......|+|+|.+|+|||||...+...
T Consensus        20 ~~~~~~~~~~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           20 LFSRIFGKKQMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             GGGGTTTTSCEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             HHHHhccCCccEEEEECCCCCCHHHHHHHHHhC
Confidence            344444555668999999999999999998653

>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=94.74  E-value=0.02  Score=43.81  Aligned_cols=24  Identities=29%  Similarity=0.537  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|.++|.+|+|||||+..+....
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            478999999999999999998764

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=94.74  E-value=0.021  Score=45.69  Aligned_cols=26  Identities=31%  Similarity=0.240  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -..++|.|++|+||||+|+.+.....
T Consensus         8 ~~~~~~~G~pGsGKsT~a~~L~~~~g   33 (230)
T 3gmt_A            8 HMRLILLGAPGAGKGTQANFIKEKFG   33 (230)
T ss_dssp             -CEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             ccceeeECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999988764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.73  E-value=0.02  Score=54.11  Aligned_cols=35  Identities=29%  Similarity=0.472  Sum_probs=28.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .++..+......-+.++|++|+|||++|+.+.+..
T Consensus       191 ~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l  225 (758)
T 3pxi_A          191 RVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQI  225 (758)
T ss_dssp             HHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            56666655556678999999999999999999886

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=94.72  E-value=0.021  Score=43.63  Aligned_cols=26  Identities=15%  Similarity=0.247  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+++|.+|+|||||...+.+..
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            45689999999999999999998775

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=94.71  E-value=0.017  Score=47.99  Aligned_cols=27  Identities=30%  Similarity=0.398  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl~~p   90 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGELEP   90 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTSSCE
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            458999999999999999999877653

>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=94.68  E-value=0.019  Score=42.58  Aligned_cols=23  Identities=30%  Similarity=0.631  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         5 ki~v~G~~~~GKssli~~l~~~~   27 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58999999999999999998754

>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=94.67  E-value=0.021  Score=42.31  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999997654

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.67  E-value=0.02  Score=45.07  Aligned_cols=24  Identities=21%  Similarity=0.397  Sum_probs=21.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+|+|.|+.|+||||+++.+....
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            579999999999999999987754

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=94.67  E-value=0.023  Score=46.28  Aligned_cols=37  Identities=24%  Similarity=0.526  Sum_probs=27.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      ++|+|.|-||+||||+|..+......++  ..+.-++..
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~G--~~VlliD~D   38 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAMG--KTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTT--CCEEEEEEC
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHCC--CcEEEEcCC
Confidence            5788899999999999999988876542  234445443

>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=94.67  E-value=0.019  Score=43.00  Aligned_cols=25  Identities=36%  Similarity=0.408  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~~   28 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGKQ   28 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC-
T ss_pred             EEEEEEECCCCccHHHHHHHHhcCC
Confidence            3468999999999999999987654

>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=94.66  E-value=0.02  Score=42.44  Aligned_cols=24  Identities=25%  Similarity=0.488  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|+++|.+|+|||||...+.+..
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            368999999999999999988664

>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=94.66  E-value=0.023  Score=42.75  Aligned_cols=26  Identities=27%  Similarity=0.507  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+++|.+|+|||||...+.+..
T Consensus         8 ~~~~i~v~G~~~~GKssli~~l~~~~   33 (181)
T 2fn4_A            8 ETHKLVVVGGGGVGKSALTIQFIQSY   33 (181)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhCc
Confidence            34579999999999999999998764

>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=94.65  E-value=0.02  Score=42.59  Aligned_cols=23  Identities=17%  Similarity=0.291  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58899999999999999988765

>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=94.64  E-value=0.018  Score=49.19  Aligned_cols=27  Identities=33%  Similarity=0.356  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus        31 Ge~~~llGpnGsGKSTLLr~iaGl~~p   57 (353)
T 1oxx_K           31 GERFGILGPSGAGKTTFMRIIAGLDVP   57 (353)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCC
Confidence            358999999999999999999876643

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=94.64  E-value=0.023  Score=45.23  Aligned_cols=27  Identities=19%  Similarity=0.087  Sum_probs=23.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.|.+.|.||+||||+|..+......+
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~   33 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQ   33 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            357888999999999999988887655

>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=94.63  E-value=0.012  Score=49.89  Aligned_cols=24  Identities=21%  Similarity=0.340  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      -+.|+|.+|+|||+||+.+.+...
T Consensus        47 ~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           47 GVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             CEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             eEEEECCCCccHHHHHHHHHHhCc
Confidence            489999999999999999998764

>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=94.63  E-value=0.022  Score=42.47  Aligned_cols=25  Identities=24%  Similarity=0.268  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|+++|.+|+|||||...+.+..
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3478999999999999999998764

>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=94.62  E-value=0.028  Score=43.51  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ....|+++|.+|+|||||...+.+.
T Consensus        24 ~~~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           24 KTGKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            3457899999999999999998753

>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=94.62  E-value=0.02  Score=42.60  Aligned_cols=24  Identities=17%  Similarity=0.273  Sum_probs=21.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|.++|.+|+|||||...+.+..
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468999999999999999998765

>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=94.61  E-value=0.02  Score=43.64  Aligned_cols=25  Identities=24%  Similarity=0.242  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus         7 ~~ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            7 KCKIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcCC
Confidence            4568999999999999999998764

>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=94.60  E-value=0.023  Score=51.29  Aligned_cols=27  Identities=19%  Similarity=0.428  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|.++|++|.||||+|+.+.....
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999987664

>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=94.59  E-value=0.023  Score=42.84  Aligned_cols=26  Identities=27%  Similarity=0.378  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+++|.+|+|||||...+.+..
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhCc
Confidence            35578999999999999999988764

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=94.59  E-value=0.019  Score=48.42  Aligned_cols=26  Identities=27%  Similarity=0.342  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..++++|.|+.|.|||||.+.+....
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhhc
Confidence            36789999999999999999998764

>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=94.58  E-value=0.024  Score=46.84  Aligned_cols=28  Identities=29%  Similarity=0.562  Sum_probs=24.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++|+|.|.||+||||+|..+......+
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~La~~   29 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAALAEM   29 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHHHHHC
Confidence            4688899999999999999988887654

>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=94.57  E-value=0.12  Score=44.26  Aligned_cols=28  Identities=25%  Similarity=0.404  Sum_probs=22.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++.++|+|+|.+|+|||||.+.+.+...
T Consensus       177 ~~~~~V~lvG~~naGKSTLln~L~~~~~  204 (364)
T 2qtf_A          177 NNIPSIGIVGYTNSGKTSLFNSLTGLTQ  204 (364)
T ss_dssp             --CCEEEEECBTTSSHHHHHHHHHCC--
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHCCCc
Confidence            4577899999999999999999887643

>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=94.56  E-value=0.024  Score=42.24  Aligned_cols=24  Identities=21%  Similarity=0.315  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+++|.+|+|||||...+.+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVEDK   27 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            468999999999999999988654

>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=94.55  E-value=0.022  Score=42.51  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      -.|+++|.+|+|||||...+..
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            4689999999999999999864

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.55  E-value=0.021  Score=42.61  Aligned_cols=24  Identities=25%  Similarity=0.610  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|.++|.+|+|||||...+.+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKGT   27 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            368999999999999999998753

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=94.53  E-value=0.74  Score=39.15  Aligned_cols=27  Identities=19%  Similarity=0.314  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+...++++|.+|+|||||...+....
T Consensus       165 ~~~~~v~lvG~~gvGKSTLin~L~~~~  191 (357)
T 2e87_A          165 LEIPTVVIAGHPNVGKSTLLKALTTAK  191 (357)
T ss_dssp             SSSCEEEEECSTTSSHHHHHHHHCSSC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            356789999999999999999987654

>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=94.53  E-value=0.022  Score=42.85  Aligned_cols=25  Identities=24%  Similarity=0.403  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~~~   31 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVTNK   31 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcCC
Confidence            4578999999999999999998654

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=94.51  E-value=0.024  Score=42.70  Aligned_cols=25  Identities=28%  Similarity=0.323  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|+++|.+|+|||||...+.+..
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~~   30 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQET   30 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhCc
Confidence            3468999999999999999987654

>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=94.51  E-value=0.022  Score=43.58  Aligned_cols=25  Identities=24%  Similarity=0.214  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|+|+|.+|+|||||...+.+..
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHSS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            4478999999999999998887664

>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=94.51  E-value=0.022  Score=49.39  Aligned_cols=24  Identities=33%  Similarity=0.594  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++|.|.|+.|+||||||..+....
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHC
Confidence            589999999999999999998765

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=94.49  E-value=0.026  Score=48.20  Aligned_cols=28  Identities=25%  Similarity=0.397  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+++|+|..|+|||||.+.+.+....
T Consensus        70 ~Gq~~gIiG~nGaGKTTLl~~I~g~~~~   97 (347)
T 2obl_A           70 IGQRIGIFAGSGVGKSTLLGMICNGASA   97 (347)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            4458999999999999999999998754

>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=94.48  E-value=0.029  Score=41.87  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||...+....
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~~   31 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVGE   31 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcCC
Confidence            3578999999999999999997654

>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=94.45  E-value=0.021  Score=43.53  Aligned_cols=27  Identities=19%  Similarity=0.218  Sum_probs=22.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .....|.++|.+|+|||||...+.+..
T Consensus        16 ~~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           16 ERELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            455689999999999999999998665

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.44  E-value=0.027  Score=48.11  Aligned_cols=27  Identities=22%  Similarity=0.329  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +..+|+|+|.+|+|||||...+.....
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~~   99 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKMLT   99 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            467999999999999999999987543

>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=94.43  E-value=0.024  Score=42.13  Aligned_cols=24  Identities=21%  Similarity=0.285  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+++|.+|+|||||...+.+..
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999998653

>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=94.42  E-value=0.024  Score=43.47  Aligned_cols=25  Identities=32%  Similarity=0.364  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|.++|.+|+|||||...+.+..
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhCC
Confidence            4578999999999999999988764

>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=94.42  E-value=0.026  Score=43.43  Aligned_cols=25  Identities=24%  Similarity=0.279  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus        23 ~~ki~~vG~~~vGKSsli~~l~~~~   47 (190)
T 1m2o_B           23 HGKLLFLGLDNAGKTTLLHMLKNDR   47 (190)
T ss_dssp             -CEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999998743

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=94.41  E-value=0.023  Score=50.04  Aligned_cols=27  Identities=26%  Similarity=0.420  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+-+.++|++|+|||++|+.+......
T Consensus        50 ~~~iLl~GppGtGKT~lar~lA~~l~~   76 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIARRLAKLANA   76 (444)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            456899999999999999999988754

>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=94.39  E-value=0.029  Score=48.06  Aligned_cols=27  Identities=15%  Similarity=0.208  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .-.+++|+|+.|+|||||.+.+.....
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~  148 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLN  148 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccc
Confidence            345999999999999999999877654

>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=94.37  E-value=0.023  Score=42.22  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -.|+++|.+|+|||||...+.+.
T Consensus         3 ~ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            3 YKVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             CEEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEEECCCCCCHHHHHHHHcCc
Confidence            36899999999999999988643

>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=94.36  E-value=0.026  Score=43.17  Aligned_cols=25  Identities=36%  Similarity=0.230  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||.+.+.+..
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhhc
Confidence            4578999999999999998776543

>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=94.35  E-value=0.025  Score=42.97  Aligned_cols=24  Identities=25%  Similarity=0.447  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|+++|.+|+|||||...+.+..
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            468999999999999999998765

>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=94.34  E-value=0.026  Score=42.42  Aligned_cols=25  Identities=28%  Similarity=0.348  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||...+.+..
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCC
Confidence            4579999999999999999998765

>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=94.33  E-value=0.028  Score=42.56  Aligned_cols=25  Identities=32%  Similarity=0.541  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus        18 ~~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           18 TYKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            4578999999999999999998764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.32  E-value=0.043  Score=43.87  Aligned_cols=49  Identities=24%  Similarity=0.312  Sum_probs=31.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEI  164 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  164 (276)
                      -.++.|.|.+|+|||++|.++..+...+. -..++|++..  .+...+.+.+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~-~~~v~~~s~E--~~~~~~~~~~   78 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEY-GEPGVFVTLE--ERARDLRREM   78 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS--SCHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCceeeccc--CCHHHHHHHH
Confidence            45899999999999999998765532210 2345565553  3455555443

>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=94.31  E-value=0.025  Score=49.08  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCC
Confidence            4589999999999999999998754

>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=94.30  E-value=0.026  Score=42.87  Aligned_cols=26  Identities=23%  Similarity=0.287  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|.++|.+|+|||||...+.+...
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~~~   35 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEKKF   35 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCCC
Confidence            45789999999999999999987643

>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=94.30  E-value=0.021  Score=43.15  Aligned_cols=24  Identities=25%  Similarity=0.303  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|.++|.+|+|||+|...+.+..
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~~~   31 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLTGS   31 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            468999999999999999988754

>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=94.28  E-value=0.026  Score=43.23  Aligned_cols=25  Identities=32%  Similarity=0.440  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            4579999999999999999988754

>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=94.28  E-value=0.032  Score=42.99  Aligned_cols=26  Identities=31%  Similarity=0.474  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+++|.+|+|||||...+.+..
T Consensus        27 ~~~ki~v~G~~~vGKSsli~~l~~~~   52 (196)
T 2atv_A           27 AEVKLAIFGRAGVGKSALVVRFLTKR   52 (196)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34579999999999999999998764

>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=94.27  E-value=0.029  Score=43.27  Aligned_cols=24  Identities=29%  Similarity=0.358  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ...|+|+|.+|+|||||...+...
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            346999999999999999998753

>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=94.27  E-value=0.027  Score=42.94  Aligned_cols=25  Identities=20%  Similarity=0.207  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        11 ~~ki~v~G~~~~GKSsli~~l~~~~   35 (195)
T 3bc1_A           11 LIKFLALGDSGVGKTSVLYQYTDGK   35 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999998754

>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=94.26  E-value=0.023  Score=43.00  Aligned_cols=25  Identities=20%  Similarity=0.355  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~~   30 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEGQ   30 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            4578999999999999999998654

>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=94.26  E-value=0.027  Score=42.33  Aligned_cols=24  Identities=25%  Similarity=0.234  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+++|.+|+|||||...+.+..
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~~   38 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYDS   38 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999998654

>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=94.25  E-value=0.027  Score=42.63  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|+++|.+|+|||||...+.+..
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~~   29 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTNA   29 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            368999999999999999988654

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=94.25  E-value=0.036  Score=42.53  Aligned_cols=26  Identities=12%  Similarity=0.263  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..-.|+|+|.+|+|||||...+.+..
T Consensus         6 ~~~ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            6 SSYKTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHhCc
Confidence            34578999999999999999998774

>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=94.24  E-value=0.018  Score=44.89  Aligned_cols=30  Identities=13%  Similarity=0.147  Sum_probs=23.6

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.......|+|+|.+|+|||||.+.+....
T Consensus        21 ~~~~~~~~v~lvG~~g~GKSTLl~~l~g~~   50 (210)
T 1pui_A           21 LPSDTGIEVAFAGRSNAGKSSALNTLTNQK   50 (210)
T ss_dssp             SSCSCSEEEEEEECTTSSHHHHHTTTCCC-
T ss_pred             CCCCCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            444455689999999999999999887554

>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=94.24  E-value=0.029  Score=49.91  Aligned_cols=29  Identities=17%  Similarity=0.328  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ....+|.++|++|+||||+++.+......
T Consensus        37 ~~~~~IvlvGlpGsGKSTia~~La~~l~~   65 (469)
T 1bif_A           37 NCPTLIVMVGLPARGKTYISKKLTRYLNF   65 (469)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            34568999999999999999999877653

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=94.22  E-value=0.032  Score=43.60  Aligned_cols=27  Identities=19%  Similarity=0.209  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..+|+|.|+.|+||||+++.+......
T Consensus         6 ~~iI~i~g~~GsGk~ti~~~la~~lg~   32 (201)
T 3fdi_A            6 QIIIAIGREFGSGGHLVAKKLAEHYNI   32 (201)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHhCc
Confidence            358999999999999999999887754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=94.22  E-value=0.025  Score=48.50  Aligned_cols=26  Identities=23%  Similarity=0.403  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..++|+|+.|+|||||.+.+......
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~~~~  201 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQEIPF  201 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTTSCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            48999999999999999999987754

>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=94.22  E-value=0.058  Score=45.84  Aligned_cols=28  Identities=25%  Similarity=0.363  Sum_probs=23.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+..+++|+|.+|+|||||+..+.....
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~~   81 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLLI   81 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4567999999999999999999876654

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.21  E-value=0.023  Score=45.36  Aligned_cols=28  Identities=18%  Similarity=0.325  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -..|.|.|+.|+||||+++.+.......
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l~~~   52 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRLQER   52 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            4589999999999999999999887643

>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=94.21  E-value=0.025  Score=43.05  Aligned_cols=24  Identities=21%  Similarity=0.286  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+++|.+|+|||||...+.+..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~~   25 (190)
T 2cxx_A            2 ATIIFAGRSNVGKSTLIYRLTGKK   25 (190)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHSCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCcC
Confidence            358999999999999999988764

>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=94.20  E-value=0.028  Score=44.57  Aligned_cols=27  Identities=19%  Similarity=0.362  Sum_probs=23.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .....|+++|.+|+|||||...+.+..
T Consensus        27 ~~~~kI~vvG~~~vGKSsLin~l~~~~   53 (228)
T 2qu8_A           27 PHKKTIILSGAPNVGKSSFMNIVSRAN   53 (228)
T ss_dssp             TTSEEEEEECSTTSSHHHHHHHHTTTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345789999999999999999987763

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=94.18  E-value=0.066  Score=46.86  Aligned_cols=30  Identities=17%  Similarity=0.164  Sum_probs=25.0

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...-.+++|+|+.|+|||||.+.+......
T Consensus       164 ~~~ggii~I~GpnGSGKTTlL~allg~l~~  193 (418)
T 1p9r_A          164 KRPHGIILVTGPTGSGKSTTLYAGLQELNS  193 (418)
T ss_dssp             TSSSEEEEEECSTTSCHHHHHHHHHHHHCC
T ss_pred             HhcCCeEEEECCCCCCHHHHHHHHHhhcCC
Confidence            344568999999999999999999887654

>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=94.18  E-value=0.029  Score=42.48  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||...+.+..
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhCC
Confidence            4578999999999999999998764

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=94.18  E-value=0.028  Score=47.03  Aligned_cols=25  Identities=24%  Similarity=0.303  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..|.|+|.+|+|||++|+.+.+...
T Consensus        26 ~~vLi~Ge~GtGKt~lAr~i~~~~~   50 (304)
T 1ojl_A           26 ATVLIHGDSGTGKELVARALHACSA   50 (304)
T ss_dssp             SCEEEESCTTSCHHHHHHHHHHHSS
T ss_pred             CcEEEECCCCchHHHHHHHHHHhCc
Confidence            4578999999999999999998654

>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=94.17  E-value=0.041  Score=47.38  Aligned_cols=28  Identities=14%  Similarity=0.286  Sum_probs=23.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..-.+++|+|+.|+|||||.+.+.....
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            3456899999999999999999887654

>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=94.15  E-value=0.03  Score=42.31  Aligned_cols=25  Identities=24%  Similarity=0.207  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|+++|.+|+|||||...+.+..
T Consensus         8 ~~ki~v~G~~~~GKssl~~~~~~~~   32 (182)
T 3bwd_D            8 FIKCVTVGDGAVGKTCLLISYTSNT   32 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999988654

>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=94.15  E-value=0.029  Score=42.31  Aligned_cols=25  Identities=24%  Similarity=0.270  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||...+....
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3478999999999999999988764

>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=94.15  E-value=0.072  Score=41.73  Aligned_cols=25  Identities=24%  Similarity=0.414  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|+|-|..|+||||+++.+.....
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~   27 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLV   27 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3688999999999999999998885

>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=94.13  E-value=0.031  Score=42.81  Aligned_cols=25  Identities=28%  Similarity=0.247  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|+|+|.+|+|||||...+.+..
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcCC
Confidence            4578999999999999999998765

>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=94.13  E-value=0.029  Score=44.90  Aligned_cols=27  Identities=19%  Similarity=0.217  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....|+|+|.+|+|||||...+.....
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~~~   54 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGRKV   54 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTSCC
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCCCc
Confidence            456899999999999999999987654

>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=94.12  E-value=0.033  Score=43.51  Aligned_cols=26  Identities=19%  Similarity=0.203  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|.++|.+|+|||||...+.+..
T Consensus         6 ~~~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            6 SQRAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             --CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34579999999999999999998765

>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=94.12  E-value=0.03  Score=42.15  Aligned_cols=26  Identities=23%  Similarity=0.232  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|+++|.+|+|||||...+.+...
T Consensus        10 ~~~i~v~G~~~~GKssli~~l~~~~~   35 (180)
T 2g6b_A           10 AFKVMLVGDSGVGKTCLLVRFKDGAF   35 (180)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhCCC
Confidence            45789999999999999999887653

>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=94.11  E-value=0.023  Score=47.42  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|+|+|.+|+|||||.+.++..
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g~   41 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFLT   41 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4699999999999999998754

>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=94.11  E-value=0.03  Score=43.29  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        14 ~~ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           14 LHKVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCC
Confidence            4579999999999999999988664

>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=94.09  E-value=0.028  Score=46.90  Aligned_cols=25  Identities=20%  Similarity=0.415  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+....
T Consensus         8 ~~~VaIvG~~nvGKSTLln~L~g~~   32 (301)
T 1ega_A            8 CGFIAIVGRPNVGKSTLLNKLLGQK   32 (301)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCC
Confidence            4589999999999999999998763

>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=94.06  E-value=0.031  Score=45.76  Aligned_cols=25  Identities=16%  Similarity=0.317  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+....
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~~   27 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGLR   27 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCCC
Confidence            3579999999999999999998764

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=94.04  E-value=0.14  Score=40.71  Aligned_cols=21  Identities=29%  Similarity=0.381  Sum_probs=17.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      +.+.+.|..|+||||+.....
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEEEeCCCCCcHHhHHHHH
Confidence            478999999999998665543

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=94.03  E-value=0.035  Score=42.24  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +-+.|.|.+|+||||||..+..+
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            46889999999999999998875

>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=94.02  E-value=0.034  Score=43.02  Aligned_cols=26  Identities=31%  Similarity=0.354  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcCC
Confidence            34579999999999999999998765

