Citrus Sinensis ID: 038944

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330----
Protein Sequence
MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLICVSRTPRDIQQAVISVVDS
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHcccccccccccccccccccccccccccHHHHHHHHHccccccEEEEEEccccccHHHHHHHHcccccccccccEEEEEEEcccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccccccEEEEEcccHHHHHHcHHcccccEEEcccccccHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHcEEcccccHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHccHHHHccccEEEEEEEcccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHccccccccEEEEEEccHHHHHHHcccccccHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
MDISFRLFSERLRRVLAgeevtlpdaaklpiqnlHAETEIVTSWLSEFQDDISCLLLQKmghreiknpdlttvmdeincftyESEKVIDTFINSIseqksqsscSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEaeagissssksrdtvgLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHyfdchawvpgtypydadQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLIcvsrtprdIQQAVISVVDS
Flexible Loop (DISEMBL)
MDISFRLFSERLRRVlageevtlpdaaklpiqnLHAETEIVTSWLSEFQDDISCLLLQKMGHreiknpdlttvMDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTfeaeagissssksrdtvgLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIreilpdnqnrsRVLITLTEIKMFTFLLETLFSLLICVSRTPRDIQQAVISVVDS
Low Complexity Region (SEG)
MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINsiseqksqsscseDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKSRDTVGlddrmeelldllieGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMftflletlfsllICVSRTPRDIQQAVISVVDS
Disordered region (IsUnstruct)
****FRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINSI************IFDALQGL********************IIDRI*************************EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLICVSRTPRDIQQAVI*****
Disordered Region (DISOPRED)
MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFIN**************IFDALQGLQSRITDIKQRMQQ*************************KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM************YEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLICVSRTPRDIQQAVISV***
Disordered Region (DISEMBL)
MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINSI*********SEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAE************VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLICVSRTPRDIQQAVISVVDS
Disordered Region (DISPRO)
MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLICVSRTP*************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDAxxxxxxxxxxxxxxxxxxxxxDSEIIDRIKTFEAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLFSLLICVSRTPRDIQQAVISVVDS
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	334	2.2.26 [Sep-21-2011]
Q9M667	835	Disease resistance protei	yes	no	0.724	0.289	0.269	1e-12
Q9STE5	847	Putative disease resistan	no	no	0.604	0.238	0.256	6e-11
Q9FJB5	901	Disease resistance RPP8-l	no	no	0.694	0.257	0.229	1e-10
Q8W474	907	Probable disease resistan	no	no	0.649	0.239	0.270	1e-10
Q6L403	1312	Putative late blight resi	N/A	no	0.616	0.157	0.259	2e-10
Q6L3Z7	1317	Putative late blight resi	N/A	no	0.616	0.156	0.259	2e-10
Q9XIF0	906	Putative disease resistan	no	no	0.736	0.271	0.256	3e-10
Q6L406	1326	Putative late blight resi	N/A	no	0.601	0.151	0.298	6e-10
Q39214	926	Disease resistance protei	no	no	0.440	0.158	0.286	1e-09
Q6L439	1244	Putative late blight resi	N/A	no	0.580	0.155	0.276	2e-09

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

 Score = 74.7 bits (182), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 79/293 (26%), Positives = 132/293 (45%), Gaps = 51/293 (17%)

Query: 45  LSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINC--------FTYESEKVIDTFINSIS 96
           L E + +++C+      H  +K+ +     DE++         F Y+ E V+DT+   + 
Sbjct: 31  LEELKTELTCI------HGYLKDVEAREREDEVSKEWSKLVLDFAYDVEDVLDTYHLKLE 84

Query: 97  EQKSQSSCSE------------DIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFE 144
           E+  +                  I D ++ L+ RI DI ++ +         I  +K  E
Sbjct: 85  ERSQRRGLRRLTNKIGRKMDAYSIVDDIRILKRRILDITRKRETYG------IGGLK--E 136

Query: 145 AEAGISSSS-------KSRDT------VGLDDRMEELLDLLIEGPPQLSVVV-ILDSIGL 190
            + G ++SS       ++R        VGL+D  + LL+ L++   +   ++ I    GL
Sbjct: 137 PQGGGNTSSLRVRQLRRARSVDQEEVVVGLEDDAKILLEKLLDYEEKNRFIISIFGMGGL 196

Query: 191 DKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSS--RLSEIMDKNY 248
            K A A + YNS  VK  F+  AW   +  Y    +L  +I+ L  +S   L +I     
Sbjct: 197 GKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGEELEKIRKFAE 256

Query: 249 EMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIK 301
           E  ++ L+  L  K+YL V+DD+W  E  D ++  LP N   SRV+IT T IK
Sbjct: 257 EELEVYLYGLLEGKKYLVVVDDIWEREAWDSLKRALPCNHEGSRVIIT-TRIK 308

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9STE5|R13L2_ARATH Putative disease resistance RPP13-like protein 2 OS=Arabidopsis thaliana GN=RPP13L2 PE=3 SV=1

 Score = 68.6 bits (166), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 111/246 (45%), Gaps = 44/246 (17%)

Query: 81  TYESEKVIDTFI----------------NSISEQKSQSSCSEDIFDALQGLQSRITDIKQ 124
            Y+ E V+DT+                 N IS++K     + +I D ++ L+ R  D+ +
Sbjct: 69  AYDVEDVLDTYFLKLEKRLHRLGLMRLTNIISDKKD----AYNILDDIKTLKRRTLDVTR 124

Query: 125 RMQQLKHMDSEIIDRIKTFEAEAGISSSSKSRDT------------VGLDDRMEELLDLL 172
           +++            I  F     ++S+S+ R+             VGL D  + LL  L
Sbjct: 125 KLEMYG---------IGNFNEHRVVASTSRVREVRRARSDDQEERVVGLTDDAKVLLTKL 175

Query: 173 IE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIV 230
           ++  G  ++ ++ I    GL K + A + +NSS VK  F+   W   +   +   +L  +
Sbjct: 176 LDDDGDNKIYMISIFGMEGLGKTSLARKLFNSSDVKESFEYRVWTNVSGECNTRDILMRI 235

Query: 231 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNR 290
           I  L  +S   E+     +  ++ LH+ L  KRYL V+DD+W  E  + ++  LP +   
Sbjct: 236 ISSLEETSE-GELEKMAQQELEVYLHDILQEKRYLVVVDDIWESEALESLKRALPCSYQG 294

Query: 291 SRVLIT 296
           SRV+IT
Sbjct: 295 SRVIIT 300

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJB5|RP8L3_ARATH Disease resistance RPP8-like protein 3 OS=Arabidopsis thaliana GN=RPP8L3 PE=2 SV=1

 Score = 67.8 bits (164), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/261 (22%), Positives = 119/261 (45%), Gaps = 29/261 (11%)

Query: 58  QKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFI--------NSISEQKSQSSC----S 105
           +K G   ++N      ++++    +++E +I++++          +     + +C     
Sbjct: 51  KKHGSDRVRN-----FLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKNHVRRLACFLTDR 105

Query: 106 EDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTF-------EAEAGISSSSKSRDT 158
             +   ++G+  RI+ +   MQ L  +  +IID  ++        E      +SS+S D 
Sbjct: 106 HKVASDIEGITKRISKVIGEMQSLG-IQQQIIDGGRSLSLQDIQREIRQTFPNSSES-DL 163

Query: 159 VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGT 218
           VG++  +EEL+  ++E    + VV I    G+ K   A + ++   V+ +FD  AWV  +
Sbjct: 164 VGVEQSVEELVGPMVE-IDNIQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVS 222

Query: 219 YPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCD 278
             +    +   +++ L P     EI+  +    +  L + L T RYL V+DDVW  E  D
Sbjct: 223 QQFTQKHVWQRILQELRPHD--GEILQMDEYTIQGKLFQLLETGRYLVVLDDVWKEEDWD 280

Query: 279 IIREILPDNQNRSRVLITLTE 299
            I+E+ P  +    +L +  E
Sbjct: 281 RIKEVFPRKRGWKMLLTSRNE 301

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W474|DRL7_ARATH Probable disease resistance protein At1g58390 OS=Arabidopsis thaliana GN=At1g58390 PE=2 SV=4

 Score = 67.4 bits (163), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 121/248 (48%), Gaps = 31/248 (12%)

Query: 72  TVMDEINCFTYESEKVIDTFI--------NSISEQKSQSSC--SEDIFDAL--QGLQSRI 119
            V++EI    Y++E +I+T++        + I  +  + +C  S+   +AL   G+++RI
Sbjct: 60  NVVEEIKEIVYDAEDIIETYLLKEKLWKTSGIKMRIRRHACIISDRRRNALDVGGIRTRI 119

Query: 120 TDIKQRMQQLKHMDSEIIDRI-------KTFEAEAGISSSSKSRDTVGLDDRMEELLDLL 172
           +D+ + MQ    +   I+D         +  E     S   +S D VGL+  +++L+  L
Sbjct: 120 SDVIRDMQSFG-VQQAIVDGGYMQPQGDRQREMRQTFSKDYES-DFVGLEVNVKKLVGYL 177

Query: 173 IEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK 232
           ++    + VV I    GL K   A + +N   VKH FD  AWV  +  +    +  ++++
Sbjct: 178 VD-EENVQVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQ 236

Query: 233 FLMPSSRLSEIMDKNYEMKKIILHEYLM----TKRYLNVIDDVWNIEVCDIIREILPDNQ 288
            L    +  EI+    +M++  LH+ L     T + L V DD+W  E  D+I+ I P N+
Sbjct: 237 NLTSREKKDEIL----QMEEAELHDKLFQLLETSKSLIVFDDIWKDEDWDLIKPIFPPNK 292

Query: 289 NRSRVLIT 296
              +VL+T
Sbjct: 293 G-WKVLLT 299

Possible disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L403|R1B17_SOLDE Putative late blight resistance protein homolog R1B-17 OS=Solanum demissum GN=R1B-17 PE=3 SV=1

 Score = 67.0 bits (162), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 96/216 (44%), Gaps = 10/216 (4%)

Query: 81  TYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRI 140
            YE E V+D  IN ++          DI +        IT IK ++Q+ K+   + +  +
Sbjct: 471 AYEVEYVVDACINKVAPHWCLERWLLDIIE-------EITCIKAKIQE-KNTVEDTMKTV 522

Query: 141 KTFEAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY 200
            T  +     +   + + VG  D +E L + L+ G     V+ I    GL K   A   Y
Sbjct: 523 ITHTSSQLARTPRMNEEIVGFKDVIENLRNRLLNGTKGQDVISIHGMPGLGKTTLANRLY 582

Query: 201 NSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM 260
           +   V  +FD  A    +  Y   ++L  ++   +         ++N    K  L + L+
Sbjct: 583 SDRSVVSHFDICAQCCVSQVYSYKELLLALLCDAVGDDSARRKHNENKLADK--LRKTLL 640

Query: 261 TKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
           ++RYL ++DDVW+    D +R   PD  NRSR+++T
Sbjct: 641 SRRYLILVDDVWDNSAWDDLRGCFPDANNRSRIILT 676

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. 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.

Solanum demissum (taxid: 50514)

>sp|Q6L3Z7|R1B14_SOLDE Putative late blight resistance protein homolog R1B-14 OS=Solanum demissum GN=R1B-14 PE=3 SV=1

 Score = 67.0 bits (162), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 96/216 (44%), Gaps = 10/216 (4%)

Query: 81  TYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRI 140
            YE E V+D  IN ++          DI +        IT IK ++Q+ K+   + +  +
Sbjct: 471 AYEVEYVVDACINKVAPHWCLERWLLDIIE-------EITCIKAKIQE-KNTVEDTMKTV 522

Query: 141 KTFEAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY 200
            T  +     +   + + VG  D +E L + L+ G     V+ I    GL K   A   Y
Sbjct: 523 ITHTSSQLARTPRMNEEIVGFKDVIENLRNRLLNGTKGQDVISIHGMPGLGKTTLANRLY 582

Query: 201 NSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM 260
           +   V  +FD  A    +  Y   ++L  ++   +         ++N    K  L + L+
Sbjct: 583 SDRSVVSHFDICAQCCVSQVYSYKELLLALLCDAVGDDSARRKHNENKLADK--LRKTLL 640

Query: 261 TKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
           ++RYL ++DDVW+    D +R   PD  NRSR+++T
Sbjct: 641 SRRYLILVDDVWDNSAWDDLRGCFPDANNRSRIILT 676

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. 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.

Solanum demissum (taxid: 50514)

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

 Score = 66.2 bits (160), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 68/265 (25%), Positives = 124/265 (46%), Gaps = 19/265 (7%)

Query: 45  LSEFQDDISCLL--LQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQS 102
           ++E +DD+  L+  L     ++         ++EI   TY++E +I+ F+   S      
Sbjct: 36  ITELRDDLKMLMAFLSDADAKKQTRALARNCLEEIKEITYDAEDIIEIFLLKGSVNMRSL 95

Query: 103 SC----SEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTF-------EAEAGISS 151
           +C      +I   +  +  RI+ + Q MQ L  + S+I+D + +        E     SS
Sbjct: 96  ACFPGGRREIALQITSISKRISKVIQVMQNLG-IKSDIMDGVDSHAQLERKRELRHTFSS 154

Query: 152 SSKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDC 211
            S+S + VGL+  +E+L++ L+ G      V I    GL K   A + ++   VK +FD 
Sbjct: 155 ESES-NLVGLEKNVEKLVEELV-GNDSSHGVSITGLGGLGKTTLARQIFDHDKVKSHFDG 212

Query: 212 HAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDV 271
            AWV  +  +    +   ++  L P  + S++ + + + K   L + L TK+ L V DD+
Sbjct: 213 LAWVCVSQEFTRKDVWKTILGNLSPKYKDSDLPEDDIQKK---LFQLLETKKALIVFDDL 269

Query: 272 WNIEVCDIIREILPDNQNRSRVLIT 296
           W  E    I  + P+ +   +VL+T
Sbjct: 270 WKREDWYRIAPMFPERKAGWKVLLT 294

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L406|R1B19_SOLDE Putative late blight resistance protein homolog R1B-19 OS=Solanum demissum GN=R1B-19 PE=5 SV=2

 Score = 65.5 bits (158), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 98/221 (44%), Gaps = 20/221 (9%)

Query: 81  TYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRI 140
            +E E V+D  IN    +     C E     LQ +   IT IK ++Q+   +D    D +
Sbjct: 473 AHEVEYVVDACIN----KGIPHWCLER---WLQDIIEEITCIKAKIQEKNTVD----DTM 521

Query: 141 KTFEAEAGISSSSKSR---DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAG 197
           KT         +   R   + VG +D +E L   L+ G     V+ I    GL K   A 
Sbjct: 522 KTVIVRTSSKLARTPRMKEEIVGFEDIIENLRKKLLNGTKGQDVISIHGMPGLGKTTLAN 581

Query: 198 EAYNSSYVKHYFDCHA--WVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIIL 255
             Y+   V   FD  A   V   Y Y  D +L ++   +   S   E+ D   E+  + L
Sbjct: 582 RLYSDRSVVSQFDICAQCCVSQVYSY-KDLLLSLLCDTIGEESERRELPDN--ELADM-L 637

Query: 256 HEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
            + L+ +RYL ++DDVW   V D +R   PD  NRSR+++T
Sbjct: 638 RKTLLPRRYLILVDDVWENSVWDDLRGCFPDTNNRSRIILT 678

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. 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.

Solanum demissum (taxid: 50514)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score = 64.3 bits (155), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 43/150 (28%), Positives = 72/150 (48%), Gaps = 3/150 (2%)

Query: 159 VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGT 218
           VG+D    +L+  L+   PQ  VV ++   G  K   +   + S  V+ +F+ +AWV  +
Sbjct: 173 VGIDAPKGKLIGRLLSPEPQRIVVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTIS 232

Query: 219 YPYDADQMLDIVIKFLMPSSRL---SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIE 275
             Y  + +   +IK     +     +E+    Y      L EYL +KRY+ V+DDVW   
Sbjct: 233 KSYVIEDVFRTMIKEFYKEADTQIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVWTTG 292

Query: 276 VCDIIREILPDNQNRSRVLITLTEIKMFTF 305
           +   I   LPD    SRV++T  ++ + +F
Sbjct: 293 LWREISIALPDGIYGSRVMMTTRDMNVASF 322

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. 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. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L439|R1A4_SOLDE Putative late blight resistance protein homolog R1A-4 OS=Solanum demissum GN=R1A-4 PE=5 SV=2

 Score = 63.9 bits (154), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 99/228 (43%), Gaps = 34/228 (14%)

Query: 81  TYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRI 140
            +E E V+D  IN    +     C E     LQ +   IT IK ++Q+   +D    D +
Sbjct: 463 AHEVEYVVDACIN----KGIPHWCLER---WLQDIIEEITCIKAKIQEKNTVD----DTM 511

Query: 141 KTFEAEAGISSSSKSR---DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAG 197
           KT  A      +   R   + VG  D +E L + L+ G     V+ I    GL K   A 
Sbjct: 512 KTVIARTSSKLARTPRMNEEIVGFKDVIENLRNQLLNGTKGQDVISIHGMPGLGKTTLAN 571

Query: 198 EAYNSSYVKHYFDCHA--WVPGTYPYD-------ADQMLDIVIKFLMPSSRLSEIMDKNY 248
             Y+   V  +FD  A   V   Y Y         D + +  ++  + ++ L++++ K  
Sbjct: 572 RLYSDRSVVSHFDICAQCCVSQVYSYKDLLLALLCDAIGEGSVRRELHANELADMLRKT- 630

Query: 249 EMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
                     L+ +RYL ++DDVW   V D +R   PD  NRSR+++T
Sbjct: 631 ----------LLPRRYLILVDDVWENSVWDDLRGCFPDANNRSRIILT 668

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. 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.