>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=94.02  E-value=0.031  Score=42.93  Aligned_cols=25  Identities=16%  Similarity=0.266  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|+|+|.+|+|||||...+.+..
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            4579999999999999999998765

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=94.02  E-value=0.028  Score=49.85  Aligned_cols=25  Identities=24%  Similarity=0.215  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|+|+.|+|||||++.+..-..
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl~~  163 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSYAL  163 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHTTH
T ss_pred             CEEEEECCCCCCHHHHHHHHhCccc
Confidence            5799999999999999999987653

>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=94.02  E-value=0.031  Score=43.62  Aligned_cols=25  Identities=24%  Similarity=0.242  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~~   52 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKDC   52 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999998764

>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=94.00  E-value=0.032  Score=43.45  Aligned_cols=25  Identities=24%  Similarity=0.449  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhCC
Confidence            4578999999999999999988654

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.98  E-value=0.025  Score=51.34  Aligned_cols=27  Identities=26%  Similarity=0.368  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|++|+|||||++.+......
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~L~~  395 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAARLME  395 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCChHHHHHHHHHHhhcc
Confidence            358999999999999999999988764

>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=93.96  E-value=0.034  Score=42.51  Aligned_cols=25  Identities=24%  Similarity=0.218  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcCC
Confidence            4579999999999999999998765

>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=93.95  E-value=0.034  Score=42.52  Aligned_cols=26  Identities=27%  Similarity=0.184  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|+|+|.+|+|||||...+.+...
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~~~   47 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASGQF   47 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcCCC
Confidence            35789999999999999999987543

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=93.95  E-value=0.036  Score=42.88  Aligned_cols=27  Identities=26%  Similarity=0.262  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....|+|+|.+|+|||||...+.+...
T Consensus        23 ~~~ki~vvG~~~~GKSsli~~l~~~~~   49 (201)
T 3oes_A           23 RYRKVVILGYRCVGKTSLAHQFVEGEF   49 (201)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHSCC
T ss_pred             CcEEEEEECCCCcCHHHHHHHHHhCCC
Confidence            355799999999999999999987653

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=93.94  E-value=0.039  Score=43.69  Aligned_cols=27  Identities=22%  Similarity=0.334  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...|.+.|+.|+||||+++.+......
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            358999999999999999999998764

>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=93.93  E-value=0.034  Score=42.66  Aligned_cols=26  Identities=23%  Similarity=0.285  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .-.|.++|.+|+|||||...+.+...
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~~~   48 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKGEI   48 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcCCC
Confidence            45789999999999999999987653

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=93.93  E-value=0.051  Score=41.56  Aligned_cols=26  Identities=27%  Similarity=0.322  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|.|+|.+|+|||||...+.+...
T Consensus        16 ~~ki~v~G~~~~GKSsli~~l~~~~~   41 (196)
T 3tkl_A           16 LFKLLLIGDSGVGKSCLLLRFADDTY   41 (196)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCCC
Confidence            45799999999999999999987653

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.91  E-value=0.031  Score=42.04  Aligned_cols=26  Identities=31%  Similarity=0.367  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+|+|.+|+|||||...+.+..
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~~   33 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADNT   33 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSCC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcCC
Confidence            35678999999999999999987653

>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=93.89  E-value=0.039  Score=42.59  Aligned_cols=27  Identities=11%  Similarity=0.241  Sum_probs=22.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +....|+|+|.+|+|||||...+.+..
T Consensus        26 ~~~~ki~v~G~~~~GKSsli~~l~~~~   52 (199)
T 2p5s_A           26 QKAYKIVLAGDAAVGKSSFLMRLCKNE   52 (199)
T ss_dssp             --CEEEEEESSTTSSHHHHHHHHHHCC
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHhCC
Confidence            445689999999999999999998654

>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=93.88  E-value=0.03  Score=43.32  Aligned_cols=23  Identities=26%  Similarity=0.452  Sum_probs=20.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      ....|+|+|.+|+|||||...+.
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            35589999999999999999985

>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=93.88  E-value=0.032  Score=43.14  Aligned_cols=25  Identities=24%  Similarity=0.218  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTCC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999988764

>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=93.88  E-value=0.036  Score=42.49  Aligned_cols=25  Identities=28%  Similarity=0.307  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|.|+|.+|+|||||...+.+..
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~~   45 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDKR   45 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            3478999999999999999988754

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=93.86  E-value=0.04  Score=48.58  Aligned_cols=29  Identities=24%  Similarity=0.488  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ..-.+++|+|..|+|||||.+.+.+....
T Consensus       155 ~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~  183 (438)
T 2dpy_A          155 GRGQRMGLFAGSGVGKSVLLGMMARYTRA  183 (438)
T ss_dssp             BTTCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcccCC
Confidence            34458999999999999999999988754

>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=93.85  E-value=0.036  Score=42.72  Aligned_cols=26  Identities=15%  Similarity=0.268  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|.++|.+|+|||+|.+.+.+..
T Consensus        19 ~~~ki~~vG~~~vGKTsLi~~l~~~~   44 (196)
T 3llu_A           19 SKPRILLMGLRRSGKSSIQKVVFHKM   44 (196)
T ss_dssp             -CCEEEEEESTTSSHHHHHHHHHSCC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHhcC
Confidence            35579999999999999999877643

>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=93.83  E-value=0.037  Score=42.29  Aligned_cols=26  Identities=19%  Similarity=0.232  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|.++|.+|+|||||...+.+..
T Consensus        19 ~~~ki~v~G~~~~GKSsli~~l~~~~   44 (189)
T 1z06_A           19 RIFKIIVIGDSNVGKTCLTYRFCAGR   44 (189)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHcCC
Confidence            34579999999999999999988654

>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=93.82  E-value=0.028  Score=47.61  Aligned_cols=27  Identities=22%  Similarity=0.289  Sum_probs=23.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..++|+|..|+|||||.+.+.......
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~  198 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKE  198 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCC
Confidence            489999999999999999998877543

>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=93.81  E-value=0.03  Score=49.07  Aligned_cols=22  Identities=23%  Similarity=0.371  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .++|+|.+|+|||||.+.++..
T Consensus        44 ~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           44 NILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            3999999999999999999875

>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=93.79  E-value=0.041  Score=42.02  Aligned_cols=24  Identities=25%  Similarity=0.336  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+++|.+|+|||||...+.+..
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            478999999999999999998764

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=93.78  E-value=0.041  Score=45.94  Aligned_cols=32  Identities=19%  Similarity=0.350  Sum_probs=25.4

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +|...+..   .+++++|++|+|||||.+.+. ...
T Consensus       158 ~L~~~l~G---~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          158 ELVDYLEG---FICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             HHHHHTTT---CEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             HHHhhccC---cEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            55555543   489999999999999999998 554

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.76  E-value=0.047  Score=48.35  Aligned_cols=49  Identities=16%  Similarity=0.293  Sum_probs=34.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEI  164 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  164 (276)
                      -.++.|.|.+|+|||||+..+........ =..++|++...  +...+...+
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~E~--s~~~l~~r~  251 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQNVATKT-NENVAIFSLEM--SAQQLVMRM  251 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHHHHS-SCCEEEEESSS--CHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhC-CCcEEEEECCC--CHHHHHHHH
Confidence            45899999999999999999988876431 12577776543  445555554

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=93.73  E-value=0.026  Score=44.37  Aligned_cols=27  Identities=11%  Similarity=0.137  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .....|+|+|.+|+|||||...+.+..
T Consensus        27 ~~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           27 TVQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CCSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            456789999999999999999998775

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=93.72  E-value=0.077  Score=41.05  Aligned_cols=39  Identities=21%  Similarity=0.335  Sum_probs=27.7

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc
Q 041612          114 NMLGIY-GMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN  154 (276)
Q Consensus       114 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~  154 (276)
                      ++|+|+ +.||+||||+|..+......++  ..+..++....
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~~g--~~vlliD~D~~   41 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSRSG--YNIAVVDTDPQ   41 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHHTT--CCEEEEECCTT
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHHCC--CeEEEEECCCC
Confidence            578887 6799999999999888776542  23555555433

>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=93.71  E-value=0.053  Score=41.56  Aligned_cols=26  Identities=23%  Similarity=0.506  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~ki~vvG~~~~GKSsli~~l~~~~   32 (199)
T 2gf0_A            7 NDYRVVVFGAGGVGKSSLVLRFVKGT   32 (199)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             CeeEEEEECCCCCcHHHHHHHHHcCC
Confidence            34578999999999999999998754

>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=93.71  E-value=0.034  Score=43.03  Aligned_cols=25  Identities=20%  Similarity=0.321  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~~   49 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIENK   49 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC--
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhCC
Confidence            4578999999999999999987553

>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=93.70  E-value=0.042  Score=48.00  Aligned_cols=25  Identities=20%  Similarity=0.238  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+++|+|.+|+|||||.+.+....
T Consensus        69 ~~~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           69 VLNVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHTCC
T ss_pred             CeEEEEECCCCCcHHHHHHHHhCCC
Confidence            4589999999999999999999843

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=93.70  E-value=0.035  Score=42.82  Aligned_cols=25  Identities=24%  Similarity=0.193  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||...+.+..
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~~   44 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTNG   44 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            4578999999999999999987654

>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=93.70  E-value=0.039  Score=47.18  Aligned_cols=25  Identities=20%  Similarity=0.296  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|+|++|+|||||.+.+.....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            4899999999999999999987654

>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=93.70  E-value=0.038  Score=42.83  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y            8 LFKLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999998764

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=93.64  E-value=0.042  Score=44.70  Aligned_cols=24  Identities=21%  Similarity=0.185  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|+++|.+|+|||||...+....
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~g~~   25 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALTNAN   25 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCC
Confidence            578999999999999999998763

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=93.62  E-value=0.077  Score=45.64  Aligned_cols=41  Identities=17%  Similarity=0.306  Sum_probs=30.5

Q ss_pred             CCccEEEEEc-CCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC
Q 041612          111 PDVNMLGIYG-MGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ  153 (276)
Q Consensus       111 ~~~~vi~I~G-~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~  153 (276)
                      ...++|+|+| .||+||||+|..+......++  ..+..++...
T Consensus       141 ~~~kvIav~s~KGGvGKTT~a~nLA~~La~~g--~rVlliD~D~  182 (373)
T 3fkq_A          141 DKSSVVIFTSPCGGVGTSTVAAACAIAHANMG--KKVFYLNIEQ  182 (373)
T ss_dssp             TSCEEEEEECSSTTSSHHHHHHHHHHHHHHHT--CCEEEEECCT
T ss_pred             CCceEEEEECCCCCChHHHHHHHHHHHHHhCC--CCEEEEECCC
Confidence            4578999985 899999999999887765541  2466666553

>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=93.59  E-value=0.047  Score=42.42  Aligned_cols=27  Identities=22%  Similarity=0.209  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..-.|+++|.+|+|||||...+.+...
T Consensus        29 ~~~ki~vvG~~~~GKSsLi~~l~~~~~   55 (204)
T 4gzl_A           29 QAIKCVVVGDGAVGKTCLLISYTTNAF   55 (204)
T ss_dssp             -CEEEEEEESTTSSHHHHHHHHHHSCC
T ss_pred             CeEEEEEECcCCCCHHHHHHHHHhCCC
Confidence            345789999999999999999886543

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.59  E-value=0.044  Score=42.06  Aligned_cols=26  Identities=15%  Similarity=0.247  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+|+|.+|+|||||...+.+..
T Consensus        16 ~~~ki~v~G~~~~GKSsl~~~l~~~~   41 (199)
T 4bas_A           16 TKLQVVMCGLDNSGKTTIINQVKPAQ   41 (199)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHSCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            46689999999999999999987654

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=93.58  E-value=0.042  Score=43.28  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=20.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      ...|+|+|.+|+|||||...+..
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            45799999999999999999874

>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=93.57  E-value=0.058  Score=49.23  Aligned_cols=27  Identities=15%  Similarity=0.149  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|.|.|++|+||||+|+.+.....
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHHHhc
Confidence            346899999999999999999988765

>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=93.56  E-value=0.039  Score=41.86  Aligned_cols=25  Identities=20%  Similarity=0.252  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.++|.+|+|||||...+.+..
T Consensus        21 ~~~i~v~G~~~~GKSsli~~l~~~~   45 (181)
T 2h17_A           21 EHKVIIVGLDNAGKTTILYQFSMNE   45 (181)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHTTS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999998653

>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=93.55  E-value=0.043  Score=42.06  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus        18 ~~ki~v~G~~~~GKssli~~l~~~~   42 (194)
T 2atx_A           18 MLKCVVVGDGAVGKTCLLMSYANDA   42 (194)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcCC
Confidence            3478999999999999999998764

>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=93.54  E-value=0.042  Score=42.72  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~~~   49 (207)
T 2fv8_A           25 RKKLVVVGDGACGKTCLLIVFSKDE   49 (207)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             CcEEEEECcCCCCHHHHHHHHhcCC
Confidence            3579999999999999999998754

>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=93.50  E-value=0.044  Score=42.50  Aligned_cols=25  Identities=20%  Similarity=0.296  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~~   53 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTGA   53 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhCC
Confidence            4579999999999999999987654

>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=93.49  E-value=0.039  Score=43.28  Aligned_cols=25  Identities=32%  Similarity=0.311  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~~   58 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADGA   58 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC--
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            3479999999999999999987643

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.48  E-value=0.043  Score=49.70  Aligned_cols=26  Identities=35%  Similarity=0.580  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||++.++.....
T Consensus       313 e~~~i~G~NGsGKSTLlk~l~Gl~~p  338 (538)
T 1yqt_A          313 EVIGIVGPNGIGKTTFVKMLAGVEEP  338 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            48999999999999999999987654

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=93.48  E-value=0.044  Score=42.67  Aligned_cols=26  Identities=19%  Similarity=0.128  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..-.|.|+|.+|+|||||...+.+..
T Consensus         8 ~~~ki~i~G~~~~GKTsli~~l~~~~   33 (212)
T 2j0v_A            8 KFIKCVTVGDGAVGKTCMLICYTSNK   33 (212)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEEECCCCCCHHHHHHHHhcCC
Confidence            34578999999999999999988654

>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=93.47  E-value=0.051  Score=42.23  Aligned_cols=25  Identities=20%  Similarity=0.344  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+....
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~~   44 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVEDK   44 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            4579999999999999999988654

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=93.45  E-value=0.13  Score=40.16  Aligned_cols=41  Identities=17%  Similarity=0.323  Sum_probs=29.6

Q ss_pred             EEEEE-cCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHH
Q 041612          115 MLGIY-GMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIR  158 (276)
Q Consensus       115 vi~I~-G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~  158 (276)
                      +|+++ +.||+||||++..+......++   .+.-++.....+..
T Consensus         2 vI~v~s~KGGvGKTT~a~~LA~~la~~g---~VlliD~D~q~~~~   43 (209)
T 3cwq_A            2 IITVASFKGGVGKTTTAVHLSAYLALQG---ETLLIDGDPNRSAT   43 (209)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHTTS---CEEEEEECTTCHHH
T ss_pred             EEEEEcCCCCCcHHHHHHHHHHHHHhcC---CEEEEECCCCCCHH
Confidence            56665 6799999999999998887652   56666665544433

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=93.44  E-value=0.046  Score=43.22  Aligned_cols=23  Identities=26%  Similarity=0.289  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|-+|+|||+|...+.+..
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~~   37 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYDS   37 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCcCHHHHHHHHHhCC
Confidence            58899999999999999987654

>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=93.44  E-value=0.05  Score=50.05  Aligned_cols=27  Identities=19%  Similarity=0.274  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|.+.|++|+||||+|+.+.....
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~   77 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLV   77 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            467899999999999999999988763

>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=93.42  E-value=0.046  Score=42.28  Aligned_cols=25  Identities=32%  Similarity=0.321  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~~~   49 (201)
T 2gco_A           25 RKKLVIVGDGACGKTCLLIVFSKDQ   49 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCc
Confidence            3478999999999999999998754

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.41  E-value=0.045  Score=49.59  Aligned_cols=25  Identities=28%  Similarity=0.465  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|+|+.|+|||||.+.+.....
T Consensus        48 e~~~LvG~NGaGKSTLlk~l~Gl~~   72 (538)
T 1yqt_A           48 MVVGIVGPNGTGKSTAVKILAGQLI   72 (538)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            5899999999999999999987654

>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=93.40  E-value=0.042  Score=45.99  Aligned_cols=27  Identities=22%  Similarity=0.351  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +....|+|+|.+|+|||||...+....
T Consensus         8 ~~~g~v~ivG~~nvGKSTLin~l~g~~   34 (308)
T 3iev_A            8 MKVGYVAIVGKPNVGKSTLLNNLLGTK   34 (308)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHTSC
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            346789999999999999999998764

>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=93.39  E-value=0.061  Score=39.82  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+.+|+|+.|.|||||...++.-.
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999887543

>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=93.39  E-value=0.049  Score=44.11  Aligned_cols=26  Identities=27%  Similarity=0.312  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+|+|.+|+|||||...+....
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~~~   46 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILRKQ   46 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHTSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHhCCC
Confidence            35689999999999999999997654

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.38  E-value=0.083  Score=48.57  Aligned_cols=27  Identities=26%  Similarity=0.469  Sum_probs=23.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..+.|+|++|+||||||+.+.......
T Consensus        61 ~~vll~Gp~GtGKTtlar~ia~~l~~~   87 (604)
T 3k1j_A           61 RHVLLIGEPGTGKSMLGQAMAELLPTE   87 (604)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHTSCCS
T ss_pred             CEEEEEeCCCCCHHHHHHHHhccCCcc
Confidence            578999999999999999999877543

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=93.36  E-value=0.097  Score=45.21  Aligned_cols=50  Identities=18%  Similarity=0.113  Sum_probs=31.9

Q ss_pred             HHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccC-CCCCeEEEEEecCc
Q 041612          104 ILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSD-KLFDQVVFVEVSQN  154 (276)
Q Consensus       104 l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~f~~~~wv~~~~~  154 (276)
                      .++.+.. ..-..++|+|.+|+|||||++.+.+....+ ..+.+ +++-+++.
T Consensus       164 aID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~-I~~lIGER  215 (422)
T 3ice_A          164 VLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVL-MVLLIDER  215 (422)
T ss_dssp             HHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEE-EEEEESSC
T ss_pred             eeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeE-EEEEecCC
Confidence            3344433 234589999999999999999988776432 11333 34555544

>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=93.35  E-value=0.058  Score=42.91  Aligned_cols=28  Identities=18%  Similarity=-0.114  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.++.++|..|+||||++..+.++...+
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~   39 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYA   39 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            4688999999999999999988887654

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.33  E-value=0.079  Score=46.75  Aligned_cols=49  Identities=18%  Similarity=0.197  Sum_probs=34.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIG  165 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  165 (276)
                      -.++.|.|.+|+|||++|..+..+...++  ..+.|++.-.  +..++...++
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~g--~~vl~fSlEm--s~~ql~~R~~  245 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEM--GKKENIKRLI  245 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHTT--CEEEEECSSS--CTTHHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHcC--CEEEEEECCC--CHHHHHHHHH
Confidence            45899999999999999999988876542  3567766543  3444444443

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=93.33  E-value=0.039  Score=49.95  Aligned_cols=28  Identities=29%  Similarity=0.591  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .-.+++|+|+.|+|||||.+.+......
T Consensus        24 ~Gei~gLiGpNGaGKSTLlkiL~Gl~~p   51 (538)
T 3ozx_A           24 NNTILGVLGKNGVGKTTVLKILAGEIIP   51 (538)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            3468999999999999999999876543

>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=93.33  E-value=0.049  Score=42.71  Aligned_cols=25  Identities=24%  Similarity=0.226  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .-.|.|+|.+|+|||||...+.+..
T Consensus        27 ~~ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           27 RCKLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcCC
Confidence            3478999999999999999988764

>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP- binding, hydrolase, magnesium, metal-binding, nucleotide- binding, potassium; HET: GDP FON; 2.95A {Chlorobium tepidum} PDB: 3gei_A*

Probab=93.32  E-value=0.024  Score=50.50  Aligned_cols=22  Identities=23%  Similarity=0.235  Sum_probs=18.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|+|+|.+|+|||||...+.+.
T Consensus       235 kV~ivG~~nvGKSSLln~L~~~  256 (476)
T 3gee_A          235 STVIAGKPNAGKSTLLNTLLGQ  256 (476)
T ss_dssp             EEEEECCTTSSHHHHHHHCC--
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4999999999999999988765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.31  E-value=0.15  Score=44.98  Aligned_cols=51  Identities=16%  Similarity=0.027  Sum_probs=36.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGD  166 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  166 (276)
                      -.++.|.|.+|+|||+|+..+........ =..++|++..  .+...+...++.
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~~-g~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALKE-GVGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESS--SCHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhC-CCeEEEEECC--CCHHHHHHHHHH
Confidence            45899999999999999999988775431 1356776653  455666666554

>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=93.30  E-value=0.055  Score=48.17  Aligned_cols=26  Identities=15%  Similarity=0.193  Sum_probs=23.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||.+.+..-...
T Consensus        30 e~~~liG~nGsGKSTLl~~l~Gl~~p   55 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVTALIP   55 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             ceEEEECCCCCcHHHHHHHHhcCCCC
Confidence            79999999999999999999877654

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=93.29  E-value=0.041  Score=49.87  Aligned_cols=26  Identities=35%  Similarity=0.682  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||++.++.-...
T Consensus       295 ei~~i~G~nGsGKSTLl~~l~Gl~~p  320 (538)
T 3ozx_A          295 EIIGILGPNGIGKTTFARILVGEITA  320 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            47999999999999999999987654

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=93.29  E-value=0.066  Score=42.60  Aligned_cols=27  Identities=15%  Similarity=0.231  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+|+|.|+.|+||||+|+.+.....
T Consensus        13 ~~~iI~i~g~~gsGk~~i~~~la~~lg   39 (223)
T 3hdt_A           13 KNLIITIEREYGSGGRIVGKKLAEELG   39 (223)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHcC
Confidence            346999999999999999999987654

>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=93.27  E-value=0.028  Score=42.63  Aligned_cols=25  Identities=24%  Similarity=0.325  Sum_probs=10.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus         8 ~~ki~v~G~~~~GKssl~~~l~~~~   32 (183)
T 2fu5_C            8 LFKLLLIGDSGVGKTCVLFRFSEDA   32 (183)
T ss_dssp             EEEEEEECCCCC-------------
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            4579999999999999999887553