Solanum demissum (taxid: 50514)

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	334
356524195	946	PREDICTED: disease resistance protein RP	0.676	0.238	0.276	4e-19
147856116	1894	hypothetical protein VITISV_006820 [Viti	0.676	0.119	0.271	4e-18
224064832	920	cc-nbs-lrr resistance protein [Populus t	0.697	0.253	0.263	2e-17
255582947	935	Disease resistance protein RPM1, putativ	0.817	0.291	0.272	3e-17
359489792	916	PREDICTED: probable disease resistance p	0.703	0.256	0.288	3e-17
297745275	1136	unnamed protein product [Vitis vinifera]	0.697	0.205	0.298	6e-17
224138292	916	nbs-lrr resistance protein [Populus tric	0.652	0.237	0.268	1e-16
359489796	795	PREDICTED: disease susceptibility protei	0.697	0.293	0.295	1e-16
297745279	920	unnamed protein product [Vitis vinifera]	0.697	0.253	0.295	1e-16
356531473	937	PREDICTED: disease resistance protein RP	0.691	0.246	0.275	3e-16

>gi|356524195|ref|XP_003530717.1| PREDICTED: disease resistance protein RPM1-like [Glycine max]

 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/264 (27%), Positives = 131/264 (49%), Gaps = 38/264 (14%)

Query: 67  NPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQSSCSE-----DIFDALQGLQSRITD 121
           N  + T++ ++   ++  E VID ++  + +Q     C+      DI   ++ L+ R   
Sbjct: 60  NEGIRTLVKQLREASFRIEDVIDEYLIFVEQQPDALGCAALFFECDITHFIEYLKRR-HH 118

Query: 122 IKQRMQQLKHMDSEIIDRIKTFE------AEAGISSSSKSR-----------------DT 158
           I   +QQ+K +   I+ R K +        E G SS++ S+                 + 
Sbjct: 119 IASEIQQIKSVVDGIMQRGKKYNFLRQPSVEQGQSSNAGSQSIQWHDPRIASRYLDEAEV 178

Query: 159 VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGT 218
           VG +   +EL+D L+EGP + +V+ ++   GL K   A   +N+  V  +FD HAW+  +
Sbjct: 179 VGFEGPRDELIDWLVEGPAERTVISVVGMGGLGKTTLASRVFNNQKVVGHFDFHAWITVS 238

Query: 219 YPYDADQMLDIVIKFLM------PSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW 272
             Y  + M+  ++K L       P   +SE MD++  + ++    YL  KRY+ ++DDVW
Sbjct: 239 QSYTVEGMMRDLLKKLCKEKRENPPQDISE-MDRDSLIDEV--RNYLQQKRYVVILDDVW 295

Query: 273 NIEVCDIIREILPDNQNRSRVLIT 296
           ++E+   I+  + DN+N SR+LIT
Sbjct: 296 SVELWGQIKSAMFDNKNGSRILIT 319

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147856116|emb|CAN80288.1| hypothetical protein VITISV_006820 [Vitis vinifera]

 Score = 98.6 bits (244), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 123/258 (47%), Gaps = 32/258 (12%)

Query: 95  ISEQKSQSSCSEDIFD--------------ALQGLQSRITDIKQRMQQLKHMDSEIIDRI 140
           + E +  + C ED+ D               L  L S++ D+K ++ +LK   S     I
Sbjct: 65  VQELRETAYCIEDLVDEYILHFANPPHRRGVLGFLSSKVQDLKLKVGKLKEASS-TYGFI 123

Query: 141 KTFEAEAGISSSS--------------KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILD 186
            +FE  +G  S +              +  + VG++    EL+  L+EG P+ +V+ ++ 
Sbjct: 124 SSFELGSGSCSGTSVPWHDPGVTSLFIEDAEIVGIESHKGELIKWLVEGAPERTVISVVG 183

Query: 187 SIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK--FLMPSSRLSEIM 244
             GL K   A + Y++  +  +FDC AW+  +  +  +++L  VIK  +L     + +  
Sbjct: 184 MGGLGKTTLAKKVYDNKRMVEHFDCRAWITVSQSFKMEEVLRNVIKQFYLARKESIPDGT 243

Query: 245 DKNYEMKKII-LHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMF 303
           D   EM  I  L EYL  KRY+ V  DVW +E    I+ ILP+N+  SR++IT   +++ 
Sbjct: 244 DAMDEMSLITRLREYLEDKRYVVVFXDVWKLEFWRFIKYILPENKRGSRIVITTRNVEVG 303

Query: 304 TFLLETLFSLLICVSRTP 321
           + + E+ F  +  +   P
Sbjct: 304 SAVKESSFHYIHNLQALP 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224064832|ref|XP_002301573.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222843299|gb|EEE80846.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/258 (26%), Positives = 124/258 (48%), Gaps = 25/258 (9%)

Query: 63  REIKNPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITD- 121
           R+ K+  + T + ++    YE E +ID F++    +K   +  + I + +      IT  
Sbjct: 51  RKEKSDSVETWVRQVREVAYEVEDIIDEFMHH-KYKKPLENGFKGIVEGVVKFPKNITSR 109

Query: 122 --IKQRMQQLKHMDSEIIDRIKTF-------EAEAGISSSSKSR-----------DTVGL 161
             I  ++Q++     E+ +R K +       EA   ++                 D VG+
Sbjct: 110 HRISSKLQKVIAKVHEVSERSKRYGFDQLDEEATRNVAGDRWQHYGESATFVDDDDIVGM 169

Query: 162 DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY 221
           ++  E+LL  L+E  P+ +V+ I+   GL K       YN+  +K  FDC AW+  +   
Sbjct: 170 EESTEQLLGWLMEDEPRRTVISIVGMGGLGKTTLVTRVYNNHIIKRGFDCWAWISVSQTC 229

Query: 222 DADQMLDIVIKFLMPSSRL---SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCD 278
              ++L  +IK L  ++ +   + +   NY     +L +YL  KRY+ V+DDVW+I++  
Sbjct: 230 GTGELLRSIIKELFGATSVVIPNNVGSMNYRQLVGMLIDYLHQKRYVIVLDDVWSIDLWS 289

Query: 279 IIREILPDNQNRSRVLIT 296
           IIR   P+N+  SR+++T
Sbjct: 290 IIRTAFPNNRYGSRIILT 307

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582947|ref|XP_002532244.1| Disease resistance protein RPM1, putative [Ricinus communis] gi|223528062|gb|EEF30138.1| Disease resistance protein RPM1, putative [Ricinus communis]

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 138/308 (44%), Gaps = 35/308 (11%)

Query: 11  RLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDL 70
           +L  +L GE V L       +Q L  E E + S+L     D      Q+     IK    
Sbjct: 12  KLDTLLTGE-VKLLRNVHTELQGLRDELEAIESFLR----DADVRFYQENSDSRIK---- 62

Query: 71  TTVMDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLK 130
            T + ++    +E E  ID ++  +   + Q      I   ++ L+ R  +I  ++Q LK
Sbjct: 63  -TWVKQVRQVAFEIEDAIDVYMLHLVRHQDQHGFFHKISRLVRKLKPR-HEIASKIQDLK 120

Query: 131 HMDSEIIDRIKTFEAEAGISSSSKSRDT-----------------VGLDDRMEELLDLLI 173
               EI +R   ++        S  RD                  VG++    EL+  L+
Sbjct: 121 KSVCEIRERSDRYKFNLSSEQGSSDRDNTWHDPRVHSLFIDEAELVGIESPKAELISKLV 180

Query: 174 EGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF 233
           EG  +  V+ ++   GL K   A + ++S  V  YFDC AW+  T  Y   ++L I+I+ 
Sbjct: 181 EGASENVVISVVGMGGLGKTTLAKKVFDSERVTVYFDCKAWITVTQSYKMAKLLRIMIRQ 240

Query: 234 L-----MPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQ 288
           L     +P+   ++ M +   ++K  L EYL+ KRYL + DDVW+I +   I   LP+N 
Sbjct: 241 LHQENVLPAFEGTDTMSELSLIEK--LREYLIEKRYLVIFDDVWDIFLWGYIMTALPNNG 298

Query: 289 NRSRVLIT 296
             +R++IT
Sbjct: 299 KGNRIIIT 306

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489792|ref|XP_002274076.2| PREDICTED: probable disease resistance protein RDL6/RF9-like [Vitis vinifera]

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 132/274 (48%), Gaps = 39/274 (14%)

Query: 55  LLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFI----------NSISEQKSQSSC 104
           L L+    + + N  +   +++I   T+++E VID FI          N++   K   +C
Sbjct: 42  LFLKDADSQSLYNEKIKLWVEQIRNVTHDAEDVIDEFILDMDHRQLRLNTLKFLKCLPTC 101

Query: 105 S--EDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKS------- 155
               D    +  L  R+ +I  R++++      + +R K +  EA ++SSS S       
Sbjct: 102 VGFADKLPFIHELDGRVKEINIRIERI------MANRSK-YGLEALMASSSSSTTDQVVA 154

Query: 156 -----------RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSY 204
                       D VG++D  E +  +L++G  + +VV I+   GL K   A + YN S 
Sbjct: 155 HKEKWAQVVEGSDVVGIEDGTEVVTQMLMKGEMRRAVVSIVGMGGLGKTTLAKKVYNHSD 214

Query: 205 VKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSS--RLSEIMDKNYEMKKIILHEYLMTK 262
           VK +FDCHAWV  +  + A ++L  V   +M  S  +  E+ +         + EYL  K
Sbjct: 215 VKQHFDCHAWVYVSQEFKAREILLGVAYCVMSLSDEKKKEVKEMGEAELGRNVREYLKEK 274

Query: 263 RYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
           +YL  +DDVW+ EV   +R  LP+ ++ S+VLIT
Sbjct: 275 KYLVAMDDVWSREVWSSLRSYLPEAKDGSKVLIT 308

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745275|emb|CBI40355.3| unnamed protein product [Vitis vinifera]

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 81/271 (29%), Positives = 130/271 (47%), Gaps = 38/271 (14%)

Query: 55  LLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFI----------NSISEQKSQSSC 104
           L L+    + I +  +   +++I   T+++E VID FI          N++   K   +C
Sbjct: 43  LFLKDADSKRIYDERIKLWVNQIRNATHDAEDVIDEFILNMDHRQRRLNTLKFLKCLPAC 102

Query: 105 S--EDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKS------- 155
               D    +  L SR+ DI   +  +      + +R K    +   SSSS +       
Sbjct: 103 VGFADKLPFIHELDSRVKDINVMIGAI------MANRSKYGLGDLVASSSSTTDQVAAHK 156

Query: 156 ---------RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVK 206
                     D VG++D +EE+  +L++   + SVV I+   GL K  FA + YN   V+
Sbjct: 157 EKRPPVVEESDVVGIEDGIEEVKQMLMKEETRRSVVSIVGMGGLGKTTFAKKVYNQRDVQ 216

Query: 207 HYFDCHAWVPGTYPYDADQ-MLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYL 265
            +FDC AWV  +  + A + +LDI   F+  S +  E+ +     K   L EYL  K+YL
Sbjct: 217 QHFDCKAWVYVSQEFRAREILLDIANHFMSLSEKEKEMRESELGEK---LCEYLKEKKYL 273

Query: 266 NVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
            V+DDVW+ EV   +R  LP+ ++ S+VLIT
Sbjct: 274 IVMDDVWSSEVWSRLRSHLPEAKDGSKVLIT 304

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138292|ref|XP_002326566.1| nbs-lrr resistance protein [Populus trichocarpa] gi|222833888|gb|EEE72365.1| nbs-lrr resistance protein [Populus trichocarpa]

 Score = 94.0 bits (232), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 119/250 (47%), Gaps = 32/250 (12%)

Query: 74  MDEINCFTYESEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQ---QLK 130
           + +I    +E+E ++D F   ++   +       ++  +  +   I ++K R +   Q+K
Sbjct: 62  VKQIRDVAHETEDILDEFTILLAHDHASG-----LYGLIHKMSCCIKNMKARYRIASQIK 116

Query: 131 HMDSEIID--------RIKTFEAEAGISSSSKS-------------RDTVGLDDRMEELL 169
            M+S I +        R K F AE G SS+S                D VG+++R  +L+
Sbjct: 117 AMNSRIRNISDGHRRLRQKFFVAEHGSSSASTGWQDRREDALLLDMTDLVGIEERKSKLV 176

Query: 170 DLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDI 229
             L++G     VV +    GL K   A + Y+ + VK +F  HAW+  +  Y  +++L  
Sbjct: 177 GWLVDGRSGREVVSLAGMGGLGKTTLAKQVYDDAEVKKHFSVHAWITVSRSYKMEELLKD 236

Query: 230 VIKFLMPSSRL---SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPD 286
           +++ L  + R      +  +N    K I+ E L  +RYL V+DDVW++   D ++  LP 
Sbjct: 237 ILQQLFAADRKPVPKNLESQNSSQLKSIIKEVLQKRRYLIVLDDVWHVNEWDAVKYALPT 296

Query: 287 NQNRSRVLIT 296
           N   SRV++T
Sbjct: 297 NNCGSRVMLT 306

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489796|ref|XP_003633980.1| PREDICTED: disease susceptibility protein LOV1-like [Vitis vinifera]

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/271 (29%), Positives = 129/271 (47%), Gaps = 38/271 (14%)

Query: 55  LLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFI----------NSISEQKSQSSC 104
           L L+    + I +  +   +++I   T+++E VID FI          N++   K   +C
Sbjct: 43  LFLKDADSKRIHDERIKLWVNQIRNATHDAEDVIDEFIVNMDHRQRRLNTLKLLKCLPTC 102

Query: 105 S--EDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKS------- 155
               D    +  L SR+ DI   +  +      + +R K    +   SSSS +       
Sbjct: 103 VGFADKLPFIHELDSRVKDINVMIGAI------MANRSKYGLGDLVASSSSTTDQVAAHK 156

Query: 156 ---------RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVK 206
                     D VG++D  EE+  +L++   + SVV I+   GL K   A + YN   V+
Sbjct: 157 EKRPPVVEESDVVGIEDGTEEVKQMLMKEETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQ 216

Query: 207 HYFDCHAWVPGTYPYDADQ-MLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYL 265
            +FDC AWV  +  + A + +LDI  +F+  S +  E+ +     K   L EYL  K+YL
Sbjct: 217 QHFDCKAWVYVSQEFRAREILLDIANRFMSLSEKEKEMRESELGEK---LCEYLKEKKYL 273

Query: 266 NVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
            V+DDVW+ EV   +R  LP+ ++ S+VLIT
Sbjct: 274 VVMDDVWSSEVWSRLRSHLPEAKDGSKVLIT 304

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745279|emb|CBI40359.3| unnamed protein product [Vitis vinifera]

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/271 (29%), Positives = 129/271 (47%), Gaps = 38/271 (14%)

Query: 55  LLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFI----------NSISEQKSQSSC 104
           L L+    + I +  +   +++I   T+++E VID FI          N++   K   +C
Sbjct: 43  LFLKDADSKRIHDERIKLWVNQIRNATHDAEDVIDEFIVNMDHRQRRLNTLKLLKCLPTC 102

Query: 105 S--EDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKS------- 155
               D    +  L SR+ DI   +  +      + +R K    +   SSSS +       
Sbjct: 103 VGFADKLPFIHELDSRVKDINVMIGAI------MANRSKYGLGDLVASSSSTTDQVAAHK 156

Query: 156 ---------RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVK 206
                     D VG++D  EE+  +L++   + SVV I+   GL K   A + YN   V+
Sbjct: 157 EKRPPVVEESDVVGIEDGTEEVKQMLMKEETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQ 216

Query: 207 HYFDCHAWVPGTYPYDADQ-MLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYL 265
            +FDC AWV  +  + A + +LDI  +F+  S +  E+ +     K   L EYL  K+YL
Sbjct: 217 QHFDCKAWVYVSQEFRAREILLDIANRFMSLSEKEKEMRESELGEK---LCEYLKEKKYL 273

Query: 266 NVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
            V+DDVW+ EV   +R  LP+ ++ S+VLIT
Sbjct: 274 VVMDDVWSSEVWSRLRSHLPEAKDGSKVLIT 304

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531473|ref|XP_003534302.1| PREDICTED: disease resistance protein RPM1-like [Glycine max]

 Score = 92.4 bits (228), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 64  EIKNPDLTTVMDEINCFTYESEKVIDTFINSISEQKSQSSCS---------EDIFDALQG 114
           E KNP+L   +  +    ++ E  ID F   + +Q  Q + S           I   +QG
Sbjct: 52  EDKNPELKAWVKRVRDVAHDMEDAIDEFSLGLVDQHGQGNNSSFHMNFFTRHKIASNIQG 111

Query: 115 LQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKSRDTVGLDDRMEELLDLLIE 174
           ++SR+  I Q+   +  + S    R+ +     G +   +  D VG+D   ++L DLL  
Sbjct: 112 IKSRLDIISQKRPDIPWIGSGSSQRLSSRLDSQGDALLLEEADLVGIDKPKKQLSDLLFN 171

Query: 175 GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL 234
                +V+ +    GL K   A + Y+   VK  F  HAW+  +  +  D++L  +++ L
Sbjct: 172 EEAGRAVIPVYGMGGLGKTTLAKQVYDDPKVKKRFRIHAWINVSQSFKLDELLKDLVQQL 231

Query: 235 M-----PSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQN 289
                 P+      M K+ ++K++I    L   RYL V+DDVW ++V D ++  LP+N  
Sbjct: 232 HTVIGKPAPEAVGQM-KSDQLKEVI-KNLLQRSRYLVVLDDVWQVKVWDSVKLALPNNNR 289

Query: 290 RSRVLIT 296
            SRV++T
Sbjct: 290 GSRVMLT 296

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	334
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.359	0.143	0.365	2.8e-09
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.359	0.141	0.322	2.7e-08
TAIR|locus:2102857	847	AT3G46710 [Arabidopsis thalian	0.377	0.148	0.304	3.4e-08
UNIPROTKB|Q84UB1	928	Pi-ta "Pi-ta protein" [Oryza s	0.497	0.178	0.289	6.6e-08
UNIPROTKB|Q9AY26	928	Pi-ta "Pi-ta protein" [Oryza s	0.497	0.178	0.289	6.6e-08
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.553	0.199	0.252	6.8e-07
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.350	0.137	0.306	3.1e-06
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.754	0.278	0.224	4e-06
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.350	0.128	0.305	5.3e-06
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.547	0.203	0.256	4.1e-05

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

 Score = 164 (62.8 bits), Expect = 2.8e-09, Sum P(2) = 2.8e-09
 Identities = 45/123 (36%), Positives = 63/123 (51%)

Query:   181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL-MPSSR 239
             ++ I    GL K A A + YNS  VK  F+  AW   +  Y    +L  +I+ L M S  
Sbjct:   187 IISIFGMGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGE 246

Query:   240 -LSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLT 298
              L +I     E  ++ L+  L  K+YL V+DD+W  E  D ++  LP N   SRV+IT T
Sbjct:   247 ELEKIRKFAEEELEVYLYGLLEGKKYLVVVDDIWEREAWDSLKRALPCNHEGSRVIIT-T 305

Query:   299 EIK 301
              IK
Sbjct:   306 RIK 308

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

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

GO:0005886 "plasma membrane" evidence=IDA

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

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

 Score = 157 (60.3 bits), Expect = 2.7e-08, P = 2.7e-08
 Identities = 40/124 (32%), Positives = 66/124 (53%)

Query:   181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL--MPSS 238
             ++ I    GL K A A + YNS  VK  FDC AW   +  Y    +L  +I+ L  + + 
Sbjct:   187 IISIFGMGGLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTRDILIRIIRSLGIVSAE 246

Query:   239 RLSEI-MDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITL 297
              + +I M +  E  ++ L+  L  K Y+ V+DDVW+ +  + ++  LP +   S+V+IT 
Sbjct:   247 EMEKIKMFEEDEELEVYLYGLLEGKNYMVVVDDVWDPDAWESLKRALPCDHRGSKVIIT- 305

Query:   298 TEIK 301
             T I+
Sbjct:   306 TRIR 309

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2102857 AT3G46710 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 3.4e-08, P = 3.4e-08
 Identities = 39/128 (30%), Positives = 66/128 (51%)

Query:   175 GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL 234
             G  ++ ++ I    GL K + A + +NSS VK  F+   W   +   +   +L  +I  L
Sbjct:   180 GDNKIYMISIFGMEGLGKTSLARKLFNSSDVKESFEYRVWTNVSGECNTRDILMRIISSL 239

Query:   235 MPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVL 294
               +S   E+     +  ++ LH+ L  KRYL V+DD+W  E  + ++  LP +   SRV+
Sbjct:   240 EETSE-GELEKMAQQELEVYLHDILQEKRYLVVVDDIWESEALESLKRALPCSYQGSRVI 298

Query:   295 ITLTEIKM 302
             IT T I++
Sbjct:   299 IT-TSIRV 305

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q84UB1 Pi-ta "Pi-ta protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 154 (59.3 bits), Expect = 6.6e-08, P = 6.6e-08
 Identities = 50/173 (28%), Positives = 80/173 (46%)

Query:   133 DSEIIDRIKTFEAEAGISSSSKSRDTVGXXXXXXXXXXXXXXGPPQLSVVVILDSIGLDK 192
             DS   +R +      G+  ++     VG              G P+L V  I+ S G+ K
Sbjct:   183 DSAGNERRRFLSLTFGMDDAAVHGQLVGRDISMQKLVRWLADGEPKLKVASIVGSGGVGK 242

Query:   193 AAFAGEAY--NSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR--LSEIMDKNY 248
                A E Y  +   +   FDC A+V      D  ++L  ++  L P  +   S++ + + 
Sbjct:   243 TTLATEFYRLHGRRLDAPFDCRAFVRTPRKPDMTKILTDMLSQLRPQHQHQSSDVWEVDR 302

Query:   249 EMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIK 301
              ++ I  H  L  KRY  +I+D+W   + DI+   LPDN + SR+LIT TEI+
Sbjct:   303 LLETIRTH--LQDKRYFIIIEDLWASSMWDIVSRGLPDNNSCSRILIT-TEIE 352

GO:0006952 "defense response" evidence=IMP

UNIPROTKB|Q9AY26 Pi-ta "Pi-ta protein" [Oryza sativa (taxid:4530)]

 Score = 154 (59.3 bits), Expect = 6.6e-08, P = 6.6e-08
 Identities = 50/173 (28%), Positives = 80/173 (46%)

Query:   133 DSEIIDRIKTFEAEAGISSSSKSRDTVGXXXXXXXXXXXXXXGPPQLSVVVILDSIGLDK 192
             DS   +R +      G+  ++     VG              G P+L V  I+ S G+ K
Sbjct:   183 DSAGNERRRFLSLTFGMDDAAVHGQLVGRDISMQKLVRWLADGEPKLKVASIVGSGGVGK 242

Query:   193 AAFAGEAY--NSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR--LSEIMDKNY 248
                A E Y  +   +   FDC A+V      D  ++L  ++  L P  +   S++ + + 
Sbjct:   243 TTLATEFYRLHGRRLDAPFDCRAFVRTPRKPDMTKILTDMLSQLRPQHQHQSSDVWEVDR 302

Query:   249 EMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIK 301
              ++ I  H  L  KRY  +I+D+W   + DI+   LPDN + SR+LIT TEI+
Sbjct:   303 LLETIRTH--LQDKRYFIIIEDLWASSMWDIVSRGLPDNNSCSRILIT-TEIE 352

GO:0006952 "defense response" evidence=IMP

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 6.8e-07, P = 6.8e-07
 Identities = 50/198 (25%), Positives = 91/198 (45%)

Query:   115 LQSRITDIKQRMQQLKHMDSEIIDRIKTFEAE--AGISSSS---KSRDTVGXXXXXXXXX 169
             +QS I+D  +R    ++  + ++  I   +A+    IS SS        VG         
Sbjct:   125 IQS-ISDSMKRYYHSENYQAALLPPIDDGDAKWVNNISESSLFFSENSLVGIDAPKGKLI 183

Query:   170 XXXXXGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDI 229
                    PQ  VV ++   G  K   +   + S  V+ +F+ +AWV  +  Y  + +   
Sbjct:   184 GRLLSPEPQRIVVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRT 243

Query:   230 VIK--FLMPSSRL-SEIMDKNYE--MKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREIL 284
             +IK  +    +++ +E+    Y   ++K++  EYL +KRY+ V+DDVW   +   I   L
Sbjct:   244 MIKEFYKEADTQIPAELYSLGYRELVEKLV--EYLQSKRYIVVLDDVWTTGLWREISIAL 301

Query:   285 PDNQNRSRVLITLTEIKM 302
             PD    SRV++T  ++ +
Sbjct:   302 PDGIYGSRVMMTTRDMNV 319

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

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

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

 Score = 140 (54.3 bits), Expect = 3.1e-06, Sum P(2) = 3.1e-06
 Identities = 38/124 (30%), Positives = 65/124 (52%)

Query:   178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPS 237
             QL ++  +   GL K   A E +N   ++H F+   WV  +  +  +Q++  +++ L  +
Sbjct:   181 QLLIMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRNLGDA 240

Query:   238 SRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW--NIEVCDIIREILPDNQNRSRVLI 295
             S   +I      ++KI   +YL+ KRYL V+DDVW  N+   D I + LP  Q  S ++ 
Sbjct:   241 SVGDDI---GTLLRKI--QQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRGQGGSVIVT 295

Query:   296 TLTE 299
             T +E
Sbjct:   296 TRSE 299

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 138 (53.6 bits), Expect = 4.0e-06, P = 4.0e-06
 Identities = 60/267 (22%), Positives = 111/267 (41%)

Query:    41 VTSWLSEFQDDISCLL--LQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTFINXXXXX 98
             V   ++E +DD+  L+  L     ++         ++EI   TY++E +I+ F+      
Sbjct:    32 VEEQITELRDDLKMLMAFLSDADAKKQTRALARNCLEEIKEITYDAEDIIEIFLLKGSVN 91

Query:    99 XXXXX----XXXDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTF-----EAEAGI 149
                         +I   +  +  RI+ + Q MQ L  + S+I+D + +      + E   
Sbjct:    92 MRSLACFPGGRREIALQITSISKRISKVIQVMQNLG-IKSDIMDGVDSHAQLERKRELRH 150

Query:   150 SSSSKSRDTVGXXXXXXXXXXXXXXGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF 209
             + SS+S   +               G      V I    GL K   A + ++   VK +F
Sbjct:   151 TFSSESESNLVGLEKNVEKLVEELVGNDSSHGVSITGLGGLGKTTLARQIFDHDKVKSHF 210

Query:   210 DCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVID 269
             D  AWV  +  +    +   ++  L P  + S++ + + + K   L + L TK+ L V D
Sbjct:   211 DGLAWVCVSQEFTRKDVWKTILGNLSPKYKDSDLPEDDIQKK---LFQLLETKKALIVFD 267

Query:   270 DVWNIEVCDIIREILPDNQNRSRVLIT 296
             D+W  E    I  + P+ +   +VL+T
Sbjct:   268 DLWKREDWYRIAPMFPERKAGWKVLLT 294

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 5.3e-06, Sum P(2) = 5.3e-06
 Identities = 36/118 (30%), Positives = 56/118 (47%)

Query:   179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSS 238
             + VV I    GL K   A + +N   VKH FD  AWV  +  +    +  ++++ L    
Sbjct:   183 VQVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSRE 242

Query:   239 RLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
             +  EI+          L + L T + L V DD+W  E  D+I+ I P N+   +VL+T
Sbjct:   243 KKDEILQMEEAELHDKLFQLLETSKSLIVFDDIWKDEDWDLIKPIFPPNKGW-KVLLT 299

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 4.1e-05, P = 4.1e-05
 Identities = 50/195 (25%), Positives = 84/195 (43%)

Query:   112 LQGLQSRITDIKQRMQQLKHMDSEIIDRIKTF-------EAEAGISSSSKSRDTVGXXXX 164
             ++G+  RI+ +   MQ L  +  +IID  ++        E      +SS+S D VG    
Sbjct:   112 IEGITKRISKVIGEMQSLG-IQQQIIDGGRSLSLQDIQREIRQTFPNSSES-DLVGVEQS 169

Query:   165 XXXXXXXXXXGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDAD 224
                           + VV I    G+ K   A + ++   V+ +FD  AWV  +  +   
Sbjct:   170 VEELVGPMVE-IDNIQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQK 228

Query:   225 QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREIL 284
              +   +++ L P     EI+  +    +  L + L T RYL V+DDVW  E  D I+E+ 
Sbjct:   229 HVWQRILQELRPHD--GEILQMDEYTIQGKLFQLLETGRYLVVLDDVWKEEDWDRIKEVF 286

Query:   285 PDNQNRSRVLITLTE 299
             P  +    +L +  E
Sbjct:   287 PRKRGWKMLLTSRNE 301

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	334
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	1e-19

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

 Score = 87.0 bits (216), Expect = 1e-19
 Identities = 44/135 (32%), Positives = 70/135 (51%), Gaps = 2/135 (1%)

Query: 162 DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY 221
           +D +E L++ L+E    L VV I+   G+ K   A + YN   V  +FD  AWV  +  Y
Sbjct: 2   EDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTY 61

Query: 222 DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIR 281
              ++   +++ L      S+ ++KN     + + E L+ KR+L V+DDVW     D I 
Sbjct: 62  TEFRLQKDILQELGLDD--SDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKIG 119