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=93.25  E-value=0.37  Score=40.62  Aligned_cols=156  Identities=7%  Similarity=0.009  Sum_probs=87.6

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHH--HhCCC------cccc
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGD--KLGLK------FHEE  175 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~--~l~~~------~~~~  175 (276)
                      +.+.+...-.++..++|..|.||++.+..+....... .|+....+.+....+...+...+..  .++..      ..+.
T Consensus         9 l~~~l~~~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~plf~~~kvvii~~~~~   87 (343)
T 1jr3_D            9 LRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQ-GFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPEN   87 (343)
T ss_dssp             HHHHHHHCCCSEEEEEESCHHHHHHHHHHHHHHHHHH-TCCEEEEEECCTTCCHHHHHHHHHHHHHCCSCEEEEEECCSS
T ss_pred             HHHHHhcCCCcEEEEECCcHHHHHHHHHHHHHHHHhC-CCCeeEEEEecCCCCHHHHHHHhcCcCCccCCeEEEEECCCC
Confidence            4444443446789999999999999999988776432 1433222234455677777655422  12211      0011


Q ss_pred             -cchh---hhhhccccCCCCcEEEEEeccc-------cccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHH
Q 041612          176 -SESG---RANSLFTHGHKGCKVLLTARSQ-------DVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSI  244 (276)
Q Consensus       176 -~~~~---~~~~l~~~~~~gs~IivTTR~~-------~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  244 (276)
                       ....   .+....+..++++.+|++|-..       .+..........++..+++.++....+.+.+..... .--.+.
T Consensus        88 kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~~~~~g~-~i~~~a  166 (343)
T 1jr3_D           88 GPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNL-ELDDAA  166 (343)
T ss_dssp             CCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHHHHHTTC-EECHHH
T ss_pred             CCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHHHHHcCC-CCCHHH
Confidence             1111   1223333556678888776431       222222333457888899998888877776641111 011234


Q ss_pred             HHHHHHHcCCCcHHHHH
Q 041612          245 ARDVAKECAGLPVSIVT  261 (276)
Q Consensus       245 ~~~i~~~c~G~PLai~~  261 (276)
                      ...++..++|-+..+..
T Consensus       167 ~~~l~~~~~gdl~~~~~  183 (343)
T 1jr3_D          167 NQVLCYCYEGNLLALAQ  183 (343)
T ss_dssp             HHHHHHSSTTCHHHHHH
T ss_pred             HHHHHHHhchHHHHHHH
Confidence            66788888887776654

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=93.24  E-value=0.035  Score=42.68  Aligned_cols=25  Identities=32%  Similarity=0.385  Sum_probs=20.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus        26 ~~ki~vvG~~~~GKSsLi~~l~~~~   50 (192)
T 2il1_A           26 KLQVIIIGSRGVGKTSLMERFTDDT   50 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHCC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcCC
Confidence            3468999999999999999987554

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=93.24  E-value=0.05  Score=44.69  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ...|+++|.+|+|||||...+...
T Consensus         3 ~~kI~lvG~~nvGKSTL~n~L~g~   26 (272)
T 3b1v_A            3 MTEIALIGNPNSGKTSLFNLITGH   26 (272)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHCC
Confidence            357999999999999999999875

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=93.23  E-value=0.13  Score=43.30  Aligned_cols=27  Identities=30%  Similarity=0.414  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++...|.||+||||+|..+.......
T Consensus        15 ~i~v~sgKGGvGKTTvA~~LA~~lA~~   41 (324)
T 3zq6_A           15 TFVFIGGKGGVGKTTISAATALWMARS   41 (324)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEEeCCCCchHHHHHHHHHHHHHHC
Confidence            455566899999999999988776554

>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=93.22  E-value=0.05  Score=45.39  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+....
T Consensus         7 ~g~V~ivG~~nvGKSTLln~l~g~~   31 (301)
T 1wf3_A            7 SGFVAIVGKPNVGKSTLLNNLLGVK   31 (301)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCc
Confidence            4579999999999999999998764

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=93.17  E-value=0.046  Score=45.57  Aligned_cols=34  Identities=24%  Similarity=0.423  Sum_probs=26.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ++...+..   .+++++|++|+|||||.+.+......
T Consensus       162 ~lf~~l~g---eiv~l~G~sG~GKSTll~~l~g~~~~  195 (301)
T 1u0l_A          162 ELKEYLKG---KISTMAGLSGVGKSSLLNAINPGLKL  195 (301)
T ss_dssp             HHHHHHSS---SEEEEECSTTSSHHHHHHHHSTTCCC
T ss_pred             HHHHHhcC---CeEEEECCCCCcHHHHHHHhcccccc
Confidence            55555543   48999999999999999999876654

>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=93.14  E-value=0.039  Score=48.26  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|+|+|.+|+|||||.+.++....
T Consensus        33 ~I~lvG~sGaGKSTLln~L~g~~~   56 (418)
T 2qag_C           33 TLMVVGESGLGKSTLINSLFLTDL   56 (418)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTCCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCC
Confidence            469999999999999999987643

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=93.13  E-value=0.052  Score=49.88  Aligned_cols=27  Identities=37%  Similarity=0.551  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|+|||||.+.+..-...
T Consensus       103 Gei~~LvGpNGaGKSTLLkiL~Gll~P  129 (608)
T 3j16_B          103 GQVLGLVGTNGIGKSTALKILAGKQKP  129 (608)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCCCC
Confidence            358999999999999999999876654

>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=93.11  E-value=0.053  Score=49.84  Aligned_cols=26  Identities=35%  Similarity=0.580  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||.+.+......
T Consensus       383 ei~~i~G~NGsGKSTLlk~l~Gl~~p  408 (607)
T 3bk7_A          383 EVIGIVGPNGIGKTTFVKMLAGVEEP  408 (607)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            48999999999999999999987654

>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=93.06  E-value=0.048  Score=42.62  Aligned_cols=25  Identities=24%  Similarity=0.255  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus        25 ~~ki~vvG~~~~GKSsLi~~l~~~~   49 (217)
T 2f7s_A           25 LIKLLALGDSGVGKTTFLYRYTDNK   49 (217)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHCSC
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcCC
Confidence            4578999999999999999988653

>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=93.01  E-value=0.037  Score=42.33  Aligned_cols=25  Identities=16%  Similarity=0.191  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+.+..
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            4578999999999999999988765

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=93.00  E-value=0.066  Score=40.77  Aligned_cols=26  Identities=15%  Similarity=0.139  Sum_probs=21.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .....|+++|.+|+|||||...+...
T Consensus        20 ~~~~~i~v~G~~~~GKssli~~l~~~   45 (189)
T 2x77_A           20 DRKIRVLMLGLDNAGKTSILYRLHLG   45 (189)
T ss_dssp             TSCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHcC
Confidence            44567999999999999999988543

>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=93.00  E-value=0.052  Score=48.73  Aligned_cols=28  Identities=4%  Similarity=-0.091  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      ...+|.+.|++|+||||+|+.+......
T Consensus       394 ~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          394 QGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            3468999999999999999999999864

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=92.87  E-value=0.06  Score=49.46  Aligned_cols=26  Identities=35%  Similarity=0.512  Sum_probs=22.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||++.+..-...
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl~~p  404 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGALKP  404 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTSSCC
T ss_pred             eEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            46899999999999999999987654

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=92.86  E-value=0.21  Score=42.64  Aligned_cols=28  Identities=29%  Similarity=0.367  Sum_probs=22.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +...++...|.||+||||+|..+.....
T Consensus        16 ~~~~i~v~sgKGGvGKTTvaanLA~~lA   43 (354)
T 2woj_A           16 TTHKWIFVGGKGGVGKTTSSCSIAIQMA   43 (354)
T ss_dssp             SSCCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            3345666679999999999998887776

>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=92.86  E-value=0.03  Score=46.92  Aligned_cols=25  Identities=24%  Similarity=0.399  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|+|++|+|||||.+.+.....
T Consensus       174 ~~~~lvG~sG~GKSTLln~L~g~~~  198 (307)
T 1t9h_A          174 KTTVFAGQSGVGKSSLLNAISPELG  198 (307)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC---
T ss_pred             CEEEEECCCCCCHHHHHHHhccccc
Confidence            5899999999999999999876543

>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=92.86  E-value=0.083  Score=48.32  Aligned_cols=27  Identities=22%  Similarity=0.327  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.+++|+|+.|.|||||++.+..-...
T Consensus       369 G~~~~ivG~sGsGKSTll~~l~g~~~p  395 (582)
T 3b5x_A          369 GKTVALVGRSGSGKSTIANLFTRFYDV  395 (582)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            358999999999999999999877654

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=92.85  E-value=0.09  Score=41.02  Aligned_cols=26  Identities=19%  Similarity=0.261  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...+|+|+|++|+||+|.|..+.+..
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~~   35 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSRL   35 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHHc
Confidence            45699999999999999999887654

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=92.83  E-value=0.087  Score=43.46  Aligned_cols=26  Identities=19%  Similarity=0.341  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....|+|+|.+|+|||||...+....
T Consensus        25 ~~~~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B           25 DLPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             CCCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             CCCeEEEEeCCCCCHHHHHHHHHCCC
Confidence            45689999999999999999998764

>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=92.83  E-value=0.053  Score=49.63  Aligned_cols=26  Identities=27%  Similarity=0.401  Sum_probs=23.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+++|+|+.|+|||||.+.+..-...
T Consensus       370 ~~~~ivG~sGsGKSTLl~~l~g~~~p  395 (582)
T 3b60_A          370 KTVALVGRSGSGKSTIASLITRFYDI  395 (582)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTTTTCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhhccCC
Confidence            48999999999999999999877654

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=92.77  E-value=0.065  Score=42.22  Aligned_cols=25  Identities=20%  Similarity=0.379  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|.|+|.+|+|||||...+.+..
T Consensus        13 ~~ki~v~G~~~vGKSsli~~l~~~~   37 (223)
T 3cpj_B           13 LFKIVLIGDSGVGKSNLLSRFTKNE   37 (223)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHHCC
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcCC
Confidence            4578999999999999999988764

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=92.76  E-value=0.17  Score=42.71  Aligned_cols=30  Identities=23%  Similarity=0.360  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +..+++.+.|.||+||||+|..+.......
T Consensus        17 ~~~~i~v~sgkGGvGKTTva~~LA~~lA~~   46 (329)
T 2woo_A           17 TSLKWIFVGGKGGVGKTTTSCSLAIQMSKV   46 (329)
T ss_dssp             TTCCEEEEECSSSSSHHHHHHHHHHHHHTS
T ss_pred             CCCEEEEEeCCCCCcHHHHHHHHHHHHHHC
Confidence            345566678999999999999988777654

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=92.57  E-value=0.28  Score=43.44  Aligned_cols=64  Identities=22%  Similarity=0.354  Sum_probs=46.2

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-HHHHHHHHHHH
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-IRKIQEEIGDK  167 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-~~~l~~~i~~~  167 (276)
                      +.++.|.. ..-..++|.|.+|+|||+|+..+.++.... +-+.++++-+++... ..++.+++...
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~~~-~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA-HGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTTTT-CSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhhHhh-CCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            66666665 234579999999999999999998876432 346778888877653 46666666554

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=92.53  E-value=0.16  Score=41.25  Aligned_cols=42  Identities=19%  Similarity=0.369  Sum_probs=30.1

Q ss_pred             CCccEEEEE-cCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          111 PDVNMLGIY-GMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       111 ~~~~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      ...++|+|+ +-||+||||+|..+..... ++  ..+.-++.....
T Consensus        25 ~~~~vI~v~s~kGGvGKTT~a~~LA~~la-~g--~~VlliD~D~~~   67 (267)
T 3k9g_A           25 KKPKIITIASIKGGVGKSTSAIILATLLS-KN--NKVLLIDMDTQA   67 (267)
T ss_dssp             -CCEEEEECCSSSSSCHHHHHHHHHHHHT-TT--SCEEEEEECTTC
T ss_pred             CCCeEEEEEeCCCCchHHHHHHHHHHHHH-CC--CCEEEEECCCCC
Confidence            456788886 5789999999999988887 53  345556655443

>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=92.53  E-value=0.059  Score=49.52  Aligned_cols=25  Identities=32%  Similarity=0.478  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+++|+|+.|+|||||.+.+.....
T Consensus       118 e~~~LiG~NGsGKSTLlkiL~Gll~  142 (607)
T 3bk7_A          118 MVVGIVGPNGTGKTTAVKILAGQLI  142 (607)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHhCCCC
Confidence            5899999999999999999987654

>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A

Probab=92.52  E-value=0.076  Score=43.18  Aligned_cols=25  Identities=20%  Similarity=0.305  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+++|.+|+|||||...+....
T Consensus         5 ~~kI~lvG~~nvGKTsL~n~l~g~~   29 (258)
T 3a1s_A            5 MVKVALAGCPNVGKTSLFNALTGTK   29 (258)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHTTC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHCCC
Confidence            3568999999999999999998754

>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=92.49  E-value=0.11  Score=46.12  Aligned_cols=37  Identities=24%  Similarity=0.372  Sum_probs=27.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+...+...+ +.+.|.|.+|+|||+++..+.......
T Consensus        36 ~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           36 IVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             HHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            3333444433 389999999999999999998887655

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=92.44  E-value=0.19  Score=46.00  Aligned_cols=40  Identities=25%  Similarity=0.338  Sum_probs=29.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      ...+++.+.|.||+||||+|..+.......+  ..+..++..
T Consensus         6 ~~~~i~~~sgkGGvGKTT~a~~lA~~lA~~G--~rVLlvd~D   45 (589)
T 1ihu_A            6 NIPPYLFFTGKGGVGKTSISCATAIRLAEQG--KRVLLVSTD   45 (589)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             CCCEEEEEeCCCcCHHHHHHHHHHHHHHHCC--CcEEEEECC
Confidence            4567888899999999999999888776542  234455444

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=92.42  E-value=0.069  Score=48.18  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=0.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEI  133 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v  133 (276)
                      .+++|+|.+|+|||||++.+
T Consensus        40 e~~~l~G~nGsGKSTL~~~~   59 (525)
T 1tf7_A           40 RSTLVSGTSGTGKTLFSIQF   59 (525)
T ss_dssp             SEEEEEESTTSSHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHH

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=92.40  E-value=0.088  Score=46.36  Aligned_cols=25  Identities=28%  Similarity=0.343  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...++|+|.+|+|||||.+.+....
T Consensus       180 ~~kvaivG~~gvGKSTLln~l~g~~  204 (439)
T 1mky_A          180 AIKVAIVGRPNVGKSTLFNAILNKE  204 (439)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTST
T ss_pred             CceEEEECCCCCCHHHHHHHHhCCc
Confidence            4689999999999999999998764

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=92.32  E-value=0.14  Score=47.53  Aligned_cols=49  Identities=22%  Similarity=0.248  Sum_probs=32.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIG  165 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  165 (276)
                      .+..|.|+||+|||+.+..+....-.+   ...+.++...+.....+...+.
T Consensus       206 ~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~  254 (646)
T 4b3f_X          206 ELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLA  254 (646)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHH
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHH
Confidence            367899999999997555444443322   2356777766666666666654

>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=92.28  E-value=0.14  Score=45.36  Aligned_cols=52  Identities=23%  Similarity=0.463  Sum_probs=35.1

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      +.++.|.. -.-..++|+|.+|+|||||+..+..+...+. -+..+++.+++..
T Consensus       140 r~ID~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~~~~~~-~~i~V~~~iGert  192 (473)
T 1sky_E          140 KVVDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNIAQEH-GGISVFAGVGERT  192 (473)
T ss_dssp             HHHHHHSCEETTCEEEEECCSSSCHHHHHHHHHHHHHHHT-CCCEEEEEESSCH
T ss_pred             hHHHHHhhhccCCEEEEECCCCCCccHHHHHHHhhhhhcc-CcEEEEeeeccCc
Confidence            44555543 1234689999999999999999988766431 2445666666554

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=92.28  E-value=0.14  Score=47.18  Aligned_cols=50  Identities=24%  Similarity=0.280  Sum_probs=34.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIG  165 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  165 (276)
                      +...|.|++|+|||+++..+.......  -...+.++.........+...+.
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~l~~~--~~~~ilv~a~tn~A~~~l~~~l~  245 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYHLARQ--GNGPVLVCAPSNIAVDQLTEKIH  245 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHTS--SSCCEEEEESSHHHHHHHHHHHH
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEeCcHHHHHHHHHHHH
Confidence            478899999999999887777665432  23466677666655566655553

---

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	276
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	7e-27

>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 =  103 bits (258), Expect = 7e-27
 Identities = 24/207 (11%), Positives = 63/207 (30%), Gaps = 35/207 (16%)

Query: 105 LSALEDPDVNMLGIYGMGGIGKTMLAEEIARK--VKSDKLFDQVVFVEVSQNQDIRKIQE 162
           L  + D D   L ++G  G GK+++A +   K        +D +V+++ S          
Sbjct: 36  LDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDL 95

Query: 163 EIGDKLGLKFHEESESG---------------------------------RANSLFTHGH 189
                L LK  ++  +                                  +  ++     
Sbjct: 96  FTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQE 155

Query: 190 KGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVA 249
              + L+T R  ++ +    +     +  L  +E +   +          + + +     
Sbjct: 156 LRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTI 215

Query: 250 KECAGLPVSIVTIARALRNKRLFEWKD 276
           +  +G P +++   ++   K   +   
Sbjct: 216 ELSSGNPATLMMFFKSCEPKTFEKMAQ 242

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	276
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.97
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.71
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.41
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.35
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.34
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.22
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.16
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.13
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.09
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.09
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.08
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.05
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.97
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.93
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.9
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.79
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.75
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.64
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.64
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.63
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.58
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.58
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.48
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.46
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.44
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.43
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.42
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.42
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.42
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.35
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.33
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.29
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.28
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.26
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.25
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.24
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.23
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.22
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.15
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.14
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	97.11
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.1
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.06
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.06
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.05
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.03
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.03
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.0
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.98
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.97
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.81
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.79
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.79
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.79
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.77
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.77
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.74
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.7
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.7
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	96.69
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.69
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.63
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.61
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.6
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.58
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.57
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.55
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.53
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.52
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.51
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	96.51
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.5
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.46
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.45
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.44
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.41
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.37
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.37
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.35
d1okkd2	207	GTPase domain of the signal recognition particle r	96.33
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	96.32
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.31
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.29
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	96.18
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.16
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.12
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.12
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	96.1
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.1
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.1
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.06
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.01
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	96.01
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.96
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.96
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.92
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	95.9
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.87
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.86
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.85
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.84
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.77
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	95.71
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.69
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.69
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	95.69
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.67
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.67
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	95.63
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.63
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	95.57
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.56
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.5
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.46
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.45
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	95.43
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	95.39
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.37
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	95.37
d1nrjb_	209	Signal recognition particle receptor beta-subunit	95.36
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.32
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.32
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.32
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.29
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.27
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	95.25
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.25
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	95.25
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	95.23
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.23
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	95.19
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	95.18
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	95.14
d2fh5b1	207	Signal recognition particle receptor beta-subunit	95.12
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	95.09
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.06
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.02
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.02
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	95.02
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	95.01
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	95.01
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	95.0
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.99
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.98
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.94
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.94
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.93
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	94.89
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.88
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.88
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.87
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	94.87
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.86
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.86
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.85
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.84
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.83
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.82
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	94.82
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.81
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	94.81
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	94.8
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.79
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.76
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.75
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	94.74
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	94.73
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.68
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	94.68
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	94.49
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.48
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	94.47
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.46
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.46
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	94.46
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.45
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.41
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	94.4
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	94.37
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	94.34
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	94.34
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	94.3
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	94.29
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	94.28
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	94.25
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	94.21
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	94.17
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	94.14
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	94.11
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.09
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	94.05
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	94.04
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.93
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.92
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	93.91
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	93.86
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	93.85
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.85
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	93.83
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.82
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	93.75
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.74
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.74
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	93.73
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.68
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	93.67
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	93.62
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.57
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	93.44
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	93.25
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	93.16
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	92.91
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.87
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	92.67
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	92.64
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.57
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	92.35
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	92.25
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	91.93
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	91.9
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	91.59
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	91.46
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	91.41
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	91.39
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	91.3
d1xpua3	289	Transcription termination factor Rho, ATPase domai	91.27
d1tuea_	205	Replication protein E1 helicase domain {Human papi	90.78
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	90.49
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	90.47
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.16
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	90.15
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	89.61
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	89.3
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	89.28
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	89.1
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	89.05
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	89.04
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	87.51
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	87.32
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	87.02
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	87.01
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	86.68
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	86.55
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	86.51
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	86.36
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	85.88
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	85.63
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	85.31
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	84.34
d1p3da1	96	UDP-N-acetylmuramate-alanine ligase MurC {Haemophi	82.89
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	82.69
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	82.13
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	81.84
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	81.73
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	81.64
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	80.75
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	80.44

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=99.97  E-value=4.1e-32  Score=226.19  Aligned_cols=173  Identities=13%  Similarity=0.152  Sum_probs=130.1

Q ss_pred             HHHHhhc---CCCccEEEEEcCCCCcHHHHHHHHHHhcc--cCCCCCeEEEEEecCcCCHHHHHHHHHH---HhCCCccc
Q 041612          103 NILSALE---DPDVNMLGIYGMGGIGKTMLAEEIARKVK--SDKLFDQVVFVEVSQNQDIRKIQEEIGD---KLGLKFHE  174 (276)
Q Consensus       103 ~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~f~~~~wv~~~~~~~~~~l~~~i~~---~l~~~~~~  174 (276)
                      +|+++|.   +++.++|+|+||||+||||||+.+|++..  ...+|++++|+++++.++...+...+..   .++.....
T Consensus        31 ~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~  110 (277)
T d2a5yb3          31 RVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLL  110 (277)
T ss_dssp             HHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCT
T ss_pred             HHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHHHHHhcchhhc
Confidence            5555553   45678999999999999999999999855  5567999999999999887776655533   33222110