Query: 282 EILPDNQNRSRVLIT 296
              PD +N SRV++T
Sbjct: 120 VPFPDGENGSRVIVT 134

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	334
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.95
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.88
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.03
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.91
PF05729	166	NACHT: NACHT domain	98.84
cd01128	249	rho_factor Transcription termination factor rho is	98.81
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.71
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.7
PRK09376	416	rho transcription termination factor Rho; Provisio	98.66
PF13173	128	AAA_14: AAA domain	98.64
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.61
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.5
TIGR00767	415	rho transcription termination factor Rho. Members	98.48
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.46
PTZ00202	550	tuzin; Provisional	98.35
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.34
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.31
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.29
PRK06893	229	DNA replication initiation factor; Validated	98.27
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.25
PRK13342	413	recombination factor protein RarA; Reviewed	98.19
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.19
PRK04841	903	transcriptional regulator MalT; Provisional	98.17
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.17
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.14
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.09
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.08
PRK13341	725	recombination factor protein RarA/unknown domain f	98.07
PRK12402	337	replication factor C small subunit 2; Reviewed	98.04
CHL00181	287	cbbX CbbX; Provisional	98.04
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.01
KOG2028	554	consensus ATPase related to the helicase subunit o	97.98
PRK08116	268	hypothetical protein; Validated	97.97
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.95
PRK04195	482	replication factor C large subunit; Provisional	97.95
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.9
PRK08118	167	topology modulation protein; Reviewed	97.89
PHA02544	316	44 clamp loader, small subunit; Provisional	97.89
smart00382	148	AAA ATPases associated with a variety of cellular	97.86
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.86
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.85
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.82
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.81
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.76
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.75
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.72
PF00004	132	AAA: ATPase family associated with various cellula	97.71
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.71
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.7
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.7
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.67
PRK09087	226	hypothetical protein; Validated	97.65
PLN03025	319	replication factor C subunit; Provisional	97.64
PRK08727	233	hypothetical protein; Validated	97.62
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.6
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.59
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.58
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.56
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.56
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.55
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.55
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.53
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.52
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.5
PRK08084	235	DNA replication initiation factor; Provisional	97.49
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.49
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.46
PRK12377	248	putative replication protein; Provisional	97.45
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.45
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.45
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.44
PRK08181	269	transposase; Validated	97.43
PRK10536	262	hypothetical protein; Provisional	97.43
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.43
PRK12608	380	transcription termination factor Rho; Provisional	97.41
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.4
PRK07952	244	DNA replication protein DnaC; Validated	97.4
PRK07261	171	topology modulation protein; Provisional	97.39
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.39
PRK05642	234	DNA replication initiation factor; Validated	97.39
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.39
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.36
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.35
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.35
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.35
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.34
PRK06835	329	DNA replication protein DnaC; Validated	97.33
CHL00095	821	clpC Clp protease ATP binding subunit	97.33
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.31
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.3
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.29
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.29
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.29
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.27
PHA00729	226	NTP-binding motif containing protein	97.27
PRK09183	259	transposase/IS protein; Provisional	97.26
PRK10865	857	protein disaggregation chaperone; Provisional	97.25
PRK06526	254	transposase; Provisional	97.25
PRK06921	266	hypothetical protein; Provisional	97.25
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.23
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.23
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.22
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.22
PRK06620	214	hypothetical protein; Validated	97.21
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.21
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.21
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.2
PRK05541	176	adenylylsulfate kinase; Provisional	97.19
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.18
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.18
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.17
PRK10865	857	protein disaggregation chaperone; Provisional	97.17
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.16
PRK12422	445	chromosomal replication initiation protein; Provis	97.15
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.15
PRK08939	306	primosomal protein DnaI; Reviewed	97.15
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.14
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.14
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.13
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.12
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.11
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.1
CHL00095	821	clpC Clp protease ATP binding subunit	97.1
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.08
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.06
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.06
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.05
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.04
PRK13695	174	putative NTPase; Provisional	97.03
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	97.02
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.02
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.02
PRK06696	223	uridine kinase; Validated	97.01
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.98
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.98
CHL00176	638	ftsH cell division protein; Validated	96.98
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.98
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.98
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.97
PRK07667	193	uridine kinase; Provisional	96.94
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.94
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.94
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.94
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.93
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.91
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.9
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.86
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.84
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.83
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.82
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.82
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.82
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.81
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.8
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.79
PRK15455	644	PrkA family serine protein kinase; Provisional	96.78
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.78
PTZ00301	210	uridine kinase; Provisional	96.7
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.7
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.7
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.7
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.69
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.69
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.68
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.67
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.66
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.66
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.66
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.65
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.65
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.65
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.63
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.6
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.6
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.6
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.6
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.57
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.56
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.56
COG3899	849	Predicted ATPase [General function prediction only	96.55
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.55
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.55
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.54
PRK08233	182	hypothetical protein; Provisional	96.54
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.53
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.53
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.53
PRK04296	190	thymidine kinase; Provisional	96.53
PRK05480	209	uridine/cytidine kinase; Provisional	96.52
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	96.51
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.49
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.48
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.47
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.45
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.45
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.45
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.43
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.41
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.39
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.39
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.37
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.35
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.34
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.33
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	96.33
PRK13531	498	regulatory ATPase RavA; Provisional	96.33
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.31
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.3
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.28
TIGR00959	428	ffh signal recognition particle protein. This mode	96.27
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.27
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.26
PRK06547	172	hypothetical protein; Provisional	96.25
cd03246	173	ABCC_Protease_Secretion This family represents the	96.23
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.23
PRK06762	166	hypothetical protein; Provisional	96.21
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.21
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.2
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	96.2
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.19
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.19
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.18
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.16
PRK03839	180	putative kinase; Provisional	96.16
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.15
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.14
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.14
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.12
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.12
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	96.12
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.11
PRK10867	433	signal recognition particle protein; Provisional	96.11
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.09
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.09
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.09
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.08
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.08
PRK01184	184	hypothetical protein; Provisional	96.07
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.06
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.05
PRK04040	188	adenylate kinase; Provisional	96.03
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	96.01
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.01
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.0
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.0
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	96.0
PRK08149	428	ATP synthase SpaL; Validated	95.99
COG2884	223	FtsE Predicted ATPase involved in cell division [C	95.97
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.96
PRK14738	206	gmk guanylate kinase; Provisional	95.95
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.95
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.95
PRK00131	175	aroK shikimate kinase; Reviewed	95.94
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.93
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.93
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.93
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.93
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.92
PRK09354	349	recA recombinase A; Provisional	95.91
PRK00625	173	shikimate kinase; Provisional	95.91
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	95.91
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.9
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.9
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.9
PTZ00185	574	ATPase alpha subunit; Provisional	95.89
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.88
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	95.88
CHL00195	489	ycf46 Ycf46; Provisional	95.87
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.81
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.8
PRK00889	175	adenylylsulfate kinase; Provisional	95.8
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.79
PRK14974	336	cell division protein FtsY; Provisional	95.78
PRK06936	439	type III secretion system ATPase; Provisional	95.78
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.77
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	95.77
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.77
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.77
PTZ00035	337	Rad51 protein; Provisional	95.76
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.75
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.74
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.73
PRK12678	672	transcription termination factor Rho; Provisional	95.72
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.71
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.71
PF07726	131	AAA_3: ATPase family associated with various cellu	95.7
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.67
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.67
PLN02318	656	phosphoribulokinase/uridine kinase	95.67
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.66
PRK13947	171	shikimate kinase; Provisional	95.66
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	95.65
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.65
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.64
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	95.64
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	95.64
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.64
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.63
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.63
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.62
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	95.62
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.62
PRK05439	311	pantothenate kinase; Provisional	95.62
PRK06217	183	hypothetical protein; Validated	95.61
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.6
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.6
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.59
PRK13949	169	shikimate kinase; Provisional	95.58
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.57
COG3903	414	Predicted ATPase [General function prediction only	95.57
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.56
PRK03846	198	adenylylsulfate kinase; Provisional	95.54
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.53
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.53
PRK00300	205	gmk guanylate kinase; Provisional	95.52
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.51
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.47
PTZ00088	229	adenylate kinase 1; Provisional	95.46
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.45
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.45
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.43
PRK05922	434	type III secretion system ATPase; Validated	95.42
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.41
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.41
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.38
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	95.38
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	95.37
PRK14530	215	adenylate kinase; Provisional	95.37
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.36
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.36
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.35
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.35
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.34
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.34
PRK09099	441	type III secretion system ATPase; Provisional	95.34
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.33
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.31
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.31
COG1084	346	Predicted GTPase [General function prediction only	95.29
KOG1969	877	consensus DNA replication checkpoint protein CHL12	95.29
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	95.28
PRK00279	215	adk adenylate kinase; Reviewed	95.26
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.26
PRK13975	196	thymidylate kinase; Provisional	95.25
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.25
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.22
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.22
PRK05057	172	aroK shikimate kinase I; Reviewed	95.21
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	95.2
PRK14737	186	gmk guanylate kinase; Provisional	95.2
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.17
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.17
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.17
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	95.16
PRK08058	329	DNA polymerase III subunit delta'; Validated	95.15
PRK07399	314	DNA polymerase III subunit delta'; Validated	95.15
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.15
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	95.14
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.11
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	95.11
CHL00059	485	atpA ATP synthase CF1 alpha subunit	95.11
PRK13946	184	shikimate kinase; Provisional	95.07
PRK13948	182	shikimate kinase; Provisional	95.05
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.02
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.01
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.01
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.0
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	95.0
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.0
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.0
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	94.99
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	94.99
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	94.98
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	94.95
PF00154	322	RecA: recA bacterial DNA recombination protein; In	94.95
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	94.94
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	94.94
PRK12339	197	2-phosphoglycerate kinase; Provisional	94.92
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	94.92
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	94.91
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.9
cd03116	159	MobB Molybdenum is an essential trace element in t	94.9
PRK09435	332	membrane ATPase/protein kinase; Provisional	94.89
PRK14527	191	adenylate kinase; Provisional	94.88
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	94.88
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	94.87
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	94.86
PRK04182	180	cytidylate kinase; Provisional	94.86
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	94.84
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	94.84
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	94.84
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	94.83
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	94.81
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	94.8
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	94.8
PLN02200	234	adenylate kinase family protein	94.79
PHA02774	613	E1; Provisional	94.79
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.79
PRK15115	444	response regulator GlrR; Provisional	94.78
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	94.78
PRK06761	282	hypothetical protein; Provisional	94.78
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	94.76
COG1100	219	GTPase SAR1 and related small G proteins [General	94.76
PLN02924	220	thymidylate kinase	94.74
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.74
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	94.74
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	94.73
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	94.72
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	94.72
PRK06820	440	type III secretion system ATPase; Validated	94.72
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	94.7
PRK05707	328	DNA polymerase III subunit delta'; Validated	94.68
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	94.68
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	94.68
PRK08356	195	hypothetical protein; Provisional	94.68
PRK13765	637	ATP-dependent protease Lon; Provisional	94.67
PLN02348	395	phosphoribulokinase	94.67
PRK09825	176	idnK D-gluconate kinase; Provisional	94.66
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	94.65
PRK03731	171	aroL shikimate kinase II; Reviewed	94.61
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	94.6
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.58
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	94.58
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	94.58
TIGR01287	275	nifH nitrogenase iron protein. This model describe	94.58
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	94.57
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	94.57
PRK13230	279	nitrogenase reductase-like protein; Reviewed	94.56
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	94.53
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	94.52
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.52
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	94.51
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	94.5
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	94.49
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	94.47
COG0714	329	MoxR-like ATPases [General function prediction onl	94.46
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	94.46
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	94.45
PLN02796	347	D-glycerate 3-kinase	94.43
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	94.43
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	94.42
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	94.42
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	94.42
PRK13232	273	nifH nitrogenase reductase; Reviewed	94.41
cd02040	270	NifH NifH gene encodes component II (iron protein)	94.41
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	94.41
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	94.41
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	94.4
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	94.4
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.39
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	94.39
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	94.38
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	94.38
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	94.38
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	94.37
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	94.37
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	94.35
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	94.35
PF14516	331	AAA_35: AAA-like domain	94.35
PRK09519	790	recA DNA recombination protein RecA; Reviewed	94.35
cd04176	163	Rap2 Rap2 subgroup. The Rap2 subgroup is part of t	94.35
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	94.35
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	94.34
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.34
PRK14532	188	adenylate kinase; Provisional	94.32
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.32
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	94.31
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	94.3
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	94.29
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	94.29
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	94.28
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	94.28
TIGR01663	526	PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	94.27
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	94.26
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	94.26
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	94.24
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	94.23
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	94.23
cd02117	212	NifH_like This family contains the NifH (iron prot	94.23
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	94.22
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	94.19
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	94.18
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	94.18
cd03269	210	ABC_putative_ATPase This subfamily is involved in	94.17
PRK08099	399	bifunctional DNA-binding transcriptional repressor	94.17
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	94.16
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	94.16
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	94.16
PRK14490	369	putative bifunctional molybdopterin-guanine dinucl	94.16
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	94.16
PF11868	192	DUF3388: Protein of unknown function (DUF3388); In	94.14
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	94.13
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	94.13
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	94.13
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	94.12
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	94.12
PRK00698	205	tmk thymidylate kinase; Validated	94.11
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	94.1

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=3e-41  Score=344.20  Aligned_cols=313  Identities=19%  Similarity=0.209  Sum_probs=260.1

Q ss_pred             CcchHHHHHHHHHHHHhhhhhccccccchhHhhhHHhHHHhhhccccchHHHHHHHHHHhcccccCCchHHHHHHHHHHH
Q 038944            1 MDISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHREIKNPDLTTVMDEINCF   80 (334)
Q Consensus         1 m~~~~~~~~~kl~~~l~~~e~~l~~~~~~~i~~L~~~l~~l~~~~~~~~~~~~~~~l~~a~~~~~~~~~v~~Wl~~lr~~   80 (334)
                      |++.++..++|+.+++ .+++..+.+.++.+..|+++|.            .++.++++++.++.....+..|...++++
T Consensus         1 ~~~~~s~~~~~~~~~l-~~~~~~~~~~~~~i~~Lk~~L~------------~l~~~l~d~~a~~~~~~~~~~~~e~~~~~   67 (889)
T KOG4658|consen    1 MGACVSFGVEKLDQLL-NRESECLDGKDNYILELKENLK------------ALQSALEDLDAKRDDLERRVNWEEDVGDL   67 (889)
T ss_pred             CCeEEEEehhhHHHHH-HHHHHHHhchHHHHHHHHHHHH------------HHHHHHHHHHhhcchHHHHHHHHHHHHHH
Confidence            5667777888999977 6888888899999999999999            99999999999988889999999999999


Q ss_pred             HHhHHHHHHHHHhhhhcccccCC-----cccchh---hhHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccCCC----CC
Q 038944           81 TYESEKVIDTFINSISEQKSQSS-----CSEDIF---DALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAE----AG  148 (334)
Q Consensus        81 ayd~ED~lD~~~~~~~~~~~~~~-----~~~~~~---~~~~~~~~~i~~i~~~l~~i~~~~~~~~~~~~~~~~~----~~  148 (334)
                      +|++||.++.|..........+.     ...+..   .+.+..+..+..+.+++..+.+..+.+  +....-..    ..
T Consensus        68 ~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l--~~~~~~~~~~~~~~  145 (889)
T KOG4658|consen   68 VYLAEDIIWLFLVEEIERKANDLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESL--GSKGVFEVVGESLD  145 (889)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHh--ccccceeccccccc
Confidence            99999999999887755432210     011111   334455777888888888888888888  64442211    11


Q ss_pred             cC---C-C--CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCC-CCCceeeEEEEEcCCCC
Q 038944          149 IS---S-S--SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSY-VKHYFDCHAWVPGTYPY  221 (334)
Q Consensus       149 ~~---~-r--~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~-~~~~F~~~~wv~vs~~~  221 (334)
                      ..   + +  .+... ||.+..++++.+.|..++.  .+++|+||||+||||||+.++|+.. ++.+|+..+||+||++|
T Consensus       146 ~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f  222 (889)
T KOG4658|consen  146 PREKVETRPIQSESD-VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEF  222 (889)
T ss_pred             chhhcccCCCCcccc-ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccc
Confidence            11   1 1  33333 9999999999999999875  8999999999999999999999987 99999999999999999


Q ss_pred             CHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          222 DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       222 ~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      +...++++|+..++............  +++..|.+.|++|||||||||||+..+|+.|..++|...+||||++|||++.
T Consensus       223 ~~~~iq~~Il~~l~~~~~~~~~~~~~--~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~  300 (889)
T KOG4658|consen  223 TTRKIQQTILERLGLLDEEWEDKEED--ELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEE  300 (889)
T ss_pred             cHHhHHHHHHHHhccCCcccchhhHH--HHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHh
Confidence            99999999999998855432222334  8999999999999999999999999999999999999999999999999999


Q ss_pred             HHhh-ccccCcccccccCC-----------------CChhHHHHHHHhcc
Q 038944          302 MFTF-LLETLFSLLICVSR-----------------TPRDIQQAVISVVD  333 (334)
Q Consensus       302 va~~-~~~~~~~~l~~l~~-----------------~~~~l~~i~~~Iv~  333 (334)
                      ||.. |++...+++.||+.                 .+|.+.++|++||+
T Consensus       301 V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~  350 (889)
T KOG4658|consen  301 VCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAE  350 (889)
T ss_pred             hhhccccCCccccccccCccccHHHHHHhhccccccccccHHHHHHHHHH
Confidence            9999 88888899999992                 55669999999986

>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=99.95  E-value=2.9e-28  Score=222.56  Aligned_cols=156  Identities=26%  Similarity=0.330  Sum_probs=126.8

Q ss_pred             chhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc
Q 038944          161 LDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL  240 (334)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~  240 (334)
                      ||.++++|.++|.....+.++|+|+||||+||||||..+|++..++.+|+.++|+.+++.++...++..|+.+++.....
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            68899999999999768899999999999999999999999766889999999999999999999999999999987542


Q ss_pred             c-ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhccc-cCcccccccC
Q 038944          241 S-EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLE-TLFSLLICVS  318 (334)
Q Consensus       241 ~-~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~-~~~~~l~~l~  318 (334)
                      . ...+..  .+...+++.|.+++|||||||||+...|+.+...++....||+||||||+..++..++. ...+.+.+|+
T Consensus        81 ~~~~~~~~--~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~  158 (287)
T PF00931_consen   81 ISDPKDIE--ELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLS  158 (287)
T ss_dssp             SSCCSSHH--HHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--
T ss_pred             cccccccc--cccccchhhhccccceeeeeeecccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            1 233445  89999999999999999999999999999999999887789999999999999988775 5677888877

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=99.88  E-value=4.7e-22  Score=212.02  Aligned_cols=171  Identities=16%  Similarity=0.197  Sum_probs=132.1

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEc---CCC----------
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPG---TYP----------  220 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~v---s~~----------  220 (334)
                      +..++||++..++++..+|..+....++++||||||+||||||+.+|+  ++..+|+..+|+..   +..          
T Consensus       182 ~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~  259 (1153)
T PLN03210        182 DFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSMEIYSSANPD  259 (1153)
T ss_pred             ccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccchhhccccccc
Confidence            345699999999999999977667899999999999999999999999  77788988877642   111          


Q ss_pred             -CC-HHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecC
Q 038944          221 -YD-ADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLT  298 (334)
Q Consensus       221 -~~-~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr  298 (334)
                       ++ ...++..++.++......    ...  . ...+++.|++||+||||||||+...|+.+.......+.||+||||||
T Consensus       260 ~~~~~~~l~~~~l~~il~~~~~----~~~--~-~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTr  332 (1153)
T PLN03210        260 DYNMKLHLQRAFLSEILDKKDI----KIY--H-LGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITK  332 (1153)
T ss_pred             ccchhHHHHHHHHHHHhCCCCc----ccC--C-HHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeC
Confidence             11 123455555555433211    111  1 14567889999999999999999999999887666678999999999


Q ss_pred             ChHHHhhccccCcccccccCC----------------CChhHHHHHHHhcc
Q 038944          299 EIKMFTFLLETLFSLLICVSR----------------TPRDIQQAVISVVD  333 (334)
Q Consensus       299 ~~~va~~~~~~~~~~l~~l~~----------------~~~~l~~i~~~Iv~  333 (334)
                      +.+++..++....|.+..++.                .++++.+++++||+
T Consensus       333 d~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~  383 (1153)
T PLN03210        333 DKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVAL  383 (1153)
T ss_pred             cHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHH
Confidence            999999887777787777762                45578999999885

syringae 6; Provisional

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.03  E-value=3e-09  Score=101.57  Aligned_cols=150  Identities=12%  Similarity=0.078  Sum_probs=98.3

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC--CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG--PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~i  230 (334)
                      ..+..++||+++.++|...|...  ......+.|+|++|+|||++++.++++.......-..++++.....+...++..|
T Consensus        27 ~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i  106 (394)
T PRK00411         27 YVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEI  106 (394)
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHH
Confidence            45667999999999999998542  2334557899999999999999999853222212345667666667888999999


Q ss_pred             HHHhCCCCCccccchhhHHHHHHHHHHHcC--CCeEEEEEeCCCCh------hHHHHHHhhCCCCCCCeE--EEEecCCh
Q 038944          231 IKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLNVIDDVWNI------EVCDIIREILPDNQNRSR--VLITLTEI  300 (334)
Q Consensus       231 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~--~kr~LlVlDdvw~~------~~w~~l~~~l~~~~~gsr--IivTTr~~  300 (334)
                      +.++..........+..  .+...+.+.+.  ++..+||||+++..      +.+..+...+.. ..+++  +|.++...
T Consensus       107 ~~~l~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~-~~~~~v~vI~i~~~~  183 (394)
T PRK00411        107 ARQLFGHPPPSSGLSFD--ELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEE-YPGARIGVIGISSDL  183 (394)
T ss_pred             HHHhcCCCCCCCCCCHH--HHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhc-cCCCeEEEEEEECCc
Confidence            99997632211122223  66677777764  56689999999763      234444333322 22334  56666665