Q ss_pred             -----c--cchhh----hhh-ccc------------------cCCCCcEEEEEeccccccccCCCCCCceeCCCCCHHHH
Q 041612          175 -----E--SESGR----ANS-LFT------------------HGHKGCKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       175 -----~--~~~~~----~~~-l~~------------------~~~~gs~IivTTR~~~va~~~~~~~~~~~l~~L~~~ea  224 (276)
                           .  .....    ... +..                  ....||+||||||+..++.......+.|++++|+.+||
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea  190 (277)
T d2a5yb3         111 NFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDEC  190 (277)
T ss_dssp             TCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHH
T ss_pred             CCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcccCceEEEEeehHHHHHhcCCCCceEECCCCCHHHH
Confidence                 0  00000    000 000                  34568999999999999876555557899999999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHhCCCccccC
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVTIARALRNKRLFEWK  275 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~~~~~~~W~  275 (276)
                      |+||.+.++.....+..++++++|+++|+|+|||++++|+.|+.++.++|.
T Consensus       191 ~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~  241 (277)
T d2a5yb3         191 YDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMA  241 (277)
T ss_dssp             HHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHH
T ss_pred             HHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHH
Confidence            999999998655566678899999999999999999999999977777774

>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=98.71  E-value=7.8e-09  Score=83.59  Aligned_cols=52  Identities=13%  Similarity=0.161  Sum_probs=39.9

Q ss_pred             CceeCCCCCHHHHHHHHHHhhCC-CCCChhHHHHHHHHHHHcCCCcHHHHHHHHHHh
Q 041612          212 PNFSIGVLNEEEAWSLFKKMAGD-YIEDSEFQSIARDVAKECAGLPVSIVTIARALR  267 (276)
Q Consensus       212 ~~~~l~~L~~~ea~~Lf~~~~~~-~~~~~~~~~~~~~i~~~c~G~PLai~~i~~~L~  267 (276)
                      ..+.|++++.+++.+++.+.... ....++    ..+|.+.++|+|..+..++..+.
T Consensus       201 ~~i~L~~l~~~e~~~~l~~~~~~~~~~~~~----~~~i~~~~~G~P~~L~~~~~~~~  253 (283)
T d2fnaa2         201 STVELKPFSREEAIEFLRRGFQEADIDFKD----YEVVYEKIGGIPGWLTYFGFIYL  253 (283)
T ss_dssp             EEEEECCCCHHHHHHHHHHHHHHHTCCCCC----HHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             eEEeeCCCCHHHHHHHHHhhhhhcCCCHHH----HHHHHHHhCCCHHHHHHHHHHHH
Confidence            46889999999999999876531 112222    45899999999999999987665

>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=98.41  E-value=3e-07  Score=72.08  Aligned_cols=154  Identities=14%  Similarity=0.153  Sum_probs=90.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC---cc------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK---FH------  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~---~~------  173 (276)
                      .|..++.+...+.+.++|++|+||||+|+.+.+....+..-....-++.+...+...+...+.......   ..      
T Consensus        26 ~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~~~~~~~kvi  105 (224)
T d1sxjb2          26 RLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIV  105 (224)
T ss_dssp             HHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEE
T ss_pred             HHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHHHHhhccCCCcceEEE
Confidence            677777777777788999999999999999988865441111234444444444444433332222111   00      


Q ss_pred             -----cccchhhhhh---ccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCCChhHH
Q 041612          174 -----EESESGRANS---LFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIEDSEFQ  242 (276)
Q Consensus       174 -----~~~~~~~~~~---l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~~~~~~  242 (276)
                           +.........   ........+++++||.+.. +..........+++++++.++-...+.+.+.  .-..+   .
T Consensus       106 iiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i~---~  182 (224)
T d1sxjb2         106 ILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYT---N  182 (224)
T ss_dssp             EEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBC---H
T ss_pred             EEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhcccCCC---H
Confidence                 0001111111   1125556667777765543 3222334445799999999999999988775  11222   2


Q ss_pred             HHHHHHHHHcCCCcHHH
Q 041612          243 SIARDVAKECAGLPVSI  259 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai  259 (276)
                      +....|++.|+|-+-.+
T Consensus       183 ~~l~~I~~~s~Gd~R~a  199 (224)
T d1sxjb2         183 DGLEAIIFTAEGDMRQA  199 (224)
T ss_dssp             HHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHcCCcHHHH
Confidence            35678999999976544

>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=98.35  E-value=1.2e-06  Score=68.49  Aligned_cols=153  Identities=13%  Similarity=0.140  Sum_probs=87.6

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhC---CCcc------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLG---LKFH------  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~---~~~~------  173 (276)
                      .|.+++..+..+.+.++|++|+||||+|+.+.+............-.+.+...+.......+.....   ....      
T Consensus        25 ~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kiii  104 (227)
T d1sxjc2          25 TVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLII  104 (227)
T ss_dssp             HHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEE
T ss_pred             HHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhccccccccCCCeEEEE
Confidence            6666777766666789999999999999999988754422222333333444333333222221111   0000      


Q ss_pred             ----cccch---hhhhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHH
Q 041612          174 ----EESES---GRANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIA  245 (276)
Q Consensus       174 ----~~~~~---~~~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~  245 (276)
                          +....   ..+..........+.++++|.+.. +..........+.+.+++.++-..++.+.+......- -.+..
T Consensus       105 iDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i-~~~~l  183 (227)
T d1sxjc2         105 LDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKL-SPNAE  183 (227)
T ss_dssp             ETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCB-CHHHH
T ss_pred             EeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccccccccccC-CHHHH
Confidence                00000   111122225556778888776543 3222234455789999999999999988775221111 12456


Q ss_pred             HHHHHHcCCCc
Q 041612          246 RDVAKECAGLP  256 (276)
Q Consensus       246 ~~i~~~c~G~P  256 (276)
                      ..|++.+.|-.
T Consensus       184 ~~i~~~s~Gd~  194 (227)
T d1sxjc2         184 KALIELSNGDM  194 (227)
T ss_dssp             HHHHHHHTTCH
T ss_pred             HHHHHHcCCcH
Confidence            78999998864

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.34  E-value=1.1e-05  Score=64.00  Aligned_cols=142  Identities=15%  Similarity=0.109  Sum_probs=76.3

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc----C-CHHHHHHHHHHHhCCCcccc---cc--
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN----Q-DIRKIQEEIGDKLGLKFHEE---SE--  177 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~----~-~~~~l~~~i~~~l~~~~~~~---~~--  177 (276)
                      +....++-+.++|++|+|||+||+.+.+.....     .+.++.+.-    . ..+..++.+++......+..   ++  
T Consensus        37 ~g~~~~~giLl~GppGtGKT~la~aia~~~~~~-----~~~i~~~~l~~~~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid  111 (247)
T d1ixza_          37 MGARIPKGVLLVGPPGVGKTHLARAVAGEARVP-----FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEID  111 (247)
T ss_dssp             TTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCC-----EEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHH
T ss_pred             cCCCCCceEEEecCCCCChhHHHHHHHHHcCCC-----EEEEEhHHhhhccccHHHHHHHHHHHHHHHcCCEEEEEEChh
Confidence            333445679999999999999999999877533     233433221    1 22333445554433221100   00  


Q ss_pred             -------------hh----hhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHh
Q 041612          178 -------------SG----RANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKM  231 (276)
Q Consensus       178 -------------~~----~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~  231 (276)
                                   ..    ....+..     ....+.-||-||....-... ..   ...+.+.++..+.++-.++|+..
T Consensus       112 ~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~  191 (247)
T d1ixza_         112 AVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIH  191 (247)
T ss_dssp             HHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHH
T ss_pred             hhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHH
Confidence                         00    0111111     12222223336655433222 11   34457899999999999999988


Q ss_pred             hCCCC--CChhHHHHHHHHHHHcCCCcHH
Q 041612          232 AGDYI--EDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       232 ~~~~~--~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      .....  .+.+    ...+++.|.|+.-+
T Consensus       192 l~~~~~~~~~~----~~~la~~t~g~s~~  216 (247)
T d1ixza_         192 ARGKPLAEDVD----LALLAKRTPGFVGA  216 (247)
T ss_dssp             HTTSCBCTTCC----HHHHHHTCTTCCHH
T ss_pred             hcccCCccccC----HHHHHHHCCCCCHH
Confidence            86222  2223    34677888886443

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.22  E-value=1.3e-05  Score=63.78  Aligned_cols=139  Identities=17%  Similarity=0.156  Sum_probs=75.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-----CHHHHHHHHHHHhCCCcc------------
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-----DIRKIQEEIGDKLGLKFH------------  173 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-----~~~~l~~~i~~~l~~~~~------------  173 (276)
                      ..++-+.++|++|+|||++|+.+.+.....     .+.++.+.-.     ..+.-++.+++......+            
T Consensus        43 ~~~~~iLL~GppGtGKT~la~~iA~~~~~~-----~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~  117 (256)
T d1lv7a_          43 KIPKGVLMVGPPGTGKTLLAKAIAGEAKVP-----FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVG  117 (256)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHHHTCC-----EEEECSCSSTTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHT
T ss_pred             CCCCeEEeeCCCCCCccHHHHHHHHHcCCC-----EEEEEhHHhhhcchhHHHHHHHHHHHHHHHcCCEEEEEEChhhhC
Confidence            346778999999999999999999887533     2333332211     113333444333211100            


Q ss_pred             ----c--ccchhh----hhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHhhCC
Q 041612          174 ----E--ESESGR----ANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKMAGD  234 (276)
Q Consensus       174 ----~--~~~~~~----~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~  234 (276)
                          .  ......    ...+..     ....+--||-||....-... ..   ...+.+.++..+.++-.++|+.....
T Consensus       118 ~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~  197 (256)
T d1lv7a_         118 RQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRR  197 (256)
T ss_dssp             CCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTT
T ss_pred             ccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccC
Confidence                0  000000    111111     23333445557765543322 22   24567889999999999999888752


Q ss_pred             CC--CChhHHHHHHHHHHHcCCCcHH
Q 041612          235 YI--EDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       235 ~~--~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      ..  .+.+    ...+++.+.|+.-|
T Consensus       198 ~~~~~~~~----~~~la~~t~G~s~a  219 (256)
T d1lv7a_         198 VPLAPDID----AAIIARGTPGFSGA  219 (256)
T ss_dssp             SCBCTTCC----HHHHHHTCTTCCHH
T ss_pred             CCcCcccC----HHHHHHhCCCCCHH
Confidence            22  2223    34677888887644

>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=98.16  E-value=3.9e-06  Score=65.86  Aligned_cols=159  Identities=12%  Similarity=0.160  Sum_probs=89.2

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCC-CCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc--------
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDK-LFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH--------  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~--------  173 (276)
                      .+.+++.....+.+.++|++|+||||+++.+.+...... .......++.+...........+-+.......        
T Consensus        23 ~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (237)
T d1sxjd2          23 VLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLE  102 (237)
T ss_dssp             HHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHH
T ss_pred             HHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhhhhhhhhhHHHHh
Confidence            777788877777789999999999999999988763221 12223344444444444433333221100000        


Q ss_pred             -------------c--ccch---hhhhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCC
Q 041612          174 -------------E--ESES---GRANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGD  234 (276)
Q Consensus       174 -------------~--~~~~---~~~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~  234 (276)
                                   +  .-..   .....+.......+++|+||.+.. +..........+++++++.++...++.+.+..
T Consensus       103 ~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~  182 (237)
T d1sxjd2         103 NYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQ  182 (237)
T ss_dssp             HSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHT
T ss_pred             hccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhccccccccccchhhhhhhhh
Confidence                         0  0000   001111114455667777765432 22221222346899999999999999887752


Q ss_pred             CCCChhHHHHHHHHHHHcCCC-cHHHHHH
Q 041612          235 YIEDSEFQSIARDVAKECAGL-PVSIVTI  262 (276)
Q Consensus       235 ~~~~~~~~~~~~~i~~~c~G~-PLai~~i  262 (276)
                      ....- -.+....|++.++|- ..|+..+
T Consensus       183 e~i~i-~~~~l~~ia~~s~gd~R~ai~~L  210 (237)
T d1sxjd2         183 ENVKC-DDGVLERILDISAGDLRRGITLL  210 (237)
T ss_dssp             TTCCC-CHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             hcCcC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            22111 124578899999775 4555544

>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=98.13  E-value=1.7e-06  Score=67.83  Aligned_cols=153  Identities=13%  Similarity=0.111  Sum_probs=82.1

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCC-eEEEEEecCcCCHHHHHHHHHHHhCC---Cc--c---
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD-QVVFVEVSQNQDIRKIQEEIGDKLGL---KF--H---  173 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l~~---~~--~---  173 (276)
                      +|..++..+..+.+.++|++|+||||+|+.+.+..... .++ ..+-++.+...+...+...+......   ..  .   
T Consensus        35 ~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~-~~~~~~~e~n~s~~~~~~~~~~~~~~~~~~~~~~~~~~~ii  113 (231)
T d1iqpa2          35 RLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKII  113 (231)
T ss_dssp             HHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEE
T ss_pred             HHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc-ccCCCeeEEecCcccchhHHHHHHHHHHhhhhccCCCceEE
Confidence            67777777777788999999999999999998876432 122 12223333322222211222111110   00  0   


Q ss_pred             ---c--ccchhhhh---hccccCCCCcEEEEEeccc-cccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHH
Q 041612          174 ---E--ESESGRAN---SLFTHGHKGCKVLLTARSQ-DVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSI  244 (276)
Q Consensus       174 ---~--~~~~~~~~---~l~~~~~~gs~IivTTR~~-~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  244 (276)
                         +  ........   ...........+|.||... .+..........+.+.+.+.++....++..+...... -..+.
T Consensus       114 lide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~-i~~~~  192 (231)
T d1iqpa2         114 FLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE-LTEEG  192 (231)
T ss_dssp             EEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE-ECHHH
T ss_pred             eehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHHHHHhCCC-CCHHH
Confidence               0  00001111   1111334445555555443 3322222233578999999999999988887522211 12345


Q ss_pred             HHHHHHHcCCCcH
Q 041612          245 ARDVAKECAGLPV  257 (276)
Q Consensus       245 ~~~i~~~c~G~PL  257 (276)
                      ...|++.|+|-+-
T Consensus       193 l~~I~~~~~gdiR  205 (231)
T d1iqpa2         193 LQAILYIAEGDMR  205 (231)
T ss_dssp             HHHHHHHHTTCHH
T ss_pred             HHHHHHHcCCCHH
Confidence            6789999988654

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.09  E-value=4.1e-05  Score=60.94  Aligned_cols=147  Identities=12%  Similarity=0.142  Sum_probs=78.0

Q ss_pred             HHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCc----C-CHHHHHHHHHHHh---CCC-----
Q 041612          105 LSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQN----Q-DIRKIQEEIGDKL---GLK-----  171 (276)
Q Consensus       105 ~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~----~-~~~~l~~~i~~~l---~~~-----  171 (276)
                      ...+.-..++-+.++|++|+|||++|+.+.+.....     .+.++.+.-    . .....++.+....   ...     
T Consensus        30 ~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~-----~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~p~il~iD  104 (258)
T d1e32a2          30 FKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID  104 (258)
T ss_dssp             HHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCE-----EEEECHHHHTTSCTTHHHHHHHHHHHHHHHTCSEEEEES
T ss_pred             HHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCe-----EEEEEchhhcccccccHHHHHHHHHHHHHhcCCeEEEeh
Confidence            333344456779999999999999999999876432     233332211    1 1122233333221   110     


Q ss_pred             cccc-------cc----hhhhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHh
Q 041612          172 FHEE-------SE----SGRANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKM  231 (276)
Q Consensus       172 ~~~~-------~~----~~~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~  231 (276)
                      ..+.       ..    ......+..     ....+.-||.||....-... ..   ...+.+.++..+.++-..+|+..
T Consensus       105 eid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~  184 (258)
T d1e32a2         105 ELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIH  184 (258)
T ss_dssp             SGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHT
T ss_pred             hhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhh
Confidence            0000       00    000011111     33334445557866543222 22   34568999999999999999888


Q ss_pred             hCCCCCChhHHHHHHHHHHHcCCCcHH
Q 041612          232 AGDYIEDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       232 ~~~~~~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      .......++..  ...|++.+.|+--|
T Consensus       185 l~~~~~~~~~~--~~~la~~t~G~s~a  209 (258)
T d1e32a2         185 TKNMKLADDVD--LEQVANETHGHVGA  209 (258)
T ss_dssp             TTTSCBCTTCC--HHHHHHHCTTCCHH
T ss_pred             ccCcccccccc--hhhhhhcccCCCHH
Confidence            75322222211  35788999887543

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.09  E-value=4.3e-05  Score=59.81  Aligned_cols=142  Identities=16%  Similarity=0.108  Sum_probs=75.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCccc-ccchhhh-----hhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHE-ESESGRA-----NSLFT  186 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-~~~~~~~-----~~l~~  186 (276)
                      .+-+.++|++|+|||++|+.+.+.....     ...++.+.......+ ..++......... .++....     ..+..
T Consensus        35 ~~~~L~~GPpGtGKT~lA~~la~~~~~~-----~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ide~~~~~~~~~~~l~~  108 (238)
T d1in4a2          35 LDHVLLAGPPGLGKTTLAHIIASELQTN-----IHVTSGPVLVKQGDM-AAILTSLERGDVLFIDEIHRLNKAVEELLYS  108 (238)
T ss_dssp             CCCEEEESSTTSSHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHH-HHHHHHCCTTCEEEEETGGGCCHHHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHhccCCC-----cccccCcccccHHHH-HHHHHhhccCCchHHHHHHHhhhHHHhhccc
Confidence            4567899999999999999999887543     223444444444433 2333332211000 0000000     00000


Q ss_pred             ---------------------cCCCCcEEEEEecccc-cccc-CCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHH
Q 041612          187 ---------------------HGHKGCKVLLTARSQD-VLSG-KMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQS  243 (276)
Q Consensus       187 ---------------------~~~~gs~IivTTR~~~-va~~-~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~  243 (276)
                                           ...+...+|.+|.+.. +... .......+.++..+.++...++......... ....+
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~~  187 (238)
T d1in4a2         109 AIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV-EIEDA  187 (238)
T ss_dssp             HHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-CBCHH
T ss_pred             ceeeeeeeeeecCcccccccccCCCCeEEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccc-hhhHH
Confidence                                 1122345555554443 2111 1233346789999999999999877752111 11223


Q ss_pred             HHHHHHHHcCCCcHHHHH
Q 041612          244 IARDVAKECAGLPVSIVT  261 (276)
Q Consensus       244 ~~~~i~~~c~G~PLai~~  261 (276)
                      ....|++.+.|-+-.+..
T Consensus       188 ~l~~i~~~s~gd~R~ai~  205 (238)
T d1in4a2         188 AAEMIAKRSRGTPRIAIR  205 (238)
T ss_dssp             HHHHHHHTSTTCHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHH
Confidence            577888998888665543

>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=98.08  E-value=2.5e-05  Score=61.69  Aligned_cols=144  Identities=13%  Similarity=0.078  Sum_probs=77.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc----------------c-
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH----------------E-  174 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~----------------~-  174 (276)
                      ..+.+.++|++|+||||+|+.+++....     ..++++.+...+...+... .........                . 
T Consensus        51 ~~~~lll~GPpG~GKTt~a~~la~~~~~-----~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (253)
T d1sxja2          51 VFRAAMLYGPPGIGKTTAAHLVAQELGY-----DILEQNASDVRSKTLLNAG-VKNALDNMSVVGYFKHNEEAQNLNGKH  124 (253)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHTTC-----EEEEECTTSCCCHHHHHHT-GGGGTTBCCSTTTTTC----CCSSTTS
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHh-----hhhccccccchhhHHHHHH-HHHHhhcchhhhhhhhhhhcccccccc
Confidence            3568999999999999999999987643     2455665555444443222 211110000                0 


Q ss_pred             ----ccchh--------hhhhccc-cCCCCcEEEEEecc--ccccccCCCCCCceeCCCCCHHHHHHHHHHhhC--CCCC
Q 041612          175 ----ESESG--------RANSLFT-HGHKGCKVLLTARS--QDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAG--DYIE  237 (276)
Q Consensus       175 ----~~~~~--------~~~~l~~-~~~~gs~IivTTR~--~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~--~~~~  237 (276)
                          .++.+        ....+.. .......|++|+-+  .............+++.+++.++-...+.....  .-..
T Consensus       125 ~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i  204 (253)
T d1sxja2         125 FVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKL  204 (253)
T ss_dssp             EEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCC
T ss_pred             eEEEeeeccccccchhhhhHHHhhhhcccccccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCC
Confidence                00000        0000111 11222345555432  222222334455899999999999988887663  1112


Q ss_pred             ChhHHHHHHHHHHHcCCCc-HHHHHHHH
Q 041612          238 DSEFQSIARDVAKECAGLP-VSIVTIAR  264 (276)
Q Consensus       238 ~~~~~~~~~~i~~~c~G~P-Lai~~i~~  264 (276)
                      ++   +....|++.++|-. .|+..+=.
T Consensus       205 ~~---~~l~~i~~~s~GDiR~ai~~L~~  229 (253)
T d1sxja2         205 DP---NVIDRLIQTTRGDIRQVINLLST  229 (253)
T ss_dssp             CT---THHHHHHHHTTTCHHHHHHHHTH
T ss_pred             CH---HHHHHHHHhCCCcHHHHHHHHHH
Confidence            22   23567999999965 55544433

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.05  E-value=8.3e-05  Score=58.89  Aligned_cols=59  Identities=19%  Similarity=0.246  Sum_probs=43.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLK  171 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  171 (276)
                      .++.+.|+|++|+|||++++.+.+....... ...+++..............+....+..
T Consensus        42 ~~~~lll~GppGtGKT~l~~~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (276)
T d1fnna2          42 HYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIARSLNIP  100 (276)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHHHHTTCC
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHhcccC-CcEEEecchhhhhhhhhhhhhHHhhhhh
Confidence            4678999999999999999999999875522 2345666666666666666666665543

>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=97.97  E-value=8e-05  Score=57.11  Aligned_cols=152  Identities=12%  Similarity=0.074  Sum_probs=87.6

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccC-------------------CCCCeEEEEEecCcC--CHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSD-------------------KLFDQVVFVEVSQNQ--DIRKI  160 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~~~~~~--~~~~l  160 (276)
                      ++.+.+..+. ++.+.++|++|+||||+|+.+.+..-..                   .......++......  -..+.
T Consensus        13 ~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~   92 (207)
T d1a5ta2          13 KLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDA   92 (207)
T ss_dssp             HHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHH
T ss_pred             HHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccch
Confidence            4555555555 4568999999999999999988764211                   011122333222211  12333


Q ss_pred             HHHHHHHhCCCccc------------ccchhh---hhhccccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHH
Q 041612          161 QEEIGDKLGLKFHE------------ESESGR---ANSLFTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEA  224 (276)
Q Consensus       161 ~~~i~~~l~~~~~~------------~~~~~~---~~~l~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea  224 (276)
                      .+.+.+.+......            .-+...   +.+..+.....+.+|+||.+.+ +......-...+++.+++.++.
T Consensus        93 ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~  172 (207)
T d1a5ta2          93 VREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYA  172 (207)
T ss_dssp             HHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHH
T ss_pred             hhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEEecCCCCHHHH
Confidence            44555555432111            011111   2222235567888888887754 4333333346899999999999


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHHHH
Q 041612          225 WSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIV  260 (276)
Q Consensus       225 ~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLai~  260 (276)
                      ...+.....   .+   .+....|++.++|.|-.+.
T Consensus       173 ~~~L~~~~~---~~---~~~~~~i~~~s~Gs~r~al  202 (207)
T d1a5ta2         173 VTWLSREVT---MS---QDALLAALRLSAGSPGAAL  202 (207)
T ss_dssp             HHHHHHHCC---CC---HHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHcCC---CC---HHHHHHHHHHcCCCHHHHH
Confidence            998876642   11   2446778899999876543

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=97.93  E-value=0.00016  Score=56.47  Aligned_cols=146  Identities=12%  Similarity=0.031  Sum_probs=77.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc------cccchhhhhhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH------EESESGRANSLF  185 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~  185 (276)
                      .++-+.++|++|+||||+|+.+.+.....     ..+++.+...........+...+.....      +.........+.
T Consensus        34 ~~~~~Ll~GPpG~GKTtla~~la~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iDe~~~~~~~~~~~l~  108 (239)
T d1ixsb2          34 PLEHLLLFGPPGLGKTTLAHVIAHELGVN-----LRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLY  108 (239)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHHHHHHHTTCCTTCEEEEETGGGCCHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhCCC-----eEeccCCccccchhhHHHHHhhccCCCeeeeecccccchhHHHhhh
Confidence            35567899999999999999999887543     2444444443433333333322222100      000000000000


Q ss_pred             c---------------------cCCCCcEEEEEe-cccccc-ccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHH
Q 041612          186 T---------------------HGHKGCKVLLTA-RSQDVL-SGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQ  242 (276)
Q Consensus       186 ~---------------------~~~~gs~IivTT-R~~~va-~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~  242 (276)
                      .                     ...+...++.+| +..... .........+.+...+.++..+++......... ....
T Consensus       109 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i-~~~~  187 (239)
T d1ixsb2         109 PAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGV-RITE  187 (239)
T ss_dssp             HHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCC-CBCH
T ss_pred             hhhhhhhhhhhhccchhhhhcccCCCCEEEEeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCC-ccch
Confidence            0                     122333444444 332221 222334557889999999999888877652111 1123


Q ss_pred             HHHHHHHHHcCCCcHHHHHHH
Q 041612          243 SIARDVAKECAGLPVSIVTIA  263 (276)
Q Consensus       243 ~~~~~i~~~c~G~PLai~~i~  263 (276)
                      +....|++.+.|-+-.+.-+-
T Consensus       188 ~~l~~ia~~s~gd~R~a~~~l  208 (239)
T d1ixsb2         188 EAALEIGRRSRGTMRVAKRLF  208 (239)
T ss_dssp             HHHHHHHHHTTSSHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHH
Confidence            467899999999876554333

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.90  E-value=2.9e-05  Score=61.19  Aligned_cols=72  Identities=10%  Similarity=0.093  Sum_probs=44.2

Q ss_pred             cCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHcCCCcHH
Q 041612          187 HGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       187 ~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      .....+++|+||.+.+ +..........+++.+++.++..+++...+......-..++....|++.+.|-+-.
T Consensus       157 ~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~  229 (252)
T d1sxje2         157 KYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRV  229 (252)
T ss_dssp             HSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHH
T ss_pred             cccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHH
Confidence            4556678788776543 21111122346889999999999988776631111111124567899999887754

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.79  E-value=0.00017  Score=57.41  Aligned_cols=130  Identities=16%  Similarity=0.175  Sum_probs=79.5

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCC----CCCeEEEE-Eec-------CcCCHHHHHHHHHHHhCC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDK----LFDQVVFV-EVS-------QNQDIRKIQEEIGDKLGL  170 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~f~~~~wv-~~~-------~~~~~~~l~~~i~~~l~~  170 (276)
                      +++..|......-+.++|.+|+|||+|+..+.......+    ..+..+|. +.+       .....+.-++.+++.+..
T Consensus        29 ~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~  108 (268)
T d1r6bx2          29 RAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQ  108 (268)
T ss_dssp             HHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSS
T ss_pred             HHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhc
Confidence            677777766667788999999999999999888765432    12344444 322       123567777777777643


Q ss_pred             Cccc-----------------ccchhhhhhcccc-CCCCcEEEEEecccccccc------CCCCCCceeCCCCCHHHHHH
Q 041612          171 KFHE-----------------ESESGRANSLFTH-GHKGCKVLLTARSQDVLSG------KMDSRPNFSIGVLNEEEAWS  226 (276)
Q Consensus       171 ~~~~-----------------~~~~~~~~~l~~~-~~~gs~IivTTR~~~va~~------~~~~~~~~~l~~L~~~ea~~  226 (276)
                      ...-                 ....+....+... ....-++|.||..+.....      .......+.+++++.+++..
T Consensus       109 ~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~  188 (268)
T d1r6bx2         109 DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQ  188 (268)
T ss_dssp             SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHH
T ss_pred             cCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHH
Confidence            2110                 0111222222222 2334678888776654321      12223478999999999999


Q ss_pred             HHHHhh
Q 041612          227 LFKKMA  232 (276)
Q Consensus       227 Lf~~~~  232 (276)
                      ++....
T Consensus       189 IL~~~~  194 (268)
T d1r6bx2         189 IINGLK  194 (268)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            987654

>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=97.75  E-value=0.00016  Score=56.56  Aligned_cols=156  Identities=13%  Similarity=0.197  Sum_probs=90.8

Q ss_pred             HHHHhhcCCC-ccEEEEEcCCCCcHHHHHHHHHHhcccCC--------------------CCCeEEEEEecCcCCHHHHH
Q 041612          103 NILSALEDPD-VNMLGIYGMGGIGKTMLAEEIARKVKSDK--------------------LFDQVVFVEVSQNQDIRKIQ  161 (276)
Q Consensus       103 ~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~~~~~~~~~~l~  161 (276)
                      .|..++..+. ++.+.++|++|+||||+|+.+.+......                    +++ .+.++.+....... .
T Consensus        23 ~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~~~~~~~i~~-i  100 (239)
T d1njfa_          23 ALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVED-T  100 (239)
T ss_dssp             HHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTT-EEEEETTCSSSHHH-H
T ss_pred             HHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCe-EEEecchhcCCHHH-H
Confidence            4555555554 45688999999999999999877653321                    112 34444444444443 3


Q ss_pred             HHHHHHhCCCccc------------ccchhhhhhc---cccCCCCcEEEEEecccc-ccccCCCCCCceeCCCCCHHHHH
Q 041612          162 EEIGDKLGLKFHE------------ESESGRANSL---FTHGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVLNEEEAW  225 (276)
Q Consensus       162 ~~i~~~l~~~~~~------------~~~~~~~~~l---~~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L~~~ea~  225 (276)
                      +.+.+.+......            .-.......+   .+.....+++|++|.+.+ +..........+.+.+++.++..
T Consensus       101 r~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~  180 (239)
T d1njfa_         101 RDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIR  180 (239)
T ss_dssp             HHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHH
T ss_pred             HHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhh
Confidence            4555554322111            0011111122   225556778888876654 22222333457899999999998


Q ss_pred             HHHHHhhC--CCCCChhHHHHHHHHHHHcCCCcH-HHHHHH
Q 041612          226 SLFKKMAG--DYIEDSEFQSIARDVAKECAGLPV-SIVTIA  263 (276)
Q Consensus       226 ~Lf~~~~~--~~~~~~~~~~~~~~i~~~c~G~PL-ai~~i~  263 (276)
                      ..+...+.  ....+   .+....|+..++|-|- |+..+=
T Consensus       181 ~~l~~i~~~e~~~~~---~~~l~~i~~~s~Gd~R~ain~l~  218 (239)
T d1njfa_         181 HQLEHILNEEHIAHE---PRALQLLARAAEGSLRDALSLTD  218 (239)
T ss_dssp             HHHHHHHHHHTCCBC---HHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             hHHHHHHhhhccCCC---HHHHHHHHHHcCCCHHHHHHHHH
Confidence            88877764  11222   2356789999999885 555543

>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=97.64  E-value=0.00012  Score=56.36  Aligned_cols=136  Identities=14%  Similarity=0.178  Sum_probs=71.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCC-H-HHH----HHHHHHHh---CCCccc----ccc-hh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQD-I-RKI----QEEIGDKL---GLKFHE----ESE-SG  179 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~-~-~~l----~~~i~~~l---~~~~~~----~~~-~~  179 (276)
                      ..+.|+|++|+|||+|++.+++....+  ...+++++...-.. . ..+    ...+.+.+   ..-.-+    ... ..
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~~~~~  114 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKR--GYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKER  114 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT--TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTTCHH
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccC--ccceEEechHHHHHHHHHHHHccchhhHHHHHhhccchhhhhhhhhcCchH
Confidence            347899999999999999999998765  34566665432211 0 000    00111111   100000    000 01


Q ss_pred             hhhhccc----cCCCCcEEEEEeccccccccC--------CCCCCceeCCCCCHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 041612          180 RANSLFT----HGHKGCKVLLTARSQDVLSGK--------MDSRPNFSIGVLNEEEAWSLFKKMAGDYIEDSEFQSIARD  247 (276)
Q Consensus       180 ~~~~l~~----~~~~gs~IivTTR~~~va~~~--------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~  247 (276)
                      ....++.    ....|.+||+||+........        ......+.++ +++++-..++++.+...... --.++..-
T Consensus       115 ~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~-l~~~v~~y  192 (213)
T d1l8qa2         115 TQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLE-LRKEVIDY  192 (213)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCC-CCHHHHHH
T ss_pred             HHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCC-CCHHHHHH
Confidence            1111111    445678999999876432211        2233467775 57777778888777421111 11245666


Q ss_pred             HHHHcC
Q 041612          248 VAKECA  253 (276)
Q Consensus       248 i~~~c~  253 (276)
                      |++++.
T Consensus       193 l~~~~~  198 (213)
T d1l8qa2         193 LLENTK  198 (213)
T ss_dssp             HHHHCS
T ss_pred             HHHhcC
Confidence            777764

>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=97.64  E-value=3.9e-05  Score=61.31  Aligned_cols=139  Identities=19%  Similarity=0.206  Sum_probs=73.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC----cC-CHHHHHHHHHHHhCCCcc--------c---
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ----NQ-DIRKIQEEIGDKLGLKFH--------E---  174 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~----~~-~~~~l~~~i~~~l~~~~~--------~---  174 (276)
                      ...+-|.++|++|+|||+||+.+++.....     .+.++.+.    .. .....++.++.......+        +   
T Consensus        39 ~~~~giLL~Gp~GtGKT~l~~ala~~~~~~-----~~~~~~~~l~~~~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~  113 (265)
T d1r7ra3          39 TPSKGVLFYGPPGCGKTLLAKAIANECQAN-----FISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIA  113 (265)
T ss_dssp             CCCCEEEEBCCTTSSHHHHHHHHHHHTTCE-----EEEECHHHHHTSCTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTC
T ss_pred             CCCCeEEEECCCCCcchhHHHHHHHHhCCc-----EEEEEHHHhhhccccchHHHHHHHHHHHHhcCCcceeHHhhhhcc
Confidence            345678999999999999999999887543     22222211    11 233444444432211100        0   


Q ss_pred             -------ccchh----hhhhccc-----cCCCCcEEEEEecccccccc-CC---CCCCceeCCCCCHHHHHHHHHHhhCC
Q 041612          175 -------ESESG----RANSLFT-----HGHKGCKVLLTARSQDVLSG-KM---DSRPNFSIGVLNEEEAWSLFKKMAGD  234 (276)
Q Consensus       175 -------~~~~~----~~~~l~~-----~~~~gs~IivTTR~~~va~~-~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~  234 (276)
                             .....    ....+..     ...++--||.||....-... ..   ...+.++++..+.++-.++|+.....
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~  193 (265)
T d1r7ra3         114 KARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRK  193 (265)
T ss_dssp             CHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTC
T ss_pred             ccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhcc
Confidence                   00000    0111111     12334455667765543222 11   24457899999999999999877652


Q ss_pred             CC--CChhHHHHHHHHHHHcCCCcHH
Q 041612          235 YI--EDSEFQSIARDVAKECAGLPVS  258 (276)
Q Consensus       235 ~~--~~~~~~~~~~~i~~~c~G~PLa  258 (276)
                      ..  .+.+    ..++++++.|+.-+
T Consensus       194 ~~~~~~~~----l~~la~~t~g~s~~  215 (265)
T d1r7ra3         194 SPVAKDVD----LEFLAKMTNGFSGA  215 (265)
T ss_dssp             C----CCC----CHHHHHHHCSSCCH
T ss_pred             CCchhhhh----HHHHHhcCCCCCHH
Confidence            21  2223    34677788877544

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.63  E-value=0.00032  Score=55.61  Aligned_cols=55  Identities=27%  Similarity=0.350  Sum_probs=35.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      ++.++|++|+|||++++.+.+.....    .......++..............+...++
T Consensus        48 ~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (287)
T d1w5sa2          48 IYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTG  106 (287)
T ss_dssp             EEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHT
T ss_pred             EEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchhhHHHHHhhhcc
Confidence            45678999999999999999886432    11234556665555555555555544443

>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=97.58  E-value=2e-05  Score=58.05  Aligned_cols=28  Identities=21%  Similarity=0.377  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++++|+|.+|+|||||++.+......+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            4689999999999999999999887655

>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=97.58  E-value=1.9e-05  Score=59.01  Aligned_cols=26  Identities=23%  Similarity=0.391  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++.|+|.|++|+||||||+.+.....
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            57899999999999999999998764

>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=3.9e-05  Score=56.84  Aligned_cols=36  Identities=14%  Similarity=0.082  Sum_probs=28.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      -.+|.|+|++|+||||+|+.+...+... +++...+.
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~L~~~-~~~~~~~~   41 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVTLNQQ-GGRSVSLL   41 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH-CSSCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhc-CCCchhhh
Confidence            4689999999999999999999888654 24555554

>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=97.46  E-value=3.1e-05  Score=56.41  Aligned_cols=25  Identities=20%  Similarity=0.412  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.|.+.|++|+||||+|+.+.....
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            5688899999999999999998864

>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=97.44  E-value=4.4e-05  Score=57.79  Aligned_cols=30  Identities=27%  Similarity=0.344  Sum_probs=26.0

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....+.+|.|+|++|+||||+|+.+.....
T Consensus         2 ~~~kp~iI~i~G~pGSGKsT~a~~La~~~g   31 (194)
T d1qf9a_           2 EKSKPNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CCCCCEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            345678999999999999999999998763

>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=97.43  E-value=8.9e-05  Score=55.77  Aligned_cols=33  Identities=27%  Similarity=0.522  Sum_probs=28.4

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +...++.+|+|.|.+|+||||||+.+.......
T Consensus        17 ~~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          17 IKTAGRLVLGIDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             SCCSSSEEEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             ccCCCCEEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            455677899999999999999999998887654

>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=97.42  E-value=4e-05  Score=55.37  Aligned_cols=24  Identities=29%  Similarity=0.367  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++|.|+|++|+||||||+.+....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            478899999999999999886543

>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=97.42  E-value=3.6e-05  Score=56.70  Aligned_cols=26  Identities=35%  Similarity=0.503  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.|.|.|++|+||||+|+.+.....
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHC
Confidence            35688999999999999999987764

>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=97.42  E-value=4.2e-05  Score=56.29  Aligned_cols=25  Identities=24%  Similarity=0.474  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|.|++|+||||+|+.+.....
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~   27 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLD   27 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcC
Confidence            5799999999999999999987653

>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=97.35  E-value=6.6e-05  Score=55.73  Aligned_cols=27  Identities=30%  Similarity=0.396  Sum_probs=24.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +.|.|+|++|+|||||++.+......+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            579999999999999999999887654

>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=97.33  E-value=7.2e-05  Score=55.05  Aligned_cols=29  Identities=28%  Similarity=0.562  Sum_probs=25.2

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +...+++.|.|++|+||||+|+.+.....
T Consensus         3 ~~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           3 NHDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             CTTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34578999999999999999999988764

>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=97.29  E-value=8.9e-05  Score=54.64  Aligned_cols=28  Identities=39%  Similarity=0.450  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +....|.|.|++|+||||+|+.+.....
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~   30 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELD   30 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhC
Confidence            3456799999999999999999998754

>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=97.28  E-value=6.1e-05  Score=56.68  Aligned_cols=28  Identities=18%  Similarity=0.274  Sum_probs=24.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..+|.++|++|+||||+|+.+.......
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            4688899999999999999999887654

>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=9.8e-05  Score=55.89  Aligned_cols=30  Identities=20%  Similarity=0.340  Sum_probs=26.3

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++..++|.|.|++|+||||+|+.+...+.
T Consensus         4 ~~~~~~iI~i~GppGSGKsT~a~~La~~~g   33 (196)
T d1ukza_           4 SPDQVSVIFVLGGPGAGKGTQCEKLVKDYS   33 (196)
T ss_dssp             CTTTCEEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346788999999999999999999988763

>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=97.25  E-value=0.00011  Score=53.92  Aligned_cols=28  Identities=25%  Similarity=0.328  Sum_probs=25.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++++|+|..|+|||||+..+...++.+
T Consensus         1 Mkii~I~G~~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_           1 MNVWQVVGYKHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHhC
Confidence            3689999999999999999999888765

>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=97.24  E-value=8.3e-05  Score=55.35  Aligned_cols=27  Identities=15%  Similarity=0.386  Sum_probs=24.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++|+|.|++|+||||+++.+......+
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            689999999999999999999887654

>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=97.23  E-value=9.9e-05  Score=54.39  Aligned_cols=26  Identities=15%  Similarity=0.225  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++|.|.|++|+||||+|+.+.....
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999998864

>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=97.22  E-value=9.8e-05  Score=54.86  Aligned_cols=27  Identities=22%  Similarity=0.395  Sum_probs=23.3

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .+.+.+|.++|++|+||||+|+.+...
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

>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=97.15  E-value=9.9e-05  Score=54.28  Aligned_cols=25  Identities=20%  Similarity=0.426  Sum_probs=21.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          116 LGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       116 i~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      |.+.|++|+||||+++.+.......
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~   28 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVG   28 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCC
Confidence            5566999999999999999887543

>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=97.14  E-value=0.00012  Score=55.74  Aligned_cols=28  Identities=18%  Similarity=0.343  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +-+|.++|.+|+||||+|+.+.......
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~~   29 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNFI   29 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            4579999999999999999999876543

>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=97.11  E-value=0.00015  Score=53.73  Aligned_cols=25  Identities=32%  Similarity=0.506  Sum_probs=22.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|+|+|++|+|||||++.+......
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            4899999999999999999987754

>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=97.10  E-value=0.00015  Score=57.49  Aligned_cols=29  Identities=24%  Similarity=0.265  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.++.|.++|++|+||||||+.+++....
T Consensus        30 ~~P~~ilL~GpPGtGKT~la~~la~~~~~   58 (273)
T d1gvnb_          30 ESPTAFLLGGQPGSGKTSLRSAIFEETQG   58 (273)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHTTT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhc
Confidence            34677999999999999999999988754

>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=97.06  E-value=0.00015  Score=54.47  Aligned_cols=27  Identities=30%  Similarity=0.208  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++..|.|.|++|+||||+|+.+.+...
T Consensus         2 ~Pm~I~i~GppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1           2 DPLKVMISGAPASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHC
Confidence            456788999999999999999988774

>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=97.06  E-value=0.00014  Score=53.63  Aligned_cols=25  Identities=36%  Similarity=0.442  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -++|.|.|++|+||||+|+.+....
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLP   28 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999997654

>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=97.05  E-value=0.00015  Score=53.09  Aligned_cols=25  Identities=28%  Similarity=0.444  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -|.|.|++|+||||+++.+......
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~   26 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDL   26 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3778899999999999999988743

>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=97.03  E-value=0.00038  Score=54.69  Aligned_cols=28  Identities=29%  Similarity=0.223  Sum_probs=24.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++-|.++|++|+|||++|+.+++....
T Consensus        39 p~~~vLL~GppGtGKT~la~alA~~~~~   66 (246)
T d1d2na_          39 PLVSVLLEGPPHSGKTALAAKIAEESNF   66 (246)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHHHHHHTC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHhhcccc
Confidence            4567899999999999999999988653

>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=97.03  E-value=0.00018  Score=55.17  Aligned_cols=27  Identities=26%  Similarity=0.406  Sum_probs=24.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .++|+|.|++|+||||+|+.+.+++.-
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~gl   29 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQW   29 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            469999999999999999999998853

>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=97.00  E-value=0.0002  Score=53.97  Aligned_cols=26  Identities=23%  Similarity=0.216  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.+|.|.|++|+||||+|+.++..+.
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~g   26 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKYG   26 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999998763

>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=96.98  E-value=0.0002  Score=52.89  Aligned_cols=25  Identities=28%  Similarity=0.384  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|.+.|++|+||||+|+.+......
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg~   28 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALGY   28 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4678899999999999999988753

>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=96.97  E-value=0.00024  Score=52.90  Aligned_cols=28  Identities=14%  Similarity=0.382  Sum_probs=24.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++|.|.|++|+||||+++.+...+..+
T Consensus         1 mkiivi~G~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           1 MKIGIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            3688999999999999999999888654

>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=96.81  E-value=0.00036  Score=51.74  Aligned_cols=24  Identities=33%  Similarity=0.408  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~~   25 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAYG   25 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478999999999999999988773

>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=96.79  E-value=0.00049  Score=51.71  Aligned_cols=27  Identities=22%  Similarity=0.369  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ....|.|.|++|+||||+|+.+...+.
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHBC
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHHC
Confidence            345778899999999999999998764

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=96.79  E-value=0.0039  Score=51.97  Aligned_cols=130  Identities=12%  Similarity=0.131  Sum_probs=70.3