Q ss_pred             HHHhh
Q 038944          301 KMFTF  305 (334)
Q Consensus       301 ~va~~  305 (334)
                      ++...
T Consensus       184 ~~~~~  188 (394)
T PRK00411        184 TFLYI  188 (394)
T ss_pred             chhhh
Confidence            54443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.91  E-value=2.3e-08  Score=94.51  Aligned_cols=119  Identities=17%  Similarity=0.039  Sum_probs=82.4

Q ss_pred             CCCCCeeechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHccCCC-CCce---eeEEEEEcCCCCCHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYV-KHYF---DCHAWVPGTYPYDADQM  226 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F---~~~~wv~vs~~~~~~~i  226 (334)
                      ..+..++||+++.++|..+|..  .......+.|+|++|+|||++++.++++..- ....   -..+|+......+...+
T Consensus        12 ~~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~   91 (365)
T TIGR02928        12 YVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQV   91 (365)
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHH
Confidence            3455799999999999999874  2233457899999999999999999974210 0010   23567777777778899


Q ss_pred             HHHHHHHhC---CCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCCh
Q 038944          227 LDIVIKFLM---PSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNI  274 (334)
Q Consensus       227 l~~il~~~~---~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~  274 (334)
                      +..|++++.   ...+. ...+..  ++...+.+.+  .++.++||||+++.-
T Consensus        92 ~~~i~~~l~~~~~~~~~-~~~~~~--~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        92 LVELANQLRGSGEEVPT-TGLSTS--EVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             HHHHHHHHhhcCCCCCC-CCCCHH--HHHHHHHHHHHhcCCeEEEEECchhhh
Confidence            999999994   22111 112222  5555666665  366889999999765

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

>PF05729 NACHT: NACHT domain

Probab=98.84  E-value=2e-08  Score=83.40  Aligned_cols=139  Identities=19%  Similarity=0.130  Sum_probs=78.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCc----eeeEEEEEcCCCCCHH---HHHHHHHHHhCCCCCccccchhhHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHY----FDCHAWVPGTYPYDAD---QMLDIVIKFLMPSSRLSEIMDKNYEMKK  252 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~---~il~~il~~~~~~~~~~~~~~~~~~~l~  252 (334)
                      +++.|+|.+|+||||+++.++..-.....    |...+|.+.....+..   .+...|..+......          ...
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~----------~~~   70 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIA----------PIE   70 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchh----------hhH
Confidence            47899999999999999999874322221    4566677665433222   333333333332211          111


Q ss_pred             HHHHHH-cCCCeEEEEEeCCCChh---------HHHHHH-hhCCC-CCCCeEEEEecCChHHHh---hccccCccccccc
Q 038944          253 IILHEY-LMTKRYLNVIDDVWNIE---------VCDIIR-EILPD-NQNRSRVLITLTEIKMFT---FLLETLFSLLICV  317 (334)
Q Consensus       253 ~~l~~~-L~~kr~LlVlDdvw~~~---------~w~~l~-~~l~~-~~~gsrIivTTr~~~va~---~~~~~~~~~l~~l  317 (334)
                      ..+... -+.++++||||++....         .+..+. ..++. ...++++|||||......   .......+.+.++
T Consensus        71 ~~~~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~  150 (166)
T PF05729_consen   71 ELLQELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPF  150 (166)
T ss_pred             HHHHHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCC
Confidence            112222 26789999999986431         133333 33333 356899999999887733   3333344566555


Q ss_pred             CCCChhHHHHHHH
Q 038944          318 SRTPRDIQQAVIS  330 (334)
Q Consensus       318 ~~~~~~l~~i~~~  330 (334)
                      ++  ++.+.+.++
T Consensus       151 ~~--~~~~~~~~~  161 (166)
T PF05729_consen  151 SE--EDIKQYLRK  161 (166)
T ss_pred             CH--HHHHHHHHH
Confidence            53  445554443

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

Probab=98.81  E-value=1.1e-08  Score=91.05  Aligned_cols=89  Identities=11%  Similarity=-0.041  Sum_probs=62.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC--CCHHHHHHHH-----HHHhCCCCCccccchhhHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP--YDADQMLDIV-----IKFLMPSSRLSEIMDKNYEMKK  252 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~il~~i-----l~~~~~~~~~~~~~~~~~~~l~  252 (334)
                      ..+.|+|++|+|||||++.+|++.... +|++.+|++++++  +++.++++.+     +.++.....  ...... ....
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~--~~~~~~-~~~~   92 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPE--RHVQVA-EMVL   92 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHH--HHHHHH-HHHH
Confidence            478999999999999999999975544 8999999998876  8999999999     333332110  001000 0222


Q ss_pred             HHHHHH-cCCCeEEEEEeCCC
Q 038944          253 IILHEY-LMTKRYLNVIDDVW  272 (334)
Q Consensus       253 ~~l~~~-L~~kr~LlVlDdvw  272 (334)
                      .....+ -.|++.++++|++-
T Consensus        93 ~~a~~~~~~G~~vll~iDei~  113 (249)
T cd01128          93 EKAKRLVEHGKDVVILLDSIT  113 (249)
T ss_pred             HHHHHHHHCCCCEEEEEECHH
Confidence            333322 35899999999995

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.

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

Probab=98.71  E-value=4.3e-08  Score=78.43  Aligned_cols=113  Identities=15%  Similarity=0.138  Sum_probs=77.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCc-----eeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHY-----FDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKI  253 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~-----F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~  253 (334)
                      -+++.|+|.+|+|||++++.+.+.  ....     -...+|+..+...+...+...|+.+++.....  ..+..  .+..
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~--~l~~   77 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKS--RQTSD--ELRS   77 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS--TS-HH--HHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccc--cCCHH--HHHH
Confidence            468999999999999999999873  2111     23456999988889999999999999987652  12333  6667


Q ss_pred             HHHHHcCC-CeEEEEEeCCCC---hhHHHHHHhhCCCCCCCeEEEEecCC
Q 038944          254 ILHEYLMT-KRYLNVIDDVWN---IEVCDIIREILPDNQNRSRVLITLTE  299 (334)
Q Consensus       254 ~l~~~L~~-kr~LlVlDdvw~---~~~w~~l~~~l~~~~~gsrIivTTr~  299 (334)
                      .+.+.+.. +..+||+|++..   ...++.|.....  ..+.+||+..+.
T Consensus        78 ~~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   78 LLIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            77777744 446999999954   345666655543  556777776543

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

Probab=98.70  E-value=4.7e-07  Score=81.79  Aligned_cols=114  Identities=18%  Similarity=0.141  Sum_probs=69.8

Q ss_pred             HHHHHHHHhcC-CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcccc
Q 038944          165 MEELLDLLIEG-PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEI  243 (334)
Q Consensus       165 ~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~  243 (334)
                      ..++...|... ..+..++.|+|++|+|||||++.+++..... .+ ..+|+. +...+..+++..|+..++..... ..
T Consensus        28 ~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~-~~~~~~-~~~~~~~~~l~~i~~~lG~~~~~-~~  103 (269)
T TIGR03015        28 HKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQE-RV-VAAKLV-NTRVDAEDLLRMVAADFGLETEG-RD  103 (269)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCC-Ce-EEeeee-CCCCCHHHHHHHHHHHcCCCCCC-CC
Confidence            34444444321 2234588999999999999999999853322 22 223433 33567889999999988765432 11


Q ss_pred             chhhHHHHHHHHHHH-cCCCeEEEEEeCCCCh--hHHHHHHh
Q 038944          244 MDKNYEMKKIILHEY-LMTKRYLNVIDDVWNI--EVCDIIRE  282 (334)
Q Consensus       244 ~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw~~--~~w~~l~~  282 (334)
                      ....+..+...+... ..++++++|+||+|..  ..++.+..
T Consensus       104 ~~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~  145 (269)
T TIGR03015       104 KAALLRELEDFLIEQFAAGKRALLVVDEAQNLTPELLEELRM  145 (269)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCeEEEEECcccCCHHHHHHHHH
Confidence            111111333333333 3788899999999874  46666654

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.66  E-value=3.2e-08  Score=92.40  Aligned_cols=90  Identities=16%  Similarity=0.016  Sum_probs=60.8

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC--CHHHHHHHHHHHhCCCCCccccchhhH---HHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY--DADQMLDIVIKFLMPSSRLSEIMDKNY---EMKKIIL  255 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~il~~il~~~~~~~~~~~~~~~~~---~~l~~~l  255 (334)
                      -..|+|++|+|||||++.||++.... ||++++||.+++++  ++.+++++|+..+-..... .......   ......-
T Consensus       171 R~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d-~~~~~~~~~a~~~ie~A  248 (416)
T PRK09376        171 RGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFD-EPAERHVQVAEMVIEKA  248 (416)
T ss_pred             eEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCC-CCHHHHHHHHHHHHHHH
Confidence            57899999999999999999975544 89999999999998  8888888887322211111 0000000   0111111


Q ss_pred             HHH-cCCCeEEEEEeCCC
Q 038944          256 HEY-LMTKRYLNVIDDVW  272 (334)
Q Consensus       256 ~~~-L~~kr~LlVlDdvw  272 (334)
                      ..+ -.|+..||++|++-
T Consensus       249 e~~~e~G~dVlL~iDsIt  266 (416)
T PRK09376        249 KRLVEHGKDVVILLDSIT  266 (416)
T ss_pred             HHHHHcCCCEEEEEEChH
Confidence            122 37899999999994

>PF13173 AAA_14: AAA domain

Probab=98.64  E-value=6.8e-08  Score=77.39  Aligned_cols=103  Identities=11%  Similarity=0.103  Sum_probs=67.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      -+++.|.|+.|+|||||++.++.+..   .....++++.........                   ...  ++...+.+.
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~-------------------~~~--~~~~~~~~~   57 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRL-------------------ADP--DLLEYFLEL   57 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHH-------------------hhh--hhHHHHHHh
Confidence            36899999999999999999997432   223445554443221000                   000  122333333


Q ss_pred             cCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          259 LMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      ...+..+|+||++-....|......+-+.....+||+|+.+......
T Consensus        58 ~~~~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~  104 (128)
T PF13173_consen   58 IKPGKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSK  104 (128)
T ss_pred             hccCCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhh
Confidence            43467889999998888888888777665566899999998776643

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

Probab=98.61  E-value=7.6e-07  Score=71.69  Aligned_cols=122  Identities=14%  Similarity=0.129  Sum_probs=69.4

Q ss_pred             echhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCC
Q 038944          160 GLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR  239 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~  239 (334)
                      |++...+.+...+...  ....+.|+|.+|+|||||++.+++...  ..-...+++..+...........+...      
T Consensus         2 ~~~~~~~~i~~~~~~~--~~~~v~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~~~~~~~~~~~~~~~~~------   71 (151)
T cd00009           2 GQEEAIEALREALELP--PPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGHF------   71 (151)
T ss_pred             chHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHhh--cCCCCeEEEehhhhhhhhHHHHHhhhh------
Confidence            6777788888887664  345788999999999999999998432  111234555544433211111100000      


Q ss_pred             ccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--h---HHHHHHhhCCCC---CCCeEEEEecCChH
Q 038944          240 LSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI--E---VCDIIREILPDN---QNRSRVLITLTEIK  301 (334)
Q Consensus       240 ~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~---~w~~l~~~l~~~---~~gsrIivTTr~~~  301 (334)
                                ............+..++++||++..  .   .+..+...+...   ..+..||+||....
T Consensus        72 ----------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 ----------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             ----------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                      0011111223456789999999853  2   233333333221   35788888888654

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.

>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=98.50  E-value=4.5e-07  Score=79.51  Aligned_cols=43  Identities=26%  Similarity=0.416  Sum_probs=35.5

Q ss_pred             eeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          158 TVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++||+.+.+.|.+++..+.  ...+.|+|+.|+|||+|++.+.+.
T Consensus         1 F~gR~~el~~l~~~l~~~~--~~~~~l~G~rg~GKTsLl~~~~~~   43 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGP--SQHILLYGPRGSGKTSLLKEFINE   43 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhc--CcEEEEEcCCcCCHHHHHHHHHHH
Confidence            5899999999999998753  568899999999999999999984

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

>TIGR00767 rho transcription termination factor Rho

Probab=98.48  E-value=5e-07  Score=84.83  Aligned_cols=92  Identities=11%  Similarity=-0.067  Sum_probs=62.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC--CCHHHHHHHHHHHhCCCCCccccchhh--HHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP--YDADQMLDIVIKFLMPSSRLSEIMDKN--YEMKKIIL  255 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~il~~il~~~~~~~~~~~~~~~~--~~~l~~~l  255 (334)
                      ..++|+|.+|+|||||++.+++.... +||+..+||.++++  .++.++++.++..+-............  ...+.+..
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~~-nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~A  247 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAITR-NHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKA  247 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhcc-cCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHH
Confidence            47899999999999999999996433 37999999999866  799999999955443222210010100  01222222


Q ss_pred             HHH-cCCCeEEEEEeCCC
Q 038944          256 HEY-LMTKRYLNVIDDVW  272 (334)
Q Consensus       256 ~~~-L~~kr~LlVlDdvw  272 (334)
                      ..+ -.|++.+|++|++-
T Consensus       248 e~~~~~GkdVVLlIDEit  265 (415)
T TIGR00767       248 KRLVEHKKDVVILLDSIT  265 (415)
T ss_pred             HHHHHcCCCeEEEEEChh
Confidence            222 36899999999995

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

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

Probab=98.46  E-value=2.5e-07  Score=78.46  Aligned_cols=79  Identities=15%  Similarity=0.120  Sum_probs=41.4

Q ss_pred             CeeechhhHHHHHHHHhc-CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC---CCHHHHHHHHHH
Q 038944          157 DTVGLDDRMEELLDLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP---YDADQMLDIVIK  232 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~---~~~~~il~~il~  232 (334)
                      .++||+++.+++...|.. .....+++.|+|.+|+|||+|.+.++........+-+..+..-...   .....++++++.
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   80 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDSERNPYSPFRSALRQLID   80 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETTTS-HHHHHHHHHHHHS-
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEeccccchhhHHHHHHHHHHH
Confidence            378999999999999942 3345689999999999999999999874322222323333322211   112555555555


Q ss_pred             HhC
Q 038944          233 FLM  235 (334)
Q Consensus       233 ~~~  235 (334)
                      ++.
T Consensus        81 ~~~   83 (185)
T PF13191_consen   81 QLL   83 (185)
T ss_dssp             ---
T ss_pred             Hhh
Confidence            543

>PTZ00202 tuzin; Provisional

Probab=98.35  E-value=8.1e-06  Score=77.24  Aligned_cols=138  Identities=15%  Similarity=0.073  Sum_probs=85.2

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCC-CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGP-PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVI  231 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il  231 (334)
                      .+..+++||+.+...|...|.+.+ ....++.|.|++|+|||||++.+...  ..  |.  +++.-+.  +..++++.|+
T Consensus       259 a~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~--l~--~~--qL~vNpr--g~eElLr~LL  330 (550)
T PTZ00202        259 AVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRK--EG--MP--AVFVDVR--GTEDTLRSVV  330 (550)
T ss_pred             CCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhc--CC--ce--EEEECCC--CHHHHHHHHH
Confidence            567789999999999999997533 34569999999999999999999973  32  21  3333333  7799999999


Q ss_pred             HHhCCCCCccccchhhHHHHHHHHHHHc-C-CCeEEEEEeCCC--Ch-hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          232 KFLMPSSRLSEIMDKNYEMKKIILHEYL-M-TKRYLNVIDDVW--NI-EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~l~~~l~~~L-~-~kr~LlVlDdvw--~~-~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      .+++....  .....-++.+.+.+.+.- . |++-+||+-==.  +- -.+++. .+|.+...-|-|++---.+.
T Consensus       331 ~ALGV~p~--~~k~dLLrqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~-v~la~drr~ch~v~evples  402 (550)
T PTZ00202        331 KALGVPNV--EACGDLLDFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEV-VALACDRRLCHVVIEVPLES  402 (550)
T ss_pred             HHcCCCCc--ccHHHHHHHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHH-HHHHccchhheeeeeehHhh
Confidence            99997432  111111224444444432 3 677777764221  11 123322 23333334455666554444

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

Probab=98.34  E-value=2.8e-06  Score=80.01  Aligned_cols=114  Identities=13%  Similarity=0.067  Sum_probs=82.5

Q ss_pred             CCCeeechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-e-EEEEEcCCCCCHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-C-HAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~-~~wv~vs~~~~~~~il~~i  230 (334)
                      +..+.+|+.+.+++...|..  .+....-+.|+|.+|+|||+.++.|.+  ++.+... . .++|+.-...++.+++..|
T Consensus        16 P~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~~~~t~~~i~~~i   93 (366)
T COG1474          16 PEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVME--ELEESSANVEVVYINCLELRTPYQVLSKI   93 (366)
T ss_pred             cccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEeeeeCCCHHHHHHHH
Confidence            44489999999999988864  122222389999999999999999998  3333321 1 6777777788899999999


Q ss_pred             HHHhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCCh
Q 038944          231 IKFLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNI  274 (334)
Q Consensus       231 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~  274 (334)
                      +.+++....  ..+...  +....+.+.+  .++.+++|||++..-
T Consensus        94 ~~~~~~~p~--~g~~~~--~~~~~l~~~~~~~~~~~IvvLDEid~L  135 (366)
T COG1474          94 LNKLGKVPL--TGDSSL--EILKRLYDNLSKKGKTVIVILDEVDAL  135 (366)
T ss_pred             HHHcCCCCC--CCCchH--HHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence            999973222  123333  5666666666  568999999999653

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.31  E-value=8.2e-06  Score=82.88  Aligned_cols=118  Identities=10%  Similarity=0.015  Sum_probs=78.9

Q ss_pred             CCCCCeeechhhHHHHHHHHhc---CCCCceEEEEEccCCccHHHHHHHHHccCC--C-CCcee--eEEEEEcCCCCCHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE---GPPQLSVVVILDSIGLDKAAFAGEAYNSSY--V-KHYFD--CHAWVPGTYPYDAD  224 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~--~-~~~F~--~~~wv~vs~~~~~~  224 (334)
                      ..+..+.||+++.++|...|..   +...-.++.|+|++|+|||+.++.|.+...  . ...++  ..++|....-.+..
T Consensus       752 YVPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~  831 (1164)
T PTZ00112        752 VVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPN  831 (1164)
T ss_pred             cCCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHH
Confidence            3456789999999999998864   233446889999999999999999986321  0 11122  24566666666788


Q ss_pred             HHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcC---CCeEEEEEeCCCC
Q 038944          225 QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM---TKRYLNVIDDVWN  273 (334)
Q Consensus       225 ~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~---~kr~LlVlDdvw~  273 (334)
                      .++..|.+++....+. ......  .....+...+.   +...+||||++..
T Consensus       832 sIYqvI~qqL~g~~P~-~GlsS~--evLerLF~~L~k~~r~v~IIILDEID~  880 (1164)
T PTZ00112        832 AAYQVLYKQLFNKKPP-NALNSF--KILDRLFNQNKKDNRNVSILIIDEIDY  880 (1164)
T ss_pred             HHHHHHHHHHcCCCCC-ccccHH--HHHHHHHhhhhcccccceEEEeehHhh
Confidence            9999999999654432 122222  44445555442   2245899999963

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.29  E-value=1.6e-05  Score=73.65  Aligned_cols=125  Identities=12%  Similarity=0.197  Sum_probs=82.3

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc----CCCCCceeeEEEEEc-CCCCCHHHHHHHH
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS----SYVKHYFDCHAWVPG-TYPYDADQMLDIV  230 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~----~~~~~~F~~~~wv~v-s~~~~~~~il~~i  230 (334)
                      .+++|.+..++.+.+++..+. -....-++|+.|+||||+|+.++..    .....|+|...|... +....+.. .+++
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~-~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-ir~~   81 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR-FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-IRNI   81 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-HHHH
Confidence            457899999999999987653 3356788999999999999988862    123456777666542 23333333 2223


Q ss_pred             HHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEe-CCCChhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          231 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVID-DVWNIEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       231 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlD-dvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      .+.+....                   +..++|++||-| |.++...|+.+...+..-..++.+|++|.+.+
T Consensus        82 ~~~~~~~p-------------------~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~  134 (313)
T PRK05564         82 IEEVNKKP-------------------YEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLE  134 (313)
T ss_pred             HHHHhcCc-------------------ccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChH
Confidence            33222110                   113455555544 55677899999999987777899998887654

>PRK06893 DNA replication initiation factor; Validated

Probab=98.27  E-value=1.3e-06  Score=77.30  Aligned_cols=109  Identities=13%  Similarity=0.088  Sum_probs=61.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      .+.+.++|.+|+|||+|++.+.+.  .........|++++...                            .....+.+.
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~~~~~----------------------------~~~~~~~~~   88 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPLSKSQ----------------------------YFSPAVLEN   88 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeHHHhh----------------------------hhhHHHHhh
Confidence            357899999999999999999984  22222344566543100                            000011112


Q ss_pred             cCCCeEEEEEeCCCCh---hHHHH-HHhhCCC-CCCCeEEEEecCC----------hHHHhhccccCcccccccC
Q 038944          259 LMTKRYLNVIDDVWNI---EVCDI-IREILPD-NQNRSRVLITLTE----------IKMFTFLLETLFSLLICVS  318 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~---~~w~~-l~~~l~~-~~~gsrIivTTr~----------~~va~~~~~~~~~~l~~l~  318 (334)
                      +. +.-+|+|||+|..   ..|+. +...+.. ...|+.+||+|.+          .+++..+.....+.+..++
T Consensus        89 ~~-~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd  162 (229)
T PRK06893         89 LE-QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLT  162 (229)
T ss_pred             cc-cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCC
Confidence            22 2348999999963   46653 3333332 1246666555443          4666666655555565555

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.25  E-value=8.6e-06  Score=81.96  Aligned_cols=141  Identities=15%  Similarity=0.067  Sum_probs=88.1

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee---eEEEEEcCC---CCCHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD---CHAWVPGTY---PYDADQMLD  228 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~---~~~wv~vs~---~~~~~~il~  228 (334)
                      -++++|.+..+..+...+....  ...+.|+|++|+||||||+.+++.......+.   ...|+.+..   ..+...+..
T Consensus       153 ~~~iiGqs~~~~~l~~~ia~~~--~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~  230 (615)
T TIGR02903       153 FSEIVGQERAIKALLAKVASPF--PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTN  230 (615)
T ss_pred             HHhceeCcHHHHHHHHHHhcCC--CCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhH
Confidence            3468999999999888775433  45799999999999999999987543333331   234555542   123333222


Q ss_pred             HH---------------HHHhCCCCC---------c-c------ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--h
Q 038944          229 IV---------------IKFLMPSSR---------L-S------EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI--E  275 (334)
Q Consensus       229 ~i---------------l~~~~~~~~---------~-~------~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~  275 (334)
                      .+               +...+....         . .      +..+ .  ..+..|.+.+.+++++++.|+.|..  .
T Consensus       231 ~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld-~--~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~  307 (615)
T TIGR02903       231 PLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELD-P--LLQNKLLKVLEDKRVEFSSSYYDPDDPN  307 (615)
T ss_pred             HhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCC-H--HHHHHHHHHHhhCeEEeecceeccCCcc
Confidence            11               111111000         0 0      1111 2  4678899999999999998877764  4


Q ss_pred             HHHHHHhhCCCCCCCeEEEE--ecCCh
Q 038944          276 VCDIIREILPDNQNRSRVLI--TLTEI  300 (334)
Q Consensus       276 ~w~~l~~~l~~~~~gsrIiv--TTr~~  300 (334)
                      .|+.+...+....+...|++  ||++.
T Consensus       308 ~~~~ik~~~~~~~~~~~VLI~aTt~~~  334 (615)
T TIGR02903       308 VPKYIKKLFEEGAPADFVLIGATTRDP  334 (615)
T ss_pred             cchhhhhhcccCccceEEEEEeccccc
Confidence            78888887777665555555  56644

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.19  E-value=9.5e-06  Score=78.07  Aligned_cols=112  Identities=17%  Similarity=0.150  Sum_probs=64.7

Q ss_pred             CCeeechhhHHH---HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          156 RDTVGLDDRMEE---LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       156 ~~~vGr~~~~~~---l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      .+++|.+..+..   +..++..+.  ...+.++|++|+||||||+.+.+.  ....|     +.++....-..-++    
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~~--~~~ilL~GppGtGKTtLA~~ia~~--~~~~~-----~~l~a~~~~~~~ir----   78 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAGR--LSSMILWGPPGTGKTTLARIIAGA--TDAPF-----EALSAVTSGVKDLR----   78 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcCC--CceEEEECCCCCCHHHHHHHHHHH--hCCCE-----EEEecccccHHHHH----
Confidence            357787766554   666665543  456788999999999999999983  33333     22222111111111    


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEE--ecCCh
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLI--TLTEI  300 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIiv--TTr~~  300 (334)
                                       .+....... ..+++.+|+||+++.-  ...+.+...+..   |+.+++  ||.+.
T Consensus        79 -----------------~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~---~~iilI~att~n~  131 (413)
T PRK13342         79 -----------------EVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED---GTITLIGATTENP  131 (413)
T ss_pred             -----------------HHHHHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhc---CcEEEEEeCCCCh
Confidence                             222222211 2467889999999854  456666665533   444444  34443

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

Probab=98.19  E-value=3.5e-05  Score=71.20  Aligned_cols=115  Identities=11%  Similarity=0.185  Sum_probs=82.3

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCc-eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQL-SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~-~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      ++.+.+|+.+...+..++..++... ..+-|+|..|.|||.+.+.+++....     ..+|+++-..|+..-++..|+.+
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~   79 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNK   79 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHH
Confidence            4567899999999999998876533 45589999999999999999995522     35899999999999999999999


Q ss_pred             hCCCCCccccchh---hHHHHHHHHHHH--c--CCCeEEEEEeCCCCh
Q 038944          234 LMPSSRLSEIMDK---NYEMKKIILHEY--L--MTKRYLNVIDDVWNI  274 (334)
Q Consensus       234 ~~~~~~~~~~~~~---~~~~l~~~l~~~--L--~~kr~LlVlDdvw~~  274 (334)
                      .+.....+.....   .+......+..+  .  .++.++||||++..-
T Consensus        80 ~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~l  127 (438)
T KOG2543|consen   80 SQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADAL  127 (438)
T ss_pred             hccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhh
Confidence            9632221111111   111333333331  1  256899999999654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.17  E-value=1.7e-05  Score=83.73  Aligned_cols=126  Identities=15%  Similarity=0.150  Sum_probs=78.7

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCCcc---
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSRLS---  241 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~~~---  241 (334)
                      .+|.+.|... ...+++.|.|++|.||||++......      +...+|+++.. +-++..++..++..+.......   
T Consensus        20 ~rl~~~l~~~-~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~   92 (903)
T PRK04841         20 ERLLAKLSGA-NNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAALQQATNGHCSK   92 (903)
T ss_pred             hHHHHHHhcc-cCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHHHHHhcCcccch
Confidence            3566666432 45789999999999999999988752      23689999964 4567777788877774221110   


Q ss_pred             --------ccchhhHHHHHHHHHHHcC--CCeEEEEEeCCCCh--hH-HHHHHhhCCCCCCCeEEEEecCCh
Q 038944          242 --------EIMDKNYEMKKIILHEYLM--TKRYLNVIDDVWNI--EV-CDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       242 --------~~~~~~~~~l~~~l~~~L~--~kr~LlVlDdvw~~--~~-w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                              ...+..  .+...+...+.  +.+++|||||+-..  .. .+.+...++....+.++|||||..
T Consensus        93 ~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~  162 (903)
T PRK04841         93 SEALAQKRQYASLS--SLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNL  162 (903)
T ss_pred             hhhhhccCCcCCHH--HHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCC
Confidence                    001111  33333333332  67899999999542  22 233433333334567788999973

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.17  E-value=9.5e-06  Score=71.24  Aligned_cols=40  Identities=13%  Similarity=0.086  Sum_probs=30.1

Q ss_pred             chhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          161 LDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....++.+..++..  .....+.++|.+|+|||+||+.+++.
T Consensus        22 ~~~~~~~l~~~~~~--~~~~~lll~G~~G~GKT~la~~~~~~   61 (226)
T TIGR03420        22 NAELLAALRQLAAG--KGDRFLYLWGESGSGKSHLLQAACAA   61 (226)
T ss_pred             cHHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            34456666666543  23568899999999999999999984

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.

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

Probab=98.14  E-value=2.9e-05  Score=74.28  Aligned_cols=119  Identities=13%  Similarity=0.062  Sum_probs=77.7

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      ..++++.+...+.+...|...    +.+.++|++|+|||++|+.+.+......+|....||++++.++..+++....   
T Consensus       174 l~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~r---  246 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYR---  246 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccC---
Confidence            456888899999999999863    4678899999999999999998654456788899999999988776654221   


Q ss_pred             CCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCChh---HHHHHHhhC
Q 038944          235 MPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNIE---VCDIIREIL  284 (334)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~~---~w~~l~~~l  284 (334)
                       ..... ......  -....+...-  .++.|++|+|++...+   .+..+...+
T Consensus       247 -P~~vg-y~~~~G--~f~~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~lL  297 (459)
T PRK11331        247 -PNGVG-FRRKDG--IFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLM  297 (459)
T ss_pred             -CCCCC-eEecCc--hHHHHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhc
Confidence             11000 011111  2222222222  2478999999996542   344444433

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

Probab=98.09  E-value=2.4e-05  Score=72.76  Aligned_cols=130  Identities=15%  Similarity=0.146  Sum_probs=75.0

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      +...+++|-+..+.++++   .  .++.-.-.||++|+||||||+.+..  .....|..     +|-.++-.+=++    
T Consensus        27 vGQ~HLlg~~~~lrr~v~---~--~~l~SmIl~GPPG~GKTTlA~liA~--~~~~~f~~-----~sAv~~gvkdlr----   90 (436)
T COG2256          27 VGQEHLLGEGKPLRRAVE---A--GHLHSMILWGPPGTGKTTLARLIAG--TTNAAFEA-----LSAVTSGVKDLR----   90 (436)
T ss_pred             cChHhhhCCCchHHHHHh---c--CCCceeEEECCCCCCHHHHHHHHHH--hhCCceEE-----eccccccHHHHH----
Confidence            445556666655555443   3  3466777899999999999999998  55555533     332222122122    


Q ss_pred             HhCCCCCccccchhhHHHHHHHH-HHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEE--ecCChHH---Hh
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIIL-HEYLMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLI--TLTEIKM---FT  304 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l-~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIiv--TTr~~~v---a~  304 (334)
                                       ...+.- +....|+|.+|.+|.|-.  ..+-+.   .||.-.+|.-|+|  ||-|..-   ..
T Consensus        91 -----------------~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~---lLp~vE~G~iilIGATTENPsF~ln~A  150 (436)
T COG2256          91 -----------------EIIEEARKNRLLGRRTILFLDEIHRFNKAQQDA---LLPHVENGTIILIGATTENPSFELNPA  150 (436)
T ss_pred             -----------------HHHHHHHHHHhcCCceEEEEehhhhcChhhhhh---hhhhhcCCeEEEEeccCCCCCeeecHH
Confidence                             222222 222358999999999953  233333   3454566887777  6766552   22


Q ss_pred             hccccCcccccccC
Q 038944          305 FLLETLFSLLICVS  318 (334)
Q Consensus       305 ~~~~~~~~~l~~l~  318 (334)
                      ..+....+.|.+|+
T Consensus       151 LlSR~~vf~lk~L~  164 (436)
T COG2256         151 LLSRARVFELKPLS  164 (436)
T ss_pred             HhhhhheeeeecCC
Confidence            23334445566665

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.08  E-value=7.3e-06  Score=75.50  Aligned_cols=135  Identities=16%  Similarity=0.088  Sum_probs=73.7

Q ss_pred             CCeeechhhHHHHHHHHhcC---CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      .+++|++..++.|..++...   ......+.++|++|+|||+||+.+.+.  ....|.   .+..+..... ..+...+.
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~--~~~~~~---~~~~~~~~~~-~~l~~~l~   77 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANE--MGVNLK---ITSGPALEKP-GDLAAILT   77 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH--hCCCEE---EeccchhcCc-hhHHHHHH
Confidence            35899999999998888642   234556789999999999999999984  332332   1121111111 22223333


Q ss_pred             HhCCCCCc-cccch--hhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHh
Q 038944          233 FLMPSSRL-SEIMD--KNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFT  304 (334)
Q Consensus       233 ~~~~~~~~-~~~~~--~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~  304 (334)
                      .+....-- .+..+  ..  ...+.+...+.+.+..+|+++.++...|..   .+|   +.+-|..||+...+..
T Consensus        78 ~~~~~~vl~iDEi~~l~~--~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~---~~~---~~~li~~t~~~~~l~~  144 (305)
T TIGR00635        78 NLEEGDVLFIDEIHRLSP--AVEELLYPAMEDFRLDIVIGKGPSARSVRL---DLP---PFTLVGATTRAGMLTS  144 (305)
T ss_pred             hcccCCEEEEehHhhhCH--HHHHHhhHHHhhhheeeeeccCccccceee---cCC---CeEEEEecCCccccCH
Confidence            33321100 00000  01  233445666666667777777665544321   222   2455666777654443

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.