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEE-EEecCc-------CCHHHHHHHHHHHhCC
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVF-VEVSQN-------QDIRKIQEEIGDKLGL  170 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~w-v~~~~~-------~~~~~l~~~i~~~l~~  170 (276)
                      +++..|...+..-+.++|.+|+|||+|+..+.......    ...+..+| ++++.-       ...+.-+..|+..+..
T Consensus        33 ~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~  112 (387)
T d1qvra2          33 RVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQ  112 (387)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhcc
Confidence            67777766555667889999999999887666654332    22344444 443321       2455556666665532


Q ss_pred             Ccccc----c-------------chhhhhhccc-cCCCCcEEEEEeccccccc-----cCCCCCCceeCCCCCHHHHHHH
Q 041612          171 KFHEE----S-------------ESGRANSLFT-HGHKGCKVLLTARSQDVLS-----GKMDSRPNFSIGVLNEEEAWSL  227 (276)
Q Consensus       171 ~~~~~----~-------------~~~~~~~l~~-~~~~gs~IivTTR~~~va~-----~~~~~~~~~~l~~L~~~ea~~L  227 (276)
                      ...+.    +             ..+....+.. .....-++|-+|.......     ........+.+++.+.+++..+
T Consensus       113 ~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~i  192 (387)
T d1qvra2         113 SQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISI  192 (387)
T ss_dssp             TCSSEEEEECCC-------------------HHHHHTTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHH
T ss_pred             CCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHH
Confidence            21110    0             0011111111 1122345666664443211     1334456899999999999999


Q ss_pred             HHHhh
Q 041612          228 FKKMA  232 (276)
Q Consensus       228 f~~~~  232 (276)
                      +....
T Consensus       193 l~~~~  197 (387)
T d1qvra2         193 LRGLK  197 (387)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87655

>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=96.79  E-value=0.00043  Score=52.91  Aligned_cols=27  Identities=19%  Similarity=0.335  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +-+|+|.|..|+||||+|+.+......
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            568999999999999999999887654

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.77  E-value=0.0025  Score=48.45  Aligned_cols=62  Identities=15%  Similarity=0.243  Sum_probs=43.2

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCH--HHHHHHHHHHhCCCccc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDI--RKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~--~~l~~~i~~~l~~~~~~  174 (276)
                      .+.+.+|.++|+.|+||||-+-++......+   ...+.+-....+..  .+-++...+.++.+...
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~---g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~   69 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIA   69 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEECCCTTCHHHHHHHHHHHHHTTCCEEC
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEecccccccchhhhhhhhhhcCCcccc
Confidence            4567899999999999999777777776643   23444444445444  55567778888877544

>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=96.77  E-value=0.00054  Score=52.31  Aligned_cols=31  Identities=23%  Similarity=0.337  Sum_probs=26.3

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...+...+|-+.|++|+||||||+.+.....
T Consensus        19 ~~~~kg~vIwltGlsGsGKTTia~~L~~~l~   49 (208)
T d1m7ga_          19 LRNQRGLTIWLTGLSASGKSTLAVELEHQLV   49 (208)
T ss_dssp             HHTSSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4456677999999999999999999987663

>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=96.74  E-value=0.00044  Score=51.46  Aligned_cols=24  Identities=29%  Similarity=0.432  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.+...+.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g   25 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYG   25 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            578999999999999999998874

>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=96.70  E-value=0.00052  Score=51.40  Aligned_cols=26  Identities=27%  Similarity=0.408  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.++| |.|++|+||||+|+.+.....
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~~g   28 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKNFC   28 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHHHT
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHHhC
Confidence            34455 789999999999999987663

>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=96.70  E-value=0.00052  Score=51.60  Aligned_cols=27  Identities=26%  Similarity=0.336  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +.++|.|.|++|+||||+|+.+...+.
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~g   33 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKYG   33 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            357899999999999999999988653

>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=96.69  E-value=0.0012  Score=52.23  Aligned_cols=36  Identities=25%  Similarity=0.446  Sum_probs=28.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      .+.|+|+|-||+||||+|-.+.......+ +...++-
T Consensus         1 mr~Iai~gKGGvGKTT~a~nLA~~LA~~G-~rVllID   36 (269)
T d1cp2a_           1 MRQVAIYGKGGIGKSTTTQNLTSGLHAMG-KTIMVVG   36 (269)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHTTT-CCEEEEE
T ss_pred             CCEEEEECCCcCCHHHHHHHHHHHHHhCC-CcEEEEe
Confidence            36899999999999999999988887653 3433443

>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=96.69  E-value=0.0005  Score=51.07  Aligned_cols=24  Identities=29%  Similarity=0.343  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.++..+.
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            578899999999999999998874

>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=96.63  E-value=0.00055  Score=52.48  Aligned_cols=26  Identities=27%  Similarity=0.299  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+|+|-|++|+||||+|+.+...+..
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~lg~   29 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKDFGF   29 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            46889999999999999999988753

>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=96.61  E-value=0.00061  Score=50.97  Aligned_cols=26  Identities=23%  Similarity=0.333  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      |-|.|+|++|+|||||++.+..+...
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~   27 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPD   27 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCc
Confidence            45889999999999999999887654

>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=96.60  E-value=0.004  Score=47.39  Aligned_cols=63  Identities=16%  Similarity=0.249  Sum_probs=43.8

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCccc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~  174 (276)
                      ...+.+|.++|+.|+||||-+-++..+...++  ..+..++... .....+-++...+.++.+...
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~   71 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAADTFRAAAIEQLKIWGERVGATVIS   71 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCEEEC
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CceEEEeecccccchhHHHHHHhhhcCccccc
Confidence            35678999999999999997777777765442  3466666543 234455677778888876543

>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=96.58  E-value=0.00073  Score=50.14  Aligned_cols=25  Identities=20%  Similarity=0.284  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..|.|.|++|+||||+|+.+.....
T Consensus         3 mrIvl~G~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3466889999999999999988763

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.57  E-value=0.00055  Score=55.66  Aligned_cols=26  Identities=27%  Similarity=0.422  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++-+.++|++|+|||.||+.+.+...
T Consensus        49 ~~~iLl~GPpG~GKT~lAkalA~~~~   74 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIARRLAKLAN   74 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHhhccc
Confidence            46678999999999999999998764

>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=96.55  E-value=0.0013  Score=53.65  Aligned_cols=30  Identities=23%  Similarity=0.367  Sum_probs=26.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+..+|+|.|+||+|||||...+......+
T Consensus        52 ~~~~~IgitG~pGaGKSTLi~~l~~~~~~~   81 (327)
T d2p67a1          52 GNTLRLGVTGTPGAGKSTFLEAFGMLLIRE   81 (327)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCceEEEeeCCCCCCHHHHHHHHHHHHHhc
Confidence            357899999999999999999998777655

>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=96.53  E-value=0.0015  Score=53.17  Aligned_cols=30  Identities=20%  Similarity=0.396  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ....+|+|.|+||+|||||...+.......
T Consensus        49 ~~~~~igitG~pGaGKSTli~~l~~~~~~~   78 (323)
T d2qm8a1          49 GRAIRVGITGVPGVGKSTTIDALGSLLTAA   78 (323)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCceEEeeeCCCCCCHHHHHHHHHHHHhhc
Confidence            457799999999999999999988765443

>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=96.52  E-value=0.00077  Score=49.88  Aligned_cols=24  Identities=25%  Similarity=0.155  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            577899999999999999997764

>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=96.51  E-value=0.0008  Score=50.01  Aligned_cols=25  Identities=12%  Similarity=0.365  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++|.|+|++|+|||||++.+..+..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5788999999999999999987653

>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=96.51  E-value=0.0013  Score=49.28  Aligned_cols=37  Identities=24%  Similarity=0.407  Sum_probs=30.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +++..|...+..-+.++|.+|+|||+++..+......
T Consensus        33 ~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~   69 (195)
T d1jbka_          33 RTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             HHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHh
Confidence            6777777766677899999999999999998887654

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.50  E-value=0.0016  Score=51.63  Aligned_cols=37  Identities=24%  Similarity=0.511  Sum_probs=29.4

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +...+..++.++|.+.|-||+||||++-.+......+
T Consensus        11 ~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~   47 (279)
T d1ihua2          11 LVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADM   47 (279)
T ss_dssp             HHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            4455567788999999999999999888877666544

>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=96.46  E-value=0.00074  Score=50.71  Aligned_cols=25  Identities=24%  Similarity=0.359  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|.|+|++|+|||||++.+......
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~   26 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSS   26 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCC
Confidence            4779999999999999999877643

>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=96.45  E-value=0.003  Score=48.02  Aligned_cols=62  Identities=19%  Similarity=0.275  Sum_probs=38.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~  174 (276)
                      ..+.+|.++|+.|+||||.+-++....+.++ . .+..++... .....+-++...+.++.+...
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~~g-~-kV~lit~Dt~R~ga~eQL~~~a~~l~v~~~~   72 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKKKG-F-KVGLVGADVYRPAALEQLQQLGQQIGVPVYG   72 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHHTT-C-CEEEEECCCSSHHHHHHHHHHHHHHTCCEEC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCC-C-ceEEEEeeccccchhHHHHHhccccCcceee
Confidence            4578999999999999997777777766442 2 355555532 223455567778888877543

>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=96.44  E-value=0.00082  Score=50.28  Aligned_cols=23  Identities=30%  Similarity=0.419  Sum_probs=20.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      .+.+|+|.|..|+||||+|..+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            36799999999999999998763

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.41  E-value=0.0024  Score=50.91  Aligned_cols=32  Identities=25%  Similarity=0.276  Sum_probs=26.7

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .++-+++|.+.|-||+||||+|..+......+
T Consensus         4 ~~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~   35 (296)
T d1ihua1           4 LQNIPPYLFFTGKGGVGKTSISCATAIRLAEQ   35 (296)
T ss_dssp             GSSCCSEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCeEEEEECCCcChHHHHHHHHHHHHHHC
Confidence            44558899999999999999998888777655

>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=96.37  E-value=0.0023  Score=48.67  Aligned_cols=27  Identities=11%  Similarity=0.287  Sum_probs=24.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..|+|.|+.|+||||+++.+.+....+
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            579999999999999999999988765

>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=96.37  E-value=0.0043  Score=47.03  Aligned_cols=61  Identities=26%  Similarity=0.373  Sum_probs=41.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~  174 (276)
                      +.+++.++|+.|+||||.+.++......++  ..+..++... .....+-++...+.++.+...
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~   70 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAADTQRPAAREQLRLLGEKVGVPVLE   70 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECCSSCHHHHHHHHHHHHHHTCCEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEecccccchHHHHHHHHHHhcCCcccc
Confidence            467899999999999998878777776542  2345554432 223455667778888877554

>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=96.35  E-value=0.019  Score=43.00  Aligned_cols=113  Identities=17%  Similarity=0.089  Sum_probs=62.0

Q ss_pred             HHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccC--CCCCeEEEEEec-CcCCHHHHHHHHHHHhCCCcccc------
Q 041612          105 LSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD--KLFDQVVFVEVS-QNQDIRKIQEEIGDKLGLKFHEE------  175 (276)
Q Consensus       105 ~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~f~~~~wv~~~-~~~~~~~l~~~i~~~l~~~~~~~------  175 (276)
                      ..++.....+.+.++|.+|+|||++|..+.+.....  .|.|. .++... ..-..+++. .+.+.+.......      
T Consensus         7 ~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~-~~i~~~~~~I~Id~IR-~i~~~~~~~~~~~~~KviI   84 (198)
T d2gnoa2           7 KRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDIR-TIKDFLNYSPELYTRKYVI   84 (198)
T ss_dssp             HHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHHH-HHHHHHTSCCSSSSSEEEE
T ss_pred             HHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCE-EEEeCCcCCCCHHHHH-HHHHHHhhCcccCCCEEEE
Confidence            344455678899999999999999999988766432  33443 333322 223455553 4666554432110      


Q ss_pred             ------cchhhhhhcc---ccCCCCcEEEEEecccc-ccccCCCCCCceeCCCC
Q 041612          176 ------SESGRANSLF---THGHKGCKVLLTARSQD-VLSGKMDSRPNFSIGVL  219 (276)
Q Consensus       176 ------~~~~~~~~l~---~~~~~gs~IivTTR~~~-va~~~~~~~~~~~l~~L  219 (276)
                            -+......+.   +..+..+.+|++|.+.. +..........+.+...
T Consensus        85 Id~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p  138 (198)
T d2gnoa2          85 VHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP  138 (198)
T ss_dssp             ETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC
T ss_pred             EeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCc
Confidence                  1111122222   25567788887776654 43332223345566543

>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=96.33  E-value=0.0065  Score=45.96  Aligned_cols=62  Identities=19%  Similarity=0.310  Sum_probs=45.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC-cCCHHHHHHHHHHHhCCCccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ-NQDIRKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~  174 (276)
                      +..++|.++|+.|+||||-+-++......++  ..+..++... .....+-++...+.++.+...
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~   66 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNLG--KKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQ   66 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTTT--CCEEEECCCCSSTTHHHHHHHHHHHHTCCEEC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEEeccccccchhhHhhcccccCceEEe
Confidence            4568999999999999998777777766442  3466666543 445667778888888887543

>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=96.32  E-value=0.0012  Score=49.01  Aligned_cols=26  Identities=19%  Similarity=0.409  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.|.|+|++|+|||||++.+..+...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~~   29 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHPD   29 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCCc
Confidence            57899999999999999999876543

>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=96.31  E-value=0.00085  Score=50.35  Aligned_cols=28  Identities=21%  Similarity=0.130  Sum_probs=23.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...+.+|+|-|..|+||||+++.+....
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3456799999999999999999987655

>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=96.29  E-value=0.0037  Score=47.31  Aligned_cols=27  Identities=22%  Similarity=0.342  Sum_probs=24.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +.|+|-|+.|+||||+++.+.......
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~   29 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQL   29 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            578999999999999999999887655

>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=96.18  E-value=0.0017  Score=50.25  Aligned_cols=28  Identities=18%  Similarity=0.264  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +++.|+|-|+-|+||||+++.+......
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            4789999999999999999999987654

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.16  E-value=0.0026  Score=49.14  Aligned_cols=40  Identities=15%  Similarity=0.312  Sum_probs=32.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQ  153 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~  153 (276)
                      .-.++.|+|.+|+|||+++.++..+...+  ...+.|++...
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~--~~~~~~is~e~   64 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACAN--KERAILFAYEE   64 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTT--TCCEEEEESSS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh--ccccceeeccC
Confidence            35689999999999999999999887554  56677877643

>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=96.12  E-value=0.0023  Score=49.57  Aligned_cols=33  Identities=33%  Similarity=0.377  Sum_probs=26.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      -+++|+|+.|+|||||.+.+..-.+..   .+.+++
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~~p~---~G~I~~   57 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIVKPD---RGEVRL   57 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSCCS---EEEEEE
T ss_pred             EEEEEECCCCChHHHHHHHHHcCCCCC---ceEEEE
Confidence            378899999999999999999887653   344444

>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=96.12  E-value=0.0014  Score=49.62  Aligned_cols=28  Identities=36%  Similarity=0.455  Sum_probs=24.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|+|||||.+.++.-.++.
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl~~p~   54 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTYLKPL   54 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcccccC
Confidence            3589999999999999999999877643

>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=96.10  E-value=0.0016  Score=52.02  Aligned_cols=28  Identities=29%  Similarity=0.562  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .+.|+|.|-||+||||+|-.+.......
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~LA~~   29 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAALAEM   29 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            4678999999999999999887777654

>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=96.10  E-value=0.0024  Score=49.53  Aligned_cols=27  Identities=26%  Similarity=0.261  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      --+++|+|+.|+|||||++.++.-...
T Consensus        29 Ge~~~liG~sGaGKSTll~~i~gl~~p   55 (240)
T d1g2912          29 GEFMILLGPSGCGKTTTLRMIAGLEEP   55 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCCCC
Confidence            358999999999999999999877654

>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=96.10  E-value=0.002  Score=49.71  Aligned_cols=34  Identities=24%  Similarity=0.368  Sum_probs=26.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEE
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFV  149 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv  149 (276)
                      --+++|+|++|+|||||.+.+..-....   .+.+++
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~gl~~p~---sG~I~~   64 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGCLDKPT---EGEVYI   64 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS---EEEEEE
T ss_pred             CCEEEEECCCCCCcchhhHhccCCCCCC---cceeEE
Confidence            4589999999999999999888766543   455555

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.06  E-value=0.0026  Score=49.08  Aligned_cols=28  Identities=25%  Similarity=0.232  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|+|||||.+.+..-.+..
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~Gl~~p~   53 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAGLETIT   53 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCCCCC
Confidence            3589999999999999999998776543

>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=96.01  E-value=0.0087  Score=46.16  Aligned_cols=48  Identities=25%  Similarity=0.362  Sum_probs=35.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIRKI  160 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~~l  160 (276)
                      -+++.|+|.+|+|||+++.++..+...+    ......+|+......+...+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            4699999999999999999988765432    12346777777666665444

>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=96.01  E-value=0.0021  Score=48.04  Aligned_cols=26  Identities=12%  Similarity=0.351  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ++.+.|+|+|.+|+|||||...+.+.
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            45678999999999999999999864

>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=95.96  E-value=0.0023  Score=49.42  Aligned_cols=25  Identities=32%  Similarity=0.519  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +|+|.|+.|.|||||...+.++...
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~   26 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLED   26 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Confidence            7899999999999999999876543

>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=95.96  E-value=0.0031  Score=48.87  Aligned_cols=28  Identities=29%  Similarity=0.280  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|+|||||.+.+..-.+..
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl~~p~   59 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGLEEPT   59 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCCS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCCC
Confidence            3589999999999999999998877653

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.92  E-value=0.0039  Score=46.94  Aligned_cols=26  Identities=27%  Similarity=0.584  Sum_probs=23.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      .|+|-|+.|+||||+++.+......+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            68999999999999999999887655

>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=95.90  E-value=0.0027  Score=49.70  Aligned_cols=28  Identities=18%  Similarity=0.278  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -..++|+|+.|+|||||++.+..-....
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~gl~~p~   67 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQNLYQPT   67 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcccCCC
Confidence            4589999999999999999998777653

>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=95.87  E-value=0.0026  Score=48.21  Aligned_cols=25  Identities=16%  Similarity=0.287  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +++.|+|++|+|||||.+.+.....
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5788999999999999999987753

>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=95.86  E-value=0.0027  Score=45.34  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.|+|.+|+|||||...+..+..
T Consensus         2 kivlvG~~~vGKSsLi~~l~~~~~   25 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKLGEI   25 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCC
Confidence            477999999999999999887653

>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=95.85  E-value=0.0049  Score=47.34  Aligned_cols=46  Identities=11%  Similarity=0.130  Sum_probs=32.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCC----CCeEEEEEecCcCCHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKL----FDQVVFVEVSQNQDIR  158 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----f~~~~wv~~~~~~~~~  158 (276)
                      -+++.|+|.+|+|||+|+.++.........    -...+|++.....+..
T Consensus        34 G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   83 (251)
T d1szpa2          34 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV   83 (251)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGG
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHH
Confidence            469999999999999999998766433211    2357777766665533

>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=95.84  E-value=0.0051  Score=49.53  Aligned_cols=28  Identities=18%  Similarity=0.215  Sum_probs=24.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+-+|+|.|.+|+||||+|+.+......
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~~  106 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLSR  106 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHTT
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHhh
Confidence            4679999999999999999999887653

>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=95.77  E-value=0.0023  Score=50.18  Aligned_cols=27  Identities=26%  Similarity=0.346  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -..++|+|+.|+|||||++.+..-...
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl~~p   67 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRFYDI   67 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTTTCC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcccCC
Confidence            458999999999999999999876654

>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=95.71  E-value=0.0029  Score=50.41  Aligned_cols=28  Identities=36%  Similarity=0.405  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|+|||||.+.+..-....
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl~~p~   89 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGELEAS   89 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSSCCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCCcCC
Confidence            3589999999999999999998877653

>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=95.69  E-value=0.0043  Score=45.26  Aligned_cols=34  Identities=18%  Similarity=0.252  Sum_probs=25.6

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++..++.+... .|.++|.+|+|||||...+....
T Consensus         6 ~~~~~~~~k~~-kI~vvG~~~~GKSsLi~rl~~~~   39 (177)
T d1zj6a1           6 RIWRLFNHQEH-KVIIVGLDNAGKTTILYQFSMNE   39 (177)
T ss_dssp             HHHHHHTTSCE-EEEEEESTTSSHHHHHHHHHTTS
T ss_pred             HHHHHhCCCeE-EEEEECCCCCCHHHHHHHHhcCC
Confidence            44555555554 57799999999999999987653

>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=95.69  E-value=0.0029  Score=45.51  Aligned_cols=25  Identities=24%  Similarity=0.294  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .|+|+|.+|+|||||...+.+....
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~~~   31 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGEVV   31 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCc
Confidence            4889999999999999999877543

>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=95.69  E-value=0.0026  Score=49.51  Aligned_cols=28  Identities=32%  Similarity=0.482  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -..++|+|..|+|||||++.+..-....
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl~~p~   56 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRFYIPE   56 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCCCC
Confidence            3589999999999999999998877543

>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=95.67  E-value=0.0025  Score=49.47  Aligned_cols=28  Identities=21%  Similarity=0.382  Sum_probs=24.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|++|+|||||++.+..-.+..
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~Gl~~p~   58 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNLLERPT   58 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCcccc
Confidence            3589999999999999999998876653

>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=95.67  E-value=0.0038  Score=49.04  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      --+++|+|+.|+|||||++.+..-.+.
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl~~p   54 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFLEKP   54 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCccC
Confidence            358999999999999999999876543

>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=95.63  E-value=0.0027  Score=49.40  Aligned_cols=27  Identities=19%  Similarity=0.293  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -..++|+|+.|+|||||++.+..-.++
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~gl~~p   54 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLERFYQP   54 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhCC
Confidence            458999999999999999999876654

>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=95.63  E-value=0.0018  Score=49.93  Aligned_cols=26  Identities=15%  Similarity=0.266  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+.|+|-|+.|+||||+++.+.....
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            47899999999999999999888764

>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=95.57  E-value=0.0043  Score=47.67  Aligned_cols=28  Identities=36%  Similarity=0.349  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      --+++|+|+.|+|||||.+.+..-....
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl~~p~   53 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGFHVPD   53 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSSCCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCcCCC
Confidence            3589999999999999999999877653

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=95.56  E-value=0.0043  Score=50.20  Aligned_cols=26  Identities=27%  Similarity=0.418  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ++.++|+||+|||.||+.+......+
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~~  150 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGGK  150 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHTT
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcCC
Confidence            45568999999999999999987644

>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=95.50  E-value=0.014  Score=46.00  Aligned_cols=56  Identities=25%  Similarity=0.332  Sum_probs=43.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFHE  174 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~  174 (276)
                      .-+++-|+|.+|+|||+||..+.......+  ..++|++.-..++.+     +++++|.+.++
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~  111 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDE  111 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGG
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchh
Confidence            467999999999999999999888765442  458899888888874     56777776443

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.46  E-value=0.0052  Score=48.91  Aligned_cols=28  Identities=18%  Similarity=0.160  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+-+|+|.|..|+|||||+..+......
T Consensus        26 ~P~iIGi~G~qGSGKSTl~~~l~~~L~~   53 (286)
T d1odfa_          26 CPLFIFFSGPQGSGKSFTSIQIYNHLME   53 (286)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCEEEEeECCCCCCHHHHHHHHHHHHHH
Confidence            4569999999999999999988776544

>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=95.45  E-value=0.024  Score=42.17  Aligned_cols=46  Identities=11%  Similarity=0.140  Sum_probs=30.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCC----CCeEEEEEecCcCCHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKL----FDQVVFVEVSQNQDIR  158 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----f~~~~wv~~~~~~~~~  158 (276)
                      -.++.|.|.+|+|||+|+.++..+......    +....++.........
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPE   72 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHH
Confidence            459999999999999999999877544321    2234454444444433

>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=95.43  E-value=0.0072  Score=46.12  Aligned_cols=38  Identities=24%  Similarity=0.398  Sum_probs=29.6

Q ss_pred             ccEEEEE-cCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          113 VNMLGIY-GMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       113 ~~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      .|+|+|. |-||+||||+|..+......+  -..+..++..
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~~la~~--g~~VlliD~D   39 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGVALAQL--GHDVTIVDAD   39 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             CEEEEEECCCCCChHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            3688888 789999999999988887755  2356677654

>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=95.39  E-value=0.0035  Score=48.59  Aligned_cols=28  Identities=32%  Similarity=0.349  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|+|||||.+.+..-....
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~gl~~p~   58 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAGLDVPS   58 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSSCCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCcCCC
Confidence            3589999999999999999998876543

>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=95.37  E-value=0.0027  Score=50.59  Aligned_cols=28  Identities=11%  Similarity=0.334  Sum_probs=20.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.++|+|.|.+|+||||+++.+.+....
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~   30 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR   30 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            3569999999999999999988776543

>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=95.37  E-value=0.0054  Score=44.31  Aligned_cols=23  Identities=17%  Similarity=0.482  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~~~   26 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCKGI   26 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999888654

>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=95.36  E-value=0.0049  Score=46.28  Aligned_cols=24  Identities=25%  Similarity=0.184  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|+|+|.+|+|||||...+.+..
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~~   27 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTDS   27 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            478999999999999999998764

>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=95.32  E-value=0.019  Score=44.07  Aligned_cols=46  Identities=13%  Similarity=0.200  Sum_probs=33.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC----CCCCeEEEEEecCcCCHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD----KLFDQVVFVEVSQNQDIR  158 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~f~~~~wv~~~~~~~~~  158 (276)
                      -+++.|+|.+|+|||++|.++..+....    ..+....|+......+..
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            4699999999999999999998764322    234567777766665543

>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=95.32  E-value=0.0041  Score=48.23  Aligned_cols=28  Identities=29%  Similarity=0.455  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|.|||||.+.+..-....
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~~~p~   55 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTLIKPS   55 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            3589999999999999999998877653

>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=95.32  E-value=0.0057  Score=50.52  Aligned_cols=29  Identities=24%  Similarity=0.181  Sum_probs=25.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +..+.+.++|++|+|||++|..+.+....
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~~~  180 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELCGG  180 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            45679999999999999999999988764

>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=95.29  E-value=0.02  Score=44.98  Aligned_cols=55  Identities=22%  Similarity=0.332  Sum_probs=42.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  173 (276)
                      .-+++-|+|.+|+|||+||..++......+  ..++|++.-..++.+.     ++++|.+.+
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d  113 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTD  113 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGG
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHH
Confidence            467999999999999999988887766552  4689999888888765     455666543

>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=95.27  E-value=0.0044  Score=48.13  Aligned_cols=28  Identities=29%  Similarity=0.425  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|.|||||.+.+..-.+..
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~~p~   59 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLVRAQ   59 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCCC
Confidence            3589999999999999999998877653

>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=95.25  E-value=0.0053  Score=48.07  Aligned_cols=28  Identities=32%  Similarity=0.376  Sum_probs=24.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.+++|+|+.|.|||||++.+..-....
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~Gl~~p~   57 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITGFLKAD   57 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHCCCcCC
Confidence            3489999999999999999999887653

>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=95.25  E-value=0.0076  Score=45.82  Aligned_cols=28  Identities=21%  Similarity=0.348  Sum_probs=24.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -+.|+|-|+.|+||||+++.+......+
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L~~~   30 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKLQPN   30 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHTTTS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHhC
Confidence            4689999999999999999999887644

>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=95.25  E-value=0.0051  Score=44.90  Aligned_cols=23  Identities=30%  Similarity=0.352  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|+..+.+..
T Consensus         5 KivvvG~~~vGKTsli~r~~~~~   27 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDKR   27 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            47899999999999999987664

>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=95.23  E-value=0.005  Score=44.81  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+|+|.+|+|||||...+.+..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~~   24 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKKK   24 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC--
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999987543

>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=95.23  E-value=0.0069  Score=44.18  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++...|+++|.+|+|||||...+....
T Consensus        11 ~k~~kI~lvG~~~vGKTsLl~~l~~~~   37 (186)
T d1f6ba_          11 KKTGKLVFLGLDNAGKTTLLHMLKDDR   37 (186)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHHSCC-
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344578899999999999999886553

>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=95.19  E-value=0.0055  Score=44.22  Aligned_cols=23  Identities=22%  Similarity=0.267  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~~   26 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAGR   26 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988764

>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=95.18  E-value=0.0056  Score=44.33  Aligned_cols=23  Identities=30%  Similarity=0.378  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||+|...+.+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~~~   28 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEKK   28 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            58899999999999999987654

>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=95.14  E-value=0.0066  Score=43.23  Aligned_cols=23  Identities=26%  Similarity=0.326  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         2 KI~liG~~nvGKSSLln~l~~~~   24 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKNDR   24 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58899999999999999988754

>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=95.12  E-value=0.0064  Score=45.73  Aligned_cols=24  Identities=21%  Similarity=0.234  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|+|+|.+|+|||||...+.+..
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~~   24 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTGQ   24 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999988754

>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=95.09  E-value=0.0058  Score=44.62  Aligned_cols=24  Identities=21%  Similarity=0.455  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +..|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999999865

>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=95.06  E-value=0.0063  Score=44.20  Aligned_cols=23  Identities=26%  Similarity=0.258  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~~   29 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADDS   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHcCC
Confidence            48899999999999999987653

>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=95.02  E-value=0.0064  Score=44.22  Aligned_cols=23  Identities=26%  Similarity=0.507  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            58899999999999999988754

>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=95.02  E-value=0.0082  Score=43.23  Aligned_cols=23  Identities=26%  Similarity=0.289  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         2 Kv~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           2 KLVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988654

>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=95.02  E-value=0.0066  Score=43.95  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.++.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            58899999999999999988764

>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=95.01  E-value=0.0082  Score=43.43  Aligned_cols=23  Identities=17%  Similarity=0.328  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988765

>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=95.01  E-value=0.0081  Score=43.73  Aligned_cols=23  Identities=30%  Similarity=0.394  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~~   26 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVNDK   26 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHcCC
Confidence            58899999999999999987654

>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=95.00  E-value=0.0068  Score=46.43  Aligned_cols=26  Identities=27%  Similarity=0.342  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..++..|.|+-|.|||||.+.+....
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhcC
Confidence            46889999999999999999988764

>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=94.99  E-value=0.0084  Score=43.47  Aligned_cols=23  Identities=35%  Similarity=0.599  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999998765

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=94.98  E-value=0.02  Score=44.89  Aligned_cols=54  Identities=22%  Similarity=0.385  Sum_probs=41.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhCCCcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLGLKFH  173 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  173 (276)
                      -+++-|+|.+|+|||||+.+++......+  ..++|++.-..++...     ++.+|.+.+
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~~-----a~~~Gvd~d  107 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDID  107 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHH-----HHHTTCCGG
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHHH-----HHHhCCCHH
Confidence            46999999999999999999988876542  4578888887777643     456666543

>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=94.94  E-value=0.0081  Score=43.58  Aligned_cols=23  Identities=26%  Similarity=0.657  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~~~   26 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVKGT   26 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            36799999999999999887654

>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=94.94  E-value=0.0066  Score=43.76  Aligned_cols=23  Identities=22%  Similarity=0.338  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||||...+.+..
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~   26 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGED   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCC
Confidence            47899999999999999987654

>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=94.93  E-value=0.0098  Score=42.98  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~~   27 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCENK   27 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999987654

>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=94.89  E-value=0.0051  Score=45.06  Aligned_cols=28  Identities=11%  Similarity=0.130  Sum_probs=23.2

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          109 EDPDVNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       109 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -.++...|+|+|.+++|||||.+.+...
T Consensus        12 p~~~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          12 PSDTGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             SCSCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCccCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3456778999999999999999887543

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.88  E-value=0.0074  Score=45.48  Aligned_cols=20  Identities=35%  Similarity=0.498  Sum_probs=18.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEI  133 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v  133 (276)
                      -+|+|.|..|+||||+|+.+
T Consensus         3 ~iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            47999999999999999865

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=94.88  E-value=0.0073  Score=45.64  Aligned_cols=19  Identities=26%  Similarity=0.455  Sum_probs=17.5

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEI  133 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v  133 (276)
                      +|+|+|..|+||||.++.+
T Consensus         5 iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHH
Confidence            8999999999999999765

>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=94.87  E-value=0.0064  Score=44.89  Aligned_cols=23  Identities=26%  Similarity=0.291  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||||+..+.+..
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~~   29 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDNK   29 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCSC
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            57899999999999999987643

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.87  E-value=0.0076  Score=44.11  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ...|+|+|.+|+|||||...+++..
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~~   29 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGVK   29 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3579999999999999999998763

>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=94.86  E-value=0.0094  Score=43.28  Aligned_cols=23  Identities=30%  Similarity=0.512  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~~   29 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQSY   29 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58899999999999999987754

>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=94.86  E-value=0.0076  Score=43.93  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|+..+....
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~~   29 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEKK   29 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            48899999999999999987653

>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=94.85  E-value=0.0097  Score=43.15  Aligned_cols=23  Identities=22%  Similarity=0.342  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988665

>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=94.84  E-value=0.011  Score=42.77  Aligned_cols=24  Identities=21%  Similarity=0.383  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|.|+|.+|+|||+|...+.+..
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~~   28 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEGQ   28 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhCC
Confidence            568899999999999999987654

>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=94.83  E-value=0.0077  Score=43.94  Aligned_cols=24  Identities=29%  Similarity=0.512  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|.|+|.+|+|||+|...+.+..
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~~   30 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQSY   30 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhCC
Confidence            368899999999999999987654

>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=94.82  E-value=0.0072  Score=43.85  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~~   25 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGVE   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC-
T ss_pred             EEEEECCCCcCHHHHHHHHhCCc
Confidence            47899999999999999887654

>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=94.82  E-value=0.018  Score=43.79  Aligned_cols=37  Identities=24%  Similarity=0.455  Sum_probs=28.5

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHhcccCCCCCeEEEEEec
Q 041612          114 NMLGIY-GMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVS  152 (276)
Q Consensus       114 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~  152 (276)
                      ++|+|+ +-||+||||+|..+.......+  ..+..++..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g--~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRG--RKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhCC--CCEEEEeCC
Confidence            588998 6799999999999988887652  346666654

>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=94.81  E-value=0.0079  Score=43.45  Aligned_cols=23  Identities=22%  Similarity=0.361  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~~   26 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVEDK   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988764

>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=94.81  E-value=0.0064  Score=44.61  Aligned_cols=22  Identities=23%  Similarity=0.342  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999865

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.80  E-value=0.0087  Score=43.74  Aligned_cols=24  Identities=33%  Similarity=0.310  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.|.|+|.+|+|||+|...+.+..
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCcCHHHHHHHHHhCC
Confidence            357899999999999999988765

>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=94.79  E-value=0.021  Score=43.64  Aligned_cols=27  Identities=19%  Similarity=0.282  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -.++.|.|.+|+|||+++..+..+...
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~~~   60 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNLQN   60 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTC
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            468999999999999999999876643

>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=94.76  E-value=0.01  Score=42.82  Aligned_cols=23  Identities=30%  Similarity=0.580  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48899999999999999988764

>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=94.75  E-value=0.0085  Score=43.74  Aligned_cols=23  Identities=26%  Similarity=0.445  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||+..+.+..
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~~   28 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRNE   28 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            58899999999999999987754

>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=94.74  E-value=0.0065  Score=46.84  Aligned_cols=24  Identities=29%  Similarity=0.434  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      --+++|+|+.|.|||||.+.+..-
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            358999999999999999999874

>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=94.73  E-value=0.0041  Score=48.72  Aligned_cols=27  Identities=30%  Similarity=0.356  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -..++|+|..|+|||||++.+..-...
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~gl~~p   70 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPRFYDV   70 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhcCCc
Confidence            458999999999999999998766654

>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=94.68  E-value=0.011  Score=44.04  Aligned_cols=23  Identities=26%  Similarity=0.405  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||||...+.+..
T Consensus         8 KivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHhhCC
Confidence            48899999999999999988765

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.68  E-value=0.011  Score=42.63  Aligned_cols=23  Identities=30%  Similarity=0.631  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         5 KivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999987765

>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=94.49  E-value=0.0075  Score=44.20  Aligned_cols=22  Identities=27%  Similarity=0.480  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -|+|+|.+|+|||||...+.+.
T Consensus         3 ~VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999998754

>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=94.48  E-value=0.013  Score=42.31  Aligned_cols=23  Identities=17%  Similarity=0.291  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            57889999999999999987764

>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=94.47  E-value=0.015  Score=42.10  Aligned_cols=23  Identities=26%  Similarity=0.353  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||+|+..+.+..
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~~   30 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDGA   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            58999999999999999887654

>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=94.46  E-value=0.011  Score=43.47  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|.|+|.+|+|||+|...+.+..
T Consensus         6 iKivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            368999999999999999988764

>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=94.46  E-value=0.0099  Score=43.25  Aligned_cols=24  Identities=25%  Similarity=0.391  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .-.|.++|.+|+|||||...+.+.
T Consensus        16 ~~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          16 EVRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcC
Confidence            446889999999999999988654

>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=94.46  E-value=0.013  Score=45.16  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=21.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++|+|.|..|+||||.|+.+.+..
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            689999999999999999987654

>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=94.45  E-value=0.011  Score=42.50  Aligned_cols=24  Identities=29%  Similarity=0.256  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.++|.+|+|||||...+....-
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~~~   27 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASGQF   27 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCC
Confidence            477899999999999998876553

>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=94.41  E-value=0.0085  Score=43.61  Aligned_cols=30  Identities=13%  Similarity=0.139  Sum_probs=22.5

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          108 LEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       108 L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +....--.|.++|.+|+|||||...+.+..
T Consensus         7 ~~~~k~~kIvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_           7 IFGNKEMRILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             HHTTCCEEEEEEEETTSSHHHHHHHTTCCC
T ss_pred             hhCCCeEEEEEECCCCCCHHHHHHHHhcCC
Confidence            333333457799999999999999987554

>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=94.40  E-value=0.011  Score=42.35  Aligned_cols=23  Identities=26%  Similarity=0.297  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||..++....
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~~   25 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGRE   25 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999998553

>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=94.37  E-value=0.012  Score=43.22  Aligned_cols=23  Identities=35%  Similarity=0.459  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.+..
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~~   26 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNKK   26 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988654

>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=94.34  E-value=0.016  Score=42.21  Aligned_cols=23  Identities=26%  Similarity=0.394  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            48899999999999999987654

>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=94.34  E-value=0.015  Score=42.03  Aligned_cols=24  Identities=25%  Similarity=0.434  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|.++|.+|+|||+|...+.+..
T Consensus         5 ~KivlvG~~~vGKTsli~~~~~~~   28 (168)
T d1u8za_           5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhCC
Confidence            468899999999999999987654

>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=94.30  E-value=0.014  Score=42.94  Aligned_cols=24  Identities=21%  Similarity=0.337  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.++|.+|+|||+|..++.....
T Consensus         4 KivllG~~~vGKTsl~~r~~~~~~   27 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKIIHE   27 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhCCC
Confidence            478999999999999998866543

>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=94.29  E-value=0.015  Score=42.54  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         4 KivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988764

>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=94.28  E-value=0.015  Score=42.78  Aligned_cols=23  Identities=30%  Similarity=0.358  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.|+|.+|+|||+|...+.+..
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            58899999999999999987764

>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=94.25  E-value=0.0089  Score=43.97  Aligned_cols=22  Identities=23%  Similarity=0.495  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -|+|+|.+++|||||...+.+.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999988654

>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=94.21  E-value=0.013  Score=42.55  Aligned_cols=23  Identities=26%  Similarity=0.456  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~~   30 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTNK   30 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48899999999999998887653

>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=94.17  E-value=0.015  Score=42.62  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +-|.|.|.+|+||||||..+..+
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            45889999999999999988765

>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=94.14  E-value=0.017  Score=41.76  Aligned_cols=23  Identities=35%  Similarity=0.608  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.++.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            46789999999999999988754

>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=94.11  E-value=0.013  Score=42.66  Aligned_cols=23  Identities=30%  Similarity=0.381  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+....
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~~~   27 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAGVH   27 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCc
Confidence            57899999999999999887543

>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=94.09  E-value=0.016  Score=46.81  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..++.++|++|+|||.||+.+....
T Consensus        52 ~~~~lf~Gp~GvGKT~lak~la~~l   76 (315)
T d1r6bx3          52 VGSFLFAGPTGVGKTEVTVQLSKAL   76 (315)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCcchhHHHHHHHHhhc
Confidence            3478899999999999999998765

>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=94.05  E-value=0.014  Score=42.87  Aligned_cols=24  Identities=29%  Similarity=0.355  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -.|+|+|.+|+|||||...+.+..
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~~   32 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNKE   32 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTST
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCC
Confidence            458999999999999999988653

>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=94.04  E-value=0.018  Score=42.51  Aligned_cols=24  Identities=25%  Similarity=0.235  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|.++|.+|+|||+|...+.+..-
T Consensus         5 KvvllG~~~vGKTSli~r~~~~~f   28 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTNKF   28 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCCC
Confidence            478999999999999998876653

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.93  E-value=0.015  Score=49.15  Aligned_cols=27  Identities=26%  Similarity=0.420  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+-|.++|+.|+|||.||+.+..-...
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l~V   75 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLANA   75 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHhCC
Confidence            457999999999999999999986643

>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=93.92  E-value=0.015  Score=43.10  Aligned_cols=19  Identities=21%  Similarity=0.468  Sum_probs=17.6

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEI  133 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v  133 (276)
                      .|.++|.+|+|||+|...+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5789999999999999988

>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=93.91  E-value=0.016  Score=42.46  Aligned_cols=23  Identities=30%  Similarity=0.351  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      +-|.|.|.+|+||||||..+..+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45789999999999999998754

>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=93.86  E-value=0.029  Score=43.95  Aligned_cols=51  Identities=12%  Similarity=0.169  Sum_probs=34.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK  167 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  167 (276)
                      .++.|.|.+|+|||+++..+..+......+ .+.+++.  ..+...+...++..
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s~--E~~~~~~~~r~~~~   86 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAML--EESVEETAEDLIGL   86 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEES--SSCHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEeee--ccchhhHHhHHHHH
Confidence            478899999999999999998775433112 3455544  34556665555543

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=93.85  E-value=0.027  Score=40.33  Aligned_cols=29  Identities=24%  Similarity=0.307  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      ..-+|.+.|.=|+||||+++.+.+....+
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            34589999999999999999999988654

>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=93.85  E-value=0.019  Score=43.50  Aligned_cols=24  Identities=21%  Similarity=0.272  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -.++.|+|.+|+|||+||.++...
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~   49 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYN   49 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            468999999999999999886544

>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=93.83  E-value=0.022  Score=44.58  Aligned_cols=26  Identities=31%  Similarity=0.519  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      .+..|+|.+|+|||||+..+......
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia~   55 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIAG   55 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHc
Confidence            47889999999999999998876543

>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=93.82  E-value=0.019  Score=43.05  Aligned_cols=28  Identities=18%  Similarity=0.240  Sum_probs=24.3

Q ss_pred             cEEEEEcCC-CCcHHHHHHHHHHhcccCC
Q 041612          114 NMLGIYGMG-GIGKTMLAEEIARKVKSDK  141 (276)
Q Consensus       114 ~vi~I~G~g-GiGKTtLa~~v~~~~~~~~  141 (276)
                      +.+-|.|-| |+||||++..+......++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G   30 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAG   30 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCC
Confidence            568899998 9999999999998887764

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.75  E-value=0.018  Score=42.05  Aligned_cols=23  Identities=26%  Similarity=0.359  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||+|...+.+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58899999999999999887765

>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=93.74  E-value=0.018  Score=42.13  Aligned_cols=28  Identities=21%  Similarity=0.233  Sum_probs=22.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          110 DPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       110 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ....-.|.++|.+|+|||||...+.+..
T Consensus        14 ~~k~~KI~lvG~~~vGKTsLi~~l~~~~   41 (182)
T d1moza_          14 SNKELRILILGLDGAGKTTILYRLQIGE   41 (182)
T ss_dssp             CSSCEEEEEEEETTSSHHHHHHHTCCSE
T ss_pred             CCceEEEEEECCCCCCHHHHHHHHhcCC
Confidence            3445568899999999999999875443

>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=93.74  E-value=0.011  Score=48.07  Aligned_cols=22  Identities=23%  Similarity=0.391  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      +-+.+.|.+|+|||+||+.+..
T Consensus        29 h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_          29 GGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CCEEEECCGGGCTTHHHHHHHH
T ss_pred             CeEEEECCCCccHHHHHHHHHH
Confidence            4689999999999999999875