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

Probab=98.07  E-value=3.9e-05  Score=78.28  Aligned_cols=50  Identities=18%  Similarity=0.265  Sum_probs=35.6

Q ss_pred             CCeeechhhHH---HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          156 RDTVGLDDRME---ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       156 ~~~vGr~~~~~---~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .+++|.+..+.   .+...+..+  ...-+.++|++|+||||||+.+++  ....+|
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~--~~~slLL~GPpGtGKTTLA~aIA~--~~~~~f   80 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKAD--RVGSLILYGPPGVGKTTLARIIAN--HTRAHF   80 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHH--HhcCcc
Confidence            35788877664   455555443  355678999999999999999998  344444

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.04  E-value=2.9e-05  Score=72.46  Aligned_cols=45  Identities=20%  Similarity=0.213  Sum_probs=37.5

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|++..++.+..++..+.  .+.+.++|++|+||||+|+.+.+.
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSPN--LPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            467899999999988887653  345789999999999999998873

>CHL00181 cbbX CbbX; Provisional

Probab=98.04  E-value=0.00011  Score=67.03  Aligned_cols=128  Identities=16%  Similarity=0.166  Sum_probs=66.5

Q ss_pred             CeeechhhHHHHHHHH---hcC----------CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCH
Q 038944          157 DTVGLDDRMEELLDLL---IEG----------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDA  223 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L---~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  223 (334)
                      +++|.+..+++|.++.   .-.          ...-..+.++|.+|+||||+|+.+.+.......-....|+.++.    
T Consensus        24 ~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~----   99 (287)
T CHL00181         24 ELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTR----   99 (287)
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecH----
Confidence            4678777666554442   210          11233578899999999999999966211001111122454441    


Q ss_pred             HHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC-----------hhHHHHHHhhCCCCCCCeE
Q 038944          224 DQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN-----------IEVCDIIREILPDNQNRSR  292 (334)
Q Consensus       224 ~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~-----------~~~w~~l~~~l~~~~~gsr  292 (334)
                      ..+    .....+...       .  .....+.+. .+  -+|+||++..           .+.-+.|...+.+...+.+
T Consensus       100 ~~l----~~~~~g~~~-------~--~~~~~l~~a-~g--gVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~  163 (287)
T CHL00181        100 DDL----VGQYIGHTA-------P--KTKEVLKKA-MG--GVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLV  163 (287)
T ss_pred             HHH----HHHHhccch-------H--HHHHHHHHc-cC--CEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEE
Confidence            222    222222111       1  222222222 23  4889999853           2344555555555555677


Q ss_pred             EEEecCChHHHh
Q 038944          293 VLITLTEIKMFT  304 (334)
Q Consensus       293 IivTTr~~~va~  304 (334)
                      ||+++....+..
T Consensus       164 vI~ag~~~~~~~  175 (287)
T CHL00181        164 VIFAGYKDRMDK  175 (287)
T ss_pred             EEEeCCcHHHHH
Confidence            888887665543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.01  E-value=9.9e-05  Score=67.38  Aligned_cols=125  Identities=15%  Similarity=0.148  Sum_probs=63.8

Q ss_pred             eeechhhHHHHHHHHh---cC----------CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHH
Q 038944          158 TVGLDDRMEELLDLLI---EG----------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDAD  224 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~---~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  224 (334)
                      ++|.++.+++|.++..   ..          ..+..-+.++|.+|+||||+|+.+..............|+.++.    .
T Consensus        24 l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~----~   99 (284)
T TIGR02880        24 LIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----D   99 (284)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH----H
Confidence            6777766666544322   11          11223578899999999999976654211011111123444442    1


Q ss_pred             HHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC-----------hhHHHHHHhhCCCCCCCeEE
Q 038944          225 QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN-----------IEVCDIIREILPDNQNRSRV  293 (334)
Q Consensus       225 ~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~-----------~~~w~~l~~~l~~~~~gsrI  293 (334)
                      ++    +..+.+...       .  .....+.+ ..  .-+|+||++..           .+.++.+...+.....+-+|
T Consensus       100 ~l----~~~~~g~~~-------~--~~~~~~~~-a~--~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~v  163 (284)
T TIGR02880       100 DL----VGQYIGHTA-------P--KTKEILKR-AM--GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVV  163 (284)
T ss_pred             HH----hHhhcccch-------H--HHHHHHHH-cc--CcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEE
Confidence            22    222222111       1  22222222 22  25889999852           23456666666555556677


Q ss_pred             EEecCChHH
Q 038944          294 LITLTEIKM  302 (334)
Q Consensus       294 ivTTr~~~v  302 (334)
                      |.+|.....
T Consensus       164 I~a~~~~~~  172 (284)
T TIGR02880       164 ILAGYKDRM  172 (284)
T ss_pred             EEeCCcHHH
Confidence            777765543

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.

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

Probab=97.98  E-value=3.1e-05  Score=71.09  Aligned_cols=118  Identities=15%  Similarity=0.185  Sum_probs=68.8

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      +....++|.+.-+.   +++..+  .++-+-.||++|+||||||+.+.+..+-..    ..||..|-.-.-..=.+.|++
T Consensus       141 vGQ~hlv~q~gllr---s~ieq~--~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife  211 (554)
T KOG2028|consen  141 VGQSHLVGQDGLLR---SLIEQN--RIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFE  211 (554)
T ss_pred             cchhhhcCcchHHH---HHHHcC--CCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHH
Confidence            44445555533332   333333  467788999999999999999998654444    345555544322233344443


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEE--ecCChH
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLI--TLTEIK  301 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIiv--TTr~~~  301 (334)
                      +....                   ..+.++|-+|.+|.|-.-  .+-   -..||.-.+|+-++|  ||-+..
T Consensus       212 ~aq~~-------------------~~l~krkTilFiDEiHRFNksQQ---D~fLP~VE~G~I~lIGATTENPS  262 (554)
T KOG2028|consen  212 QAQNE-------------------KSLTKRKTILFIDEIHRFNKSQQ---DTFLPHVENGDITLIGATTENPS  262 (554)
T ss_pred             HHHHH-------------------HhhhcceeEEEeHHhhhhhhhhh---hcccceeccCceEEEecccCCCc
Confidence            32110                   124567889999999432  121   135676677886666  676655

>PRK08116 hypothetical protein; Validated

Probab=97.97  E-value=2.1e-05  Score=71.20  Aligned_cols=102  Identities=17%  Similarity=0.133  Sum_probs=57.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL  259 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L  259 (334)
                      .-+.++|..|+|||+||..+++.  +..+-...++++      ..+++..+.........    .+..  .    +.+.+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~------~~~ll~~i~~~~~~~~~----~~~~--~----~~~~l  176 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVN------FPQLLNRIKSTYKSSGK----EDEN--E----IIRSL  176 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEE------HHHHHHHHHHHHhcccc----ccHH--H----HHHHh
Confidence            35889999999999999999994  322223345554      45566666655433211    1111  2    22333


Q ss_pred             CCCeEEEEEeCCC--ChhHHHH--HHhhCCC-CCCCeEEEEecCCh
Q 038944          260 MTKRYLNVIDDVW--NIEVCDI--IREILPD-NQNRSRVLITLTEI  300 (334)
Q Consensus       260 ~~kr~LlVlDdvw--~~~~w~~--l~~~l~~-~~~gsrIivTTr~~  300 (334)
                      .+-. ||||||+-  ....|..  +...+.. -.+|..+|+||...
T Consensus       177 ~~~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        177 VNAD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             cCCC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            3333 89999993  2234432  2222221 12456688888754

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.95  E-value=2.2e-05  Score=74.35  Aligned_cols=55  Identities=16%  Similarity=0.178  Sum_probs=41.5

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      ....++.|+++.+++|.+.+...           -...+-+.++|++|+|||+||+.+++  ....+|
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~--~l~~~~  184 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH--ETNATF  184 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH--hCCCCE
Confidence            34456899999999998877421           02345688999999999999999998  444444

Many proteins may score above the trusted cutoff because an internal

>PRK04195 replication factor C large subunit; Provisional

Probab=97.95  E-value=4.9e-05  Score=74.64  Aligned_cols=117  Identities=16%  Similarity=0.209  Sum_probs=70.2

Q ss_pred             CCeeechhhHHHHHHHHhcC--CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          156 RDTVGLDDRMEELLDLLIEG--PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      .+++|.+..++.+.+|+..-  ....+.+.|+|++|+||||+|+.+.++.  .  |+. +-++.|...+ ...+..++..
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el--~--~~~-ielnasd~r~-~~~i~~~i~~   87 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY--G--WEV-IELNASDQRT-ADVIERVAGE   87 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc--C--CCE-EEEccccccc-HHHHHHHHHH
Confidence            45899999999999998752  2236789999999999999999999843  2  222 2233333222 2233333322


Q ss_pred             hCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh------hHHHHHHhhCCCCCCCeEEEEecC
Q 038944          234 LMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI------EVCDIIREILPDNQNRSRVLITLT  298 (334)
Q Consensus       234 ~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~------~~w~~l~~~l~~~~~gsrIivTTr  298 (334)
                      .....           .       ....++-+||||++...      ..+..+...+..  .+..||+|+.
T Consensus        88 ~~~~~-----------s-------l~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n  138 (482)
T PRK04195         88 AATSG-----------S-------LFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTAN  138 (482)
T ss_pred             hhccC-----------c-------ccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEecc
Confidence            21110           0       01136779999999753      235566555542  2344666654

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.90  E-value=0.00011  Score=66.17  Aligned_cols=45  Identities=18%  Similarity=0.180  Sum_probs=32.1

Q ss_pred             CeeechhhHHHHHHH---Hhc----------CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDL---LIE----------GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~---L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.++.++.|.+.   +..          ..+...-+.++|++|+||||+|+.+.+
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHH
Confidence            478887777666443   311          123456678899999999999999976

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.

>PRK08118 topology modulation protein; Reviewed

Probab=97.89  E-value=6.4e-06  Score=69.10  Aligned_cols=35  Identities=20%  Similarity=0.367  Sum_probs=28.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCC-CceeeEEE
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVK-HYFDCHAW  214 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~-~~F~~~~w  214 (334)
                      +-|.|+|++|+||||||+.+++..... -+|+...|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            358999999999999999999965544 45777774

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.89  E-value=0.0001  Score=68.17  Aligned_cols=47  Identities=15%  Similarity=0.126  Sum_probs=39.4

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+...+.+..++..+. -..++.++|++|+||||+|+.+++.
T Consensus        20 ~~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l~~~   66 (316)
T PHA02544         20 IDECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKALCNE   66 (316)
T ss_pred             HHHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHHHHH
Confidence            3568999999999999987643 3467788999999999999999883

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.86  E-value=8.3e-05  Score=58.99  Aligned_cols=88  Identities=8%  Similarity=0.025  Sum_probs=45.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL  259 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L  259 (334)
                      ..+.|+|.+|+||||+++.+...  .........++..+........... .........   .....  .....+.+..
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~---~~~~~--~~~~~~~~~~   74 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARE--LGPPGGGVIYIDGEDILEEVLDQLL-LIIVGGKKA---SGSGE--LRLRLALALA   74 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhc--cCCCCCCEEEECCEEccccCHHHHH-hhhhhccCC---CCCHH--HHHHHHHHHH
Confidence            57899999999999999999884  3222222344444333221111111 001111111   11111  2333444444


Q ss_pred             CCC-eEEEEEeCCCChh
Q 038944          260 MTK-RYLNVIDDVWNIE  275 (334)
Q Consensus       260 ~~k-r~LlVlDdvw~~~  275 (334)
                      ... ..+|++|++....
T Consensus        75 ~~~~~~viiiDei~~~~   91 (148)
T smart00382       75 RKLKPDVLILDEITSLL   91 (148)
T ss_pred             HhcCCCEEEEECCcccC
Confidence            433 3899999998763

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.86  E-value=0.00026  Score=67.02  Aligned_cols=136  Identities=13%  Similarity=0.077  Sum_probs=72.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|.+.-++.+.+.+..+. -...+-++|+.|+||||+|+.+.+.-.-.....       +.++.....-+.+.....
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~-~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~-------~~pc~~c~~c~~~~~~~~   87 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGR-IHHAWLLSGTRGVGKTTIARLLAKSLNCQNGIT-------SNPCRKCIICKEIEKGLC   87 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCCCHHHHHHhcCCC
Confidence            468999999999988887653 235678999999999999999987321110000       011110011111111100


Q ss_pred             CCCC---ccccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCC
Q 038944          236 PSSR---LSEIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTE  299 (334)
Q Consensus       236 ~~~~---~~~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~  299 (334)
                      ....   .......+ ..++...+... ..+++-++|+|++..-  ..++.+...+.......++|++|.+
T Consensus        88 ~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~  158 (363)
T PRK14961         88 LDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTD  158 (363)
T ss_pred             CceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCC
Confidence            0000   00000001 01222222111 1345569999999754  4688888777655556777776654

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.85  E-value=0.00016  Score=73.06  Aligned_cols=137  Identities=9%  Similarity=0.022  Sum_probs=72.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+...-...+       .+..|.....-+.|...-.
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~-------~~~PCG~C~sCr~I~~G~h   87 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKALNCETGV-------TSQPCGVCRACREIDEGRF   87 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCccCC-------CCCCCcccHHHHHHhcCCC
Confidence            468999999999999987654 23355699999999999999877632111111       0111221122222211100


Q ss_pred             CCCCcc---ccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          236 PSSRLS---EIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       236 ~~~~~~---~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      ......   .....+ ...+.+.+... ..++.-++|||++...  ..|+.|+..+-.-....++|+||.+.
T Consensus        88 ~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~  159 (830)
T PRK07003         88 VDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDP  159 (830)
T ss_pred             ceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECCh
Confidence            000000   001111 00222222211 2345568889999753  57888888775544567766666553

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.82  E-value=8.1e-05  Score=69.42  Aligned_cols=48  Identities=21%  Similarity=0.238  Sum_probs=39.5

Q ss_pred             CCCeeechhhHHHHHHHHhc---CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE---GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|++..++.+..++..   .......+.++|++|+||||||+.+.+.
T Consensus        24 ~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~   74 (328)
T PRK00080         24 LDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANE   74 (328)
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHH
Confidence            45689999999998887764   2344667889999999999999999984

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.81  E-value=3.5e-05  Score=75.67  Aligned_cols=158  Identities=13%  Similarity=0.015  Sum_probs=81.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|.+..++.|.+++..+. -...+-++|++|+||||+|+.+.+...-...+...+|.|.+-.. +.......+..+.
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~-i~~~~h~dv~el~   91 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLA-VRRGAHPDVLEID   91 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHH-HhcCCCCceEEec
Confidence            458999988888888887654 23466899999999999999998743222222223333321100 0000000000001


Q ss_pred             CCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEec-CChHHHhhccc-cC
Q 038944          236 PSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITL-TEIKMFTFLLE-TL  310 (334)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTT-r~~~va~~~~~-~~  310 (334)
                      ..... ...+..  ++...+... +.+++-++|||+++..  ..++.+...+......+.+|++| ....+...+.. ..
T Consensus        92 ~~~~~-~vd~iR--~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~  168 (504)
T PRK14963         92 AASNN-SVEDVR--DLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQ  168 (504)
T ss_pred             ccccC-CHHHHH--HHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceE
Confidence            00000 011111  222222221 2356679999999754  57888888876544455555554 44444333332 22


Q ss_pred             cccccccC
Q 038944          311 FSLLICVS  318 (334)
Q Consensus       311 ~~~l~~l~  318 (334)
                      .+.+..++
T Consensus       169 ~~~f~~ls  176 (504)
T PRK14963        169 HFRFRRLT  176 (504)
T ss_pred             EEEecCCC
Confidence            34444444

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.76  E-value=0.00034  Score=64.60  Aligned_cols=45  Identities=18%  Similarity=0.206  Sum_probs=37.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|++..++.+..++..+.  .+.+.++|.+|+||||+++.+.+.
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~--~~~~ll~G~~G~GKt~~~~~l~~~   61 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKN--MPHLLFAGPPGTGKTTAALALARE   61 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999987643  345799999999999999999874

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.75  E-value=0.00026  Score=69.98  Aligned_cols=125  Identities=10%  Similarity=0.055  Sum_probs=72.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCC-------------------ceeeEEEEE
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKH-------------------YFDCHAWVP  216 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-------------------~F~~~~wv~  216 (334)
                      .+++|.+..+..|...+..+. -...+-++|+.|+||||+|+.+.+.-.-..                   .|...+++.
T Consensus        16 ~diiGq~~~v~~L~~~i~~~r-l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieid   94 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQK-VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEID   94 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEee
Confidence            468899999999998887643 234567899999999999999976211000                   011111111


Q ss_pred             cCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEE
Q 038944          217 GTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRV  293 (334)
Q Consensus       217 vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrI  293 (334)
                      ......+                    .+..  .+...+... ..+++-++++|++..  ...++.+...+-.....+.+
T Consensus        95 aas~~gv--------------------d~ir--~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~f  152 (546)
T PRK14957         95 AASRTGV--------------------EETK--EILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKF  152 (546)
T ss_pred             cccccCH--------------------HHHH--HHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceE
Confidence            1111111                    1111  333333322 246677999999863  46788888887665455665


Q ss_pred             EE-ecCChHHH
Q 038944          294 LI-TLTEIKMF  303 (334)
Q Consensus       294 iv-TTr~~~va  303 (334)
                      |+ ||....+.
T Consensus       153 IL~Ttd~~kil  163 (546)
T PRK14957        153 ILATTDYHKIP  163 (546)
T ss_pred             EEEECChhhhh
Confidence            54 55444444

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.72  E-value=0.00078  Score=66.13  Aligned_cols=156  Identities=11%  Similarity=-0.018  Sum_probs=81.8

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceee-EEEEEcCCCCCHHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDC-HAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~il~~il~~  233 (334)
                      -.+++|.+.-+..|...+..+. -..-+-++|+.|+||||+|+.+.+.-.-...+.. ..+    ..+....--..|...
T Consensus        20 f~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~----~~C~~C~~C~~i~~~   94 (507)
T PRK06645         20 FAELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTI----KTCEQCTNCISFNNH   94 (507)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCc----CCCCCChHHHHHhcC
Confidence            3467899988888887776543 2356788999999999999999873211110000 000    000000000111100


Q ss_pred             -------hCCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEE-EecCChHH
Q 038944          234 -------LMPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVL-ITLTEIKM  302 (334)
Q Consensus       234 -------~~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIi-vTTr~~~v  302 (334)
                             +...... ...+..  .+.+..... +.+++-++|+|+++.  ...|+.+...+......+.+| .||....+
T Consensus        95 ~h~Dv~eidaas~~-~vd~Ir--~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI  171 (507)
T PRK06645         95 NHPDIIEIDAASKT-SVDDIR--RIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKI  171 (507)
T ss_pred             CCCcEEEeeccCCC-CHHHHH--HHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHh
Confidence                   0000000 011111  222222211 356778999999986  467888888876555566655 46666666


Q ss_pred             HhhccccC-cccccccC
Q 038944          303 FTFLLETL-FSLLICVS  318 (334)
Q Consensus       303 a~~~~~~~-~~~l~~l~  318 (334)
                      ...+...+ .+.+..++
T Consensus       172 ~~tI~SRc~~~ef~~ls  188 (507)
T PRK06645        172 PATIISRCQRYDLRRLS  188 (507)
T ss_pred             hHHHHhcceEEEccCCC
Confidence            65544333 24444444

>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=97.71  E-value=0.00014  Score=57.78  Aligned_cols=21  Identities=14%  Similarity=0.197  Sum_probs=19.3

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |-|+|.+|+||||+|+.+.++
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            568999999999999999994

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 ....