>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=93.73  E-value=0.02  Score=41.63  Aligned_cols=24  Identities=33%  Similarity=0.331  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +-|.|.|.+|+||||||..+..+-
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~g   39 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKRG   39 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHcC
Confidence            458899999999999998877663

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.68  E-value=0.02  Score=42.22  Aligned_cols=23  Identities=22%  Similarity=0.309  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+....
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999986654

>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=93.67  E-value=0.009  Score=43.42  Aligned_cols=23  Identities=30%  Similarity=0.378  Sum_probs=17.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||+|...+.+..
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~~   27 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTGE   27 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC---
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47889999999999998876543

>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=93.62  E-value=0.018  Score=45.42  Aligned_cols=27  Identities=26%  Similarity=0.225  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++.|.|+|+|.+|.|||||+..+....
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            356889999999999999999986543

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=93.57  E-value=0.019  Score=47.23  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +..+..+|+.|+|||.||+.+....
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcceeeeCCCCccHHHHHHHHHhhc
Confidence            4568899999999999999998664

>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=93.44  E-value=0.0079  Score=43.01  Aligned_cols=23  Identities=22%  Similarity=0.332  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|+++|.+|+|||||...+.+..
T Consensus         2 kI~liG~~n~GKSSLin~l~g~~   24 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNED   24 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48999999999999999998764

>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=93.25  E-value=0.013  Score=42.58  Aligned_cols=23  Identities=26%  Similarity=0.372  Sum_probs=9.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .|.++|.+|+|||||...+.++.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSEDA   30 (173)
T ss_dssp             EEEEECCCCC-------------
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999998776543

>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=93.16  E-value=0.027  Score=42.73  Aligned_cols=23  Identities=22%  Similarity=0.374  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ..|.++|.+|+|||||...+...
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999987544

>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=92.91  E-value=0.12  Score=40.36  Aligned_cols=64  Identities=22%  Similarity=0.370  Sum_probs=45.2

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC-CHHHHHHHHHHH
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ-DIRKIQEEIGDK  167 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~  167 (276)
                      +.++.+.. ..-..++|.|..|+|||+|+..+.++.... +-+..+++.+++.. ...++.+++.+.
T Consensus        57 raID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~~~~-~~~v~V~~~iGer~~ev~~~~~~~~~~  122 (276)
T d2jdid3          57 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA-HGGYSVFAGVGERTREGNDLYHEMIES  122 (276)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHHTTT-CSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             eeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHHHhh-CCCeEEEEEeccChHHHHHHHHHHHhc
Confidence            66666665 233469999999999999999998874332 24677888888765 346666666553

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.87  E-value=0.027  Score=42.87  Aligned_cols=33  Identities=24%  Similarity=0.457  Sum_probs=26.0

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .|..+|..   +...++|.+|+|||||...+..+..
T Consensus        88 ~L~~~l~~---kt~~~~G~SGVGKSTLiN~L~~~~~  120 (225)
T d1u0la2          88 ELKEYLKG---KISTMAGLSGVGKSSLLNAINPGLK  120 (225)
T ss_dssp             HHHHHHSS---SEEEEECSTTSSHHHHHHHHSTTCC
T ss_pred             hHHHHhcC---CeEEEECCCCCCHHHHHHhhcchhh
Confidence            66666643   4778999999999999999876543

>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=92.67  E-value=0.036  Score=43.46  Aligned_cols=24  Identities=33%  Similarity=0.560  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHh
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      .|.|+|+|..|.|||||+..+.+.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHHHH
Confidence            478999999999999999988543

>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=92.64  E-value=0.057  Score=43.65  Aligned_cols=28  Identities=21%  Similarity=0.313  Sum_probs=24.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +..|.|-|.-|+||||+++.+.+....+
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l~~~   33 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAASGG   33 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGGGCS
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHhccC
Confidence            4578889999999999999999987654

>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=92.35  E-value=0.045  Score=41.62  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHh
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      ++|+|+|-++.|||||...+...
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhh
Confidence            56999999999999999988765

>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=92.25  E-value=0.037  Score=44.49  Aligned_cols=23  Identities=35%  Similarity=0.498  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ++.++|++|+|||.||+.+....
T Consensus        55 ~~lf~Gp~G~GKt~lak~la~~l   77 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAKTLAATL   77 (315)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCcchHHHHHHHHHHHh
Confidence            77889999999999999998876

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=91.93  E-value=0.049  Score=44.62  Aligned_cols=52  Identities=13%  Similarity=0.106  Sum_probs=31.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcccC-CCCCeEEEEEecCcCCHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVKSD-KLFDQVVFVEVSQNQDIRKIQEEI  164 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~f~~~~wv~~~~~~~~~~l~~~i  164 (276)
                      .++..|.|++|+||||++..+....... ..-...+.+.....-....+...+
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            4689999999999999886655443221 112345666665544444444443

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=91.90  E-value=0.044  Score=42.60  Aligned_cols=26  Identities=23%  Similarity=0.406  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.-.|.++|.+|+|||||...++.+.
T Consensus        31 ~~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          31 NSLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CCcEEEEECCCCCcHHHHHHHHhCCC
Confidence            34578899999999999999999764

>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=91.59  E-value=0.19  Score=38.59  Aligned_cols=25  Identities=28%  Similarity=0.375  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      -|.|.|..|+|||++|+.+......
T Consensus        25 pvlI~Ge~GtGK~~~A~~ih~~s~~   49 (247)
T d1ny5a2          25 PVLITGESGVGKEVVARLIHKLSDR   49 (247)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CEEEECCCCcCHHHHHHHHHHhcCC
Confidence            3788999999999999999865443

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=91.46  E-value=0.48  Score=35.90  Aligned_cols=62  Identities=23%  Similarity=0.175  Sum_probs=40.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHH
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDK  167 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  167 (276)
                      ++.+.+..+......++|..|+|||.++.......-.+   +..+-+-++...-..+....+-+.
T Consensus        66 ~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~---g~qv~~l~Pt~~La~Q~~~~~~~~  127 (233)
T d2eyqa3          66 AVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPTTLLAQQHYDNFRDR  127 (233)
T ss_dssp             HHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc---CCceEEEccHHHhHHHHHHHHHHH
Confidence            67777788888899999999999999998877665443   223333333333334444444443

>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=91.41  E-value=0.11  Score=41.32  Aligned_cols=17  Identities=35%  Similarity=0.284  Sum_probs=13.5

Q ss_pred             EEEEEcCCCCcHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAE  131 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~  131 (276)
                      .+.|.|.+|+||||.+.
T Consensus        26 ~~lV~g~aGSGKTt~l~   42 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLT   42 (318)
T ss_dssp             CEEEEECTTSCHHHHHH
T ss_pred             CEEEEecCCccHHHHHH
Confidence            36688999999998543

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=91.39  E-value=0.057  Score=43.52  Aligned_cols=26  Identities=23%  Similarity=0.266  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhccc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKS  139 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~  139 (276)
                      +.|.|.|..|+||||+.+.+......
T Consensus       167 ~nili~G~tgSGKTT~l~al~~~i~~  192 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIMEFIPK  192 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGSCT
T ss_pred             CCEEEEeeccccchHHHHHHhhhccc
Confidence            45899999999999999999877643

>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=91.30  E-value=0.056  Score=39.32  Aligned_cols=21  Identities=38%  Similarity=0.574  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .|+|+|.++.|||||...+.+
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            599999999999999999875

>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=91.27  E-value=0.15  Score=40.16  Aligned_cols=38  Identities=24%  Similarity=0.182  Sum_probs=29.2

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      +.++.+.. ..-..++|.|..|+|||+|+..+.++...+
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~   70 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN   70 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhc
Confidence            55666655 234579999999999999999998876543

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=90.78  E-value=0.1  Score=38.70  Aligned_cols=36  Identities=22%  Similarity=0.321  Sum_probs=28.3

Q ss_pred             HHHHhhcC-CCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALED-PDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+..+|.. ++...+.++|+++.|||.+|..+.+-..
T Consensus        42 ~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          42 ALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            55555543 5678999999999999999988877654

>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=90.49  E-value=0.037  Score=42.26  Aligned_cols=32  Identities=25%  Similarity=0.500  Sum_probs=23.0

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +|..+|..   +...++|.+|+|||||...+..+.
T Consensus        90 ~L~~~l~~---~~~vl~G~SGVGKSSLiN~L~~~~  121 (231)
T d1t9ha2          90 DIIPHFQD---KTTVFAGQSGVGKSSLLNAISPEL  121 (231)
T ss_dssp             TTGGGGTT---SEEEEEESHHHHHHHHHHHHCC--
T ss_pred             HHHHhhcc---ceEEEECCCCccHHHHHHhhccHh
Confidence            55555532   456789999999999999887544

>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=90.47  E-value=0.072  Score=42.99  Aligned_cols=27  Identities=33%  Similarity=0.318  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSD  140 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  140 (276)
                      -.|.|-|.-|+||||+++.+.+....+
T Consensus         6 lrI~IEG~iGsGKSTl~~~L~~~l~~~   32 (331)
T d1osna_           6 LRIYLDGAYGIGKTTAAEEFLHHFAIT   32 (331)
T ss_dssp             EEEEEEESSSSCTTHHHHHHHHTTTTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            358899999999999999999887543

>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=90.15  E-value=0.11  Score=40.69  Aligned_cols=38  Identities=18%  Similarity=0.201  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHH-HHHHHhccc-CCCCCeEEEEEec
Q 041612          115 MLGIYGMGGIGKTMLA-EEIARKVKS-DKLFDQVVFVEVS  152 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa-~~v~~~~~~-~~~f~~~~wv~~~  152 (276)
                      .+.|.|.+|+||||.+ ..+.+-.+. ......+..++.+
T Consensus        16 ~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~t   55 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFT   55 (306)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESS
T ss_pred             CEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCc
Confidence            3678899999999754 444333222 1112345566544

>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=89.61  E-value=0.018  Score=42.44  Aligned_cols=26  Identities=15%  Similarity=0.174  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .++..|+|+.|+||||+..++..-..
T Consensus        24 ~~~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          24 ELVTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc
Confidence            35778899999999999999876553

>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=89.28  E-value=0.12  Score=40.56  Aligned_cols=25  Identities=24%  Similarity=0.380  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..|+|+|+|.+|||||-..+.+...
T Consensus         3 ~~~GivG~Pn~GKSTlf~~lt~~~~   27 (278)
T d1jala1           3 FKCGIVGLPNVGKSTLFNALTKAGI   27 (278)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTC-
T ss_pred             ceEEEECCCCCCHHHHHHHHHCCCC
Confidence            3689999999999999999886643

>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=89.10  E-value=0.13  Score=38.35  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHh
Q 041612          115 MLGIYGMGGIGKTMLAEEIARK  136 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~  136 (276)
                      -|+|+|-++.|||||+.++.+.
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHH
Confidence            4899999999999999988643

>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=89.05  E-value=0.33  Score=33.02  Aligned_cols=53  Identities=11%  Similarity=0.032  Sum_probs=32.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcCCHHHHHHHHHHHhC
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQDIRKIQEEIGDKLG  169 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  169 (276)
                      ++.++..|+++.|.|||+++-.++.+.      ...+.+.+....-..+..+.+.+.++
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            345778889999999999886655432      33455665544444444444444443

>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=89.04  E-value=0.092  Score=42.27  Aligned_cols=26  Identities=23%  Similarity=0.193  Sum_probs=20.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ...|.|-|.-|+||||+++.+.+...
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC---
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHHhC
Confidence            34689999999999999999876543

>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=87.51  E-value=0.16  Score=40.08  Aligned_cols=24  Identities=33%  Similarity=0.531  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..|+|+|.|.+|||||-..+.+..
T Consensus        11 ~kiGivG~Pn~GKSTlfnalT~~~   34 (296)
T d1ni3a1          11 LKTGIVGMPNVGKSTFFRAITKSV   34 (296)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHST
T ss_pred             cEEEEECCCCCCHHHHHHHHHCCC
Confidence            469999999999999999998763

>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=87.32  E-value=0.31  Score=37.85  Aligned_cols=35  Identities=31%  Similarity=0.363  Sum_probs=27.4

Q ss_pred             HHHHhhcC--CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          103 NILSALED--PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       103 ~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      .+..+|..  +....+.++|+|+.|||+++..+..-.
T Consensus        92 ~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            45555643  457788999999999999999987765

>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=87.02  E-value=0.36  Score=37.65  Aligned_cols=40  Identities=23%  Similarity=0.200  Sum_probs=30.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHhcccCCCCCeEEEEEecCcC
Q 041612          114 NMLGIYGMGGIGKTMLAEEIARKVKSDKLFDQVVFVEVSQNQ  155 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~f~~~~wv~~~~~~  155 (276)
                      ..++|.|..|+|||+|+.........+  -+.++++.+....
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~~~~~--~~v~V~~~iGer~  107 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILNQQGQ--NVICVYVAIGQKA  107 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCCTT--TCEEEEEEESCCH
T ss_pred             ceEeeccCCCCChHHHHHHHHhhhccc--Cceeeeeeecchh
Confidence            468999999999999998866555433  4577777777654

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.01  E-value=0.19  Score=39.36  Aligned_cols=27  Identities=26%  Similarity=0.388  Sum_probs=23.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      +.+.+|+|+|+-+.|||+|...++...
T Consensus        30 ~~v~vvsi~G~~~sGKS~llN~l~~~~   56 (277)
T d1f5na2          30 QPMVVVAIVGLYRTGKSYLMNKLAGKK   56 (277)
T ss_dssp             SBEEEEEEEEBTTSSHHHHHHHHTTCS
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHcCCC
Confidence            457899999999999999999998754

>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=86.68  E-value=0.2  Score=39.02  Aligned_cols=27  Identities=26%  Similarity=0.322  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ..-.++|+|++.+|||||...+.....
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~~~~  137 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAKKNI  137 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTSCC
T ss_pred             CceEEEEEecCccchhhhhhhhhccce
Confidence            345699999999999999999987654

>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=86.55  E-value=0.18  Score=41.79  Aligned_cols=22  Identities=18%  Similarity=0.300  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      -.|+|+|.+|+|||||...+..
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            3699999999999999999985

>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=86.51  E-value=0.19  Score=40.62  Aligned_cols=25  Identities=16%  Similarity=0.345  Sum_probs=22.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 041612          111 PDVNMLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       111 ~~~~vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      +..|-|+|+|..|.|||||+-.+..
T Consensus        15 ~~IRNI~iiGhvd~GKTTL~d~Ll~   39 (341)
T d1n0ua2          15 TNVRNMSVIAHVDHGKSTLTDSLVQ   39 (341)
T ss_dssp             GGEEEEEEECCGGGTHHHHHHHHHH
T ss_pred             ccCcEEEEEeCCCCcHHHHHHHHHH
Confidence            4578899999999999999988754

>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=86.36  E-value=0.17  Score=40.24  Aligned_cols=23  Identities=17%  Similarity=0.293  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHhc
Q 041612          115 MLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      -|+|+|.|.+|||||-..+.+..
T Consensus         2 ~v~lvG~pn~GKStlfn~lt~~~   24 (319)
T d1wxqa1           2 EIGVVGKPNVGKSTFFSAATLVD   24 (319)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC--
T ss_pred             cEeEECCCCCCHHHHHHHHHCCC
Confidence            48999999999999999997654

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase 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: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.88  E-value=0.6  Score=36.02  Aligned_cols=36  Identities=19%  Similarity=0.064  Sum_probs=29.7

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      ++..-+..+....-.+.|..|+|||..|.......-
T Consensus        94 ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~  129 (264)
T d1gm5a3          94 EIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNY  129 (264)
T ss_dssp             HHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHhhccCcceeeeeccccccccHHHHHHHHHHH
Confidence            777777788888899999999999999887665543

>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=85.63  E-value=0.35  Score=39.91  Aligned_cols=35  Identities=14%  Similarity=0.117  Sum_probs=27.5

Q ss_pred             HHHhhcCCCccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       104 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      .+..+......+|.|.|+.|.||||....+.+...
T Consensus       149 ~l~~l~~~~~GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         149 NFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             HHHHHHTSSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHhhhhceEEEEcCCCCCccHHHHHHhhhhc
Confidence            34444556678999999999999999888877653

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {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: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=85.31  E-value=0.84  Score=33.25  Aligned_cols=28  Identities=25%  Similarity=0.154  Sum_probs=19.9

Q ss_pred             HHHHhhcCCCccEEEEEcCCCCcHHHHHHH
Q 041612          103 NILSALEDPDVNMLGIYGMGGIGKTMLAEE  132 (276)
Q Consensus       103 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~  132 (276)
                      +.+..+...+  -+.+.++.|.|||+.|..
T Consensus        32 ~ai~~l~~~~--~~il~apTGsGKT~~a~l   59 (202)
T d2p6ra3          32 EAVEKVFSGK--NLLLAMPTAAGKTLLAEM   59 (202)
T ss_dssp             HHHHHHTTCS--CEEEECSSHHHHHHHHHH
T ss_pred             HHHHHHHcCC--CEEEEcCCCCchhHHHHH
Confidence            5555555443  366899999999998743

>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=84.34  E-value=0.25  Score=38.73  Aligned_cols=22  Identities=27%  Similarity=0.424  Sum_probs=18.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      .++-.|+|+.|+|||++..++.
T Consensus        24 ~~lnvlvG~NgsGKS~iL~Ai~   45 (308)
T d1e69a_          24 DRVTAIVGPNGSGKSNIIDAIK   45 (308)
T ss_dssp             SSEEEEECCTTTCSTHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHH
Confidence            3588999999999999987763

>d1p3da1 c.5.1.1 (A:11-106) UDP-N-acetylmuramate-alanine ligase MurC {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: MurCD N-terminal domain
superfamily: MurCD N-terminal domain
family: MurCD N-terminal domain
domain: UDP-N-acetylmuramate-alanine ligase MurC
species: Haemophilus influenzae [TaxId: 727]

Probab=82.89  E-value=0.65  Score=29.74  Aligned_cols=26  Identities=27%  Similarity=0.451  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKV  137 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~  137 (276)
                      ..+.|-+.|.||+|-+.||+.+...-
T Consensus         7 ~~~~ihfiGigG~GMs~LA~~L~~~G   32 (96)
T d1p3da1           7 RVQQIHFIGIGGAGMSGIAEILLNEG   32 (96)
T ss_dssp             TCCEEEEETTTSTTHHHHHHHHHHHT
T ss_pred             hCCEEEEEEECHHHHHHHHHHHHhCC
Confidence            45689999999999999998877654

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=82.69  E-value=0.32  Score=38.51  Aligned_cols=18  Identities=33%  Similarity=0.702  Sum_probs=15.5

Q ss_pred             cEEEEEcCCCCcHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAE  131 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~  131 (276)
                      .+..+.|.+|.|||||..
T Consensus        15 ~~alfFGLSGTGKTTLs~   32 (313)
T d2olra1          15 DVAVFFGLSGTGKTTLST   32 (313)
T ss_dssp             CEEEEECSTTSSHHHHHC
T ss_pred             CEEEEEccCCCCccccee
Confidence            466789999999999984

>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=82.13  E-value=0.45  Score=38.88  Aligned_cols=22  Identities=32%  Similarity=0.534  Sum_probs=19.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 041612          113 VNMLGIYGMGGIGKTMLAEEIA  134 (276)
Q Consensus       113 ~~vi~I~G~gGiGKTtLa~~v~  134 (276)
                      ..+-+|+|..|+|||++..++.
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~   46 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAIS   46 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            4578899999999999998875

>d1zunb3 c.37.1.8 (B:16-237) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=81.84  E-value=0.5  Score=35.47  Aligned_cols=27  Identities=19%  Similarity=0.149  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHhcc
Q 041612          112 DVNMLGIYGMGGIGKTMLAEEIARKVK  138 (276)
Q Consensus       112 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  138 (276)
                      +...++++|-...|||||+.++.....
T Consensus         8 ~~~~i~viGHVd~GKSTL~~~Ll~~~g   34 (222)
T d1zunb3           8 EMLRFLTCGNVDDGKSTLIGRLLHDSK   34 (222)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHcC
Confidence            344588999999999999999876543

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=81.73  E-value=0.33  Score=38.56  Aligned_cols=18  Identities=33%  Similarity=0.702  Sum_probs=15.7

Q ss_pred             cEEEEEcCCCCcHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAE  131 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~  131 (276)
                      .+....|.+|.|||||..
T Consensus        15 ~valffGLSGTGKTTLs~   32 (318)
T d1j3ba1          15 DVAVFFGLSGTGKTTLST   32 (318)
T ss_dssp             CEEEEEECTTSCHHHHTC
T ss_pred             CEEEEEccCCCCcccccc
Confidence            567889999999999884

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [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: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=81.64  E-value=0.48  Score=34.80  Aligned_cols=21  Identities=33%  Similarity=0.452  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .|+|.|-.+.|||||+..+.+
T Consensus         5 ni~iiGHvd~GKSTL~~~l~~   25 (196)
T d1d2ea3           5 NVGTIGHVDHGKTTLTAAITK   25 (196)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            489999999999999998764

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {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: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=80.75  E-value=0.66  Score=34.08  Aligned_cols=21  Identities=33%  Similarity=0.480  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 041612          115 MLGIYGMGGIGKTMLAEEIAR  135 (276)
Q Consensus       115 vi~I~G~gGiGKTtLa~~v~~  135 (276)
                      .|+|+|-...|||||+..+..
T Consensus        10 ni~iiGhVd~GKSTL~~~L~~   30 (205)
T d2qn6a3          10 NIGVVGHVDHGKTTLVQAITG   30 (205)
T ss_dssp             EEEEECSTTSSHHHHHHHHHS
T ss_pred             EEEEEEccCCcHHHHHHHHHh
Confidence            599999999999999999865

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=80.44  E-value=0.42  Score=37.96  Aligned_cols=18  Identities=33%  Similarity=0.702  Sum_probs=15.3

Q ss_pred             cEEEEEcCCCCcHHHHHH
Q 041612          114 NMLGIYGMGGIGKTMLAE  131 (276)
Q Consensus       114 ~vi~I~G~gGiGKTtLa~  131 (276)
                      .+..+.|.+|.|||||..
T Consensus        15 d~alfFGLSGTGKTTLs~   32 (323)
T d1ii2a1          15 DVTVFFGLSGTGKTTLSA   32 (323)
T ss_dssp             CEEEEECCTTSSHHHHHC
T ss_pred             CEEEEEccCCCCccccee
Confidence            456789999999999993