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00033  Score=72.13  Aligned_cols=152  Identities=14%  Similarity=0.094  Sum_probs=80.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH--
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF--  233 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~--  233 (334)
                      .+++|.+.-++.|.+++..+. -...+-++|..|+||||+|+.+.+...-.....      .+ .|....--..|...  
T Consensus        16 ddIIGQe~Iv~~LknaI~~~r-l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~------~~-pCg~C~sC~~i~~g~~   87 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQR-LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVT------AT-PCGVCSSCVEIAQGRF   87 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHhccCccCCC------CC-CCCCchHHHHHhcCCC
Confidence            468999999999998887653 223457899999999999999987321111000      00 00000000000000  


Q ss_pred             -----hCCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCC--ChhHHHHHHhhCCCCCCCeEEEEe-cCChHHHh
Q 038944          234 -----LMPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVW--NIEVCDIIREILPDNQNRSRVLIT-LTEIKMFT  304 (334)
Q Consensus       234 -----~~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw--~~~~w~~l~~~l~~~~~gsrIivT-Tr~~~va~  304 (334)
                           +...... ...+..  .+...+... ..+++-++|||++.  +...++.|+..+-.-....++|++ |....+..
T Consensus        88 ~DviEidAas~~-kVDdIR--eLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~  164 (944)
T PRK14949         88 VDLIEVDAASRT-KVDDTR--ELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPV  164 (944)
T ss_pred             ceEEEecccccc-CHHHHH--HHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchH
Confidence                 0000000 011111  333333221 24677899999985  457888888877554445665554 44455543


Q ss_pred             hccc-cCcccccccC
Q 038944          305 FLLE-TLFSLLICVS  318 (334)
Q Consensus       305 ~~~~-~~~~~l~~l~  318 (334)
                      .+-. ...+++..++
T Consensus       165 TIlSRCq~f~fkpLs  179 (944)
T PRK14949        165 TVLSRCLQFNLKSLT  179 (944)
T ss_pred             HHHHhheEEeCCCCC
Confidence            3222 2344555554

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00042  Score=69.27  Aligned_cols=136  Identities=13%  Similarity=0.089  Sum_probs=73.1

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|.+...+.|.+++..+. -...+-++|+.|+||||+|+.+.+..      .|.-|+.. ..|+....-+.|...-.
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~L------nC~~~~~~-~pCg~C~sC~~I~~g~h   86 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCL------NCETGVTS-TPCEVCATCKAVNEGRF   86 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh------CCCcCCCC-CCCccCHHHHHHhcCCC
Confidence            468999999999999998654 23577899999999999999887631      11112111 11111111111111000


Q ss_pred             CCC---Cccccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCC
Q 038944          236 PSS---RLSEIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTE  299 (334)
Q Consensus       236 ~~~---~~~~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~  299 (334)
                      ...   ...+....+ ...+...+... ..+++-++|+|++..  ...++.|...+-.-..+.++|++|.+
T Consensus        87 pDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd  157 (702)
T PRK14960         87 IDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTD  157 (702)
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECC
Confidence            000   000000111 00222222111 246667899999964  46777787777554456677776654

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.70  E-value=0.00058  Score=69.13  Aligned_cols=133  Identities=17%  Similarity=0.158  Sum_probs=85.6

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC-CCHHHHHHHHHHHhCCCCCcc--
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP-YDADQMLDIVIKFLMPSSRLS--  241 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~il~~il~~~~~~~~~~--  241 (334)
                      ..+|++.|... .+.+.+-|..+.|.|||||+-....  .. ..=.-++|.+.+.+ -++..++.-++..++.-.+.-  
T Consensus        24 R~rL~~~L~~~-~~~RL~li~APAGfGKttl~aq~~~--~~-~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~   99 (894)
T COG2909          24 RPRLLDRLRRA-NDYRLILISAPAGFGKTTLLAQWRE--LA-ADGAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGD   99 (894)
T ss_pred             cHHHHHHHhcC-CCceEEEEeCCCCCcHHHHHHHHHH--hc-CcccceeEeecCCccCCHHHHHHHHHHHHHHhCccccH
Confidence            45777777665 3589999999999999999988865  11 12245799998754 588899999999887544321  


Q ss_pred             -------ccchhhHHHHHHHHHHHcC--CCeEEEEEeCCC---ChhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          242 -------EIMDKNYEMKKIILHEYLM--TKRYLNVIDDVW---NIEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       242 -------~~~~~~~~~l~~~l~~~L~--~kr~LlVlDdvw---~~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                             ......+..+...+..-+.  .+...+||||.-   ++.--..+...+.....+-..|||||+.-
T Consensus       100 ~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP  171 (894)
T COG2909         100 EAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRP  171 (894)
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCC
Confidence                   0011111134444444342  457899999964   33333333333334445678999999753

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

Probab=97.70  E-value=0.00016  Score=63.86  Aligned_cols=36  Identities=22%  Similarity=0.326  Sum_probs=29.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPG  217 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~v  217 (334)
                      -.+.|+|..|+|||||...+..  .....|.+..+++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~--~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLY--YLRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--hhcccCCEEEEEec
Confidence            3688999999999999999987  56678876666543

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

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.67  E-value=0.00092  Score=65.22  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=36.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+.....|...+..+. -...+-++|++|+||||+|+.+.+.
T Consensus        14 ~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999888777777776543 2346789999999999999999773

>PRK09087 hypothetical protein; Validated

Probab=97.65  E-value=0.00031  Score=61.90  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -+.+.|+|..|+|||+|++.+.+.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            467899999999999999998874

>PLN03025 replication factor C subunit; Provisional

Probab=97.64  E-value=0.0004  Score=64.53  Aligned_cols=45  Identities=18%  Similarity=0.233  Sum_probs=35.4

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.++.++.|..++..+.  .+-+-++|++|+||||+|+.+.+.
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~G~GKTtla~~la~~   57 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDGN--MPNLILSGPPGTGKTTSILALAHE   57 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            357888888888887776543  344678999999999999998873

>PRK08727 hypothetical protein; Validated

Probab=97.62  E-value=0.00014  Score=64.35  Aligned_cols=36  Identities=14%  Similarity=0.141  Sum_probs=26.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEE
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVP  216 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (334)
                      ...+.|+|..|+|||+|++.+.+.  ..++.....|++
T Consensus        41 ~~~l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~   76 (233)
T PRK08727         41 SDWLYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLP   76 (233)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEe
Confidence            345999999999999999999873  323333445654

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.60  E-value=0.00028  Score=67.36  Aligned_cols=50  Identities=16%  Similarity=0.175  Sum_probs=39.0

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....++.|+++.++++.+.+...           -...+-+.++|++|+|||++|+.+.+.
T Consensus       128 ~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        128 VTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            33456889999999998876421           134566889999999999999999983

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.59  E-value=0.0009  Score=65.98  Aligned_cols=45  Identities=11%  Similarity=0.126  Sum_probs=37.3

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++||-+.-++.|.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        16 ~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk   60 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAK   60 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999997653 223567899999999999998876

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

Probab=97.58  E-value=0.00054  Score=60.30  Aligned_cols=104  Identities=13%  Similarity=0.157  Sum_probs=65.1

Q ss_pred             CCCCCeeechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~i  230 (334)
                      +.-.+++|.+.+++.|++--..  ...+..-+-++|..|.|||+|++.+.+...-+.   ++ -|.|++.          
T Consensus        24 ~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~G---LR-lIev~k~----------   89 (249)
T PF05673_consen   24 IRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQG---LR-LIEVSKE----------   89 (249)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC---ce-EEEECHH----------
Confidence            5566799999999988765432  122345667799999999999999987322111   11 1222221          


Q ss_pred             HHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCC---ChhHHHHHHhhCC
Q 038944          231 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW---NIEVCDIIREILP  285 (334)
Q Consensus       231 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw---~~~~w~~l~~~l~  285 (334)
                                 +..+..  .+...|+.  ...||+|.+||+-   ++..+..++..|.
T Consensus        90 -----------~L~~l~--~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~Le  132 (249)
T PF05673_consen   90 -----------DLGDLP--ELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLE  132 (249)
T ss_pred             -----------HhccHH--HHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhc
Confidence                       111112  44444442  3579999999995   3457888887775

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.56  E-value=0.0016  Score=61.29  Aligned_cols=45  Identities=16%  Similarity=0.210  Sum_probs=37.3

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..++.+.+++..+. -...+-++|++|+||||+|+.+..
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~   58 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAK   58 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999887643 235678899999999999988875

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.56  E-value=0.00089  Score=67.15  Aligned_cols=45  Identities=13%  Similarity=0.190  Sum_probs=36.6

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|-+.-++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk   60 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAK   60 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468898888888888887754 235678899999999999998854

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

Probab=97.55  E-value=0.00049  Score=65.29  Aligned_cols=117  Identities=10%  Similarity=0.039  Sum_probs=80.0

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC--CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG--PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~i  230 (334)
                      ..+..++||+.+++.+.+|+...  .....-+.|.|.+|.|||.+...|+.+..-...=.+.+++....--....++..|
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHH
Confidence            56778999999999999998753  2445678899999999999999999863221111234555544434567888888


Q ss_pred             HHHhCCCCCccccchhhHHHHHHHHHHHcCCCe--EEEEEeCCCC
Q 038944          231 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKR--YLNVIDDVWN  273 (334)
Q Consensus       231 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr--~LlVlDdvw~  273 (334)
                      ...+-.....  .....  +.+..+.++.++.+  ||+|||.+..
T Consensus       227 ~~~~~q~~~s--~~~~~--~~~~~~~~h~~q~k~~~llVlDEmD~  267 (529)
T KOG2227|consen  227 FSSLLQDLVS--PGTGM--QHLEKFEKHTKQSKFMLLLVLDEMDH  267 (529)
T ss_pred             HHHHHHHhcC--CchhH--HHHHHHHHHHhcccceEEEEechhhH
Confidence            8777222211  11113  66777777775544  8999999854

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.55  E-value=0.00097  Score=66.63  Aligned_cols=160  Identities=11%  Similarity=-0.027  Sum_probs=80.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .++||.+.-++.|.+++..+. -...+-++|..|+||||+|+.+.+...-...-. ..-+ .+..|+....-+.|...-.
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~-~~g~-~~~PCG~C~sC~~I~aG~h   92 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADG-EGGI-TAQPCGQCRACTEIDAGRF   92 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCccc-cccC-CCCCCcccHHHHHHHcCCC
Confidence            468999999999999987654 234567899999999999998876321100000 0000 0011111111111110000


Q ss_pred             CCCCcc---ccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeE-EEEecCChHHHhhcc
Q 038944          236 PSSRLS---EIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSR-VLITLTEIKMFTFLL  307 (334)
Q Consensus       236 ~~~~~~---~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsr-IivTTr~~~va~~~~  307 (334)
                      ......   .....+ ..++.+.+... ..++.-++|||++..  ...++.|+..+-.-..+.+ |++||....+...+-
T Consensus        93 pDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIr  172 (700)
T PRK12323         93 VDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVL  172 (700)
T ss_pred             CcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHH
Confidence            000000   001111 00222222211 246667999999964  4688888887754334455 555666666665544


Q ss_pred             ccC-cccccccC
Q 038944          308 ETL-FSLLICVS  318 (334)
Q Consensus       308 ~~~-~~~l~~l~  318 (334)
                      +.+ .+.+..++
T Consensus       173 SRCq~f~f~~ls  184 (700)
T PRK12323        173 SRCLQFNLKQMP  184 (700)
T ss_pred             HHHHhcccCCCC
Confidence            433 34444444

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.53  E-value=0.00055  Score=68.06  Aligned_cols=142  Identities=9%  Similarity=0.023  Sum_probs=75.2

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      -.+++|.+..++.+.+++..+. -...+-++|+.|+||||+|+.+.+.-      .|.-|.... .|+....-+.+....
T Consensus        15 F~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk~L------~C~~~~~~~-~Cg~C~sCr~i~~~~   86 (605)
T PRK05896         15 FKQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAKAI------NCLNPKDGD-CCNSCSVCESINTNQ   86 (605)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHh------cCCCCCCCC-CCcccHHHHHHHcCC
Confidence            3468899999999999886653 23567899999999999999987631      222232211 222222222222111


Q ss_pred             CCCCCcc---ccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEE-ecCChHHHh
Q 038944          235 MPSSRLS---EIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLI-TLTEIKMFT  304 (334)
Q Consensus       235 ~~~~~~~---~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIiv-TTr~~~va~  304 (334)
                      .......   .....+ ...+...+... ..+++-++|+|++..  ...++.|...+..-...+.+|+ ||....+-.
T Consensus        87 h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~  164 (605)
T PRK05896         87 SVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPL  164 (605)
T ss_pred             CCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhH
Confidence            1000000   000111 11222222221 223445799999854  4678888877755444565554 444444443

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

Probab=97.52  E-value=0.00012  Score=63.53  Aligned_cols=55  Identities=18%  Similarity=0.183  Sum_probs=36.7

Q ss_pred             CCCCeeechhhHHHHHHHHh---cCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee
Q 038944          154 KSRDTVGLDDRMEELLDLLI---EGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD  210 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~---~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~  210 (334)
                      .-.+++|.+.-+..+.-++.   .....+.-+-.||++|+||||||..+.+  .....|.
T Consensus        22 ~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~--e~~~~~~   79 (233)
T PF05496_consen   22 SLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIAN--ELGVNFK   79 (233)
T ss_dssp             SCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHH--HCT--EE
T ss_pred             CHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHh--ccCCCeE
Confidence            45678999888877654443   3345678889999999999999999999  5555563

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.

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

Probab=97.50  E-value=0.00056  Score=70.60  Aligned_cols=118  Identities=8%  Similarity=0.152  Sum_probs=66.6

Q ss_pred             CCCeeechhhHHHHHHHHhcC-------CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQML  227 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il  227 (334)
                      ...++|.+..++.+.+.+...       +....++.++|+.|+|||+||+.+...  ....   .+.+..|.-.+..   
T Consensus       453 ~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~--l~~~---~~~~d~se~~~~~---  524 (731)
T TIGR02639       453 KAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEA--LGVH---LERFDMSEYMEKH---  524 (731)
T ss_pred             hcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHH--hcCC---eEEEeCchhhhcc---
Confidence            446889999999988887631       234557889999999999999999883  3222   2344433311111   


Q ss_pred             HHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCC
Q 038944          228 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREILPD  286 (334)
Q Consensus       228 ~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~  286 (334)
                       .+...++......+.....  .+...++.   ...-+++||++..  .+.++.+...+..
T Consensus       525 -~~~~lig~~~gyvg~~~~~--~l~~~~~~---~p~~VvllDEieka~~~~~~~Ll~~ld~  579 (731)
T TIGR02639       525 -TVSRLIGAPPGYVGFEQGG--LLTEAVRK---HPHCVLLLDEIEKAHPDIYNILLQVMDY  579 (731)
T ss_pred             -cHHHHhcCCCCCcccchhh--HHHHHHHh---CCCeEEEEechhhcCHHHHHHHHHhhcc
Confidence             1111122111000011111  23333321   2345999999975  4677777776653

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.49  E-value=0.00037  Score=61.83  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+.|+|+.|+|||+|++.+.+.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~   68 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAE   68 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999999873

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.49  E-value=0.0012  Score=63.17  Aligned_cols=149  Identities=10%  Similarity=-0.008  Sum_probs=74.5

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEE-cCCCCCHHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVP-GTYPYDADQMLDIVIKF  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~il~~il~~  233 (334)
                      -.+++|.+..++.|..++..+. -...+-++|+.|+||||+|..+.+.-.-...+....|.. +..+++.-..-+.+...
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~   93 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAG   93 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcC
Confidence            3468899988888888887653 234577899999999999998876321111111111111 01111111111111110


Q ss_pred             hCCCC---Cccccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEec-CChHHHh
Q 038944          234 LMPSS---RLSEIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITL-TEIKMFT  304 (334)
Q Consensus       234 ~~~~~---~~~~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTT-r~~~va~  304 (334)
                      .....   ........+ ..++...+... ..+++-++|+|++..  ...|+.+...+.+-...+.+|++| +...+..
T Consensus        94 ~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~  172 (397)
T PRK14955         94 TSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPA  172 (397)
T ss_pred             CCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHH
Confidence            00000   000000011 00222222111 235566889999863  467888888876655567766554 4444443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.46  E-value=0.0019  Score=64.03  Aligned_cols=45  Identities=16%  Similarity=0.183  Sum_probs=36.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        16 ~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk   60 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAK   60 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHH
Confidence            468899999999998887654 224567899999999999999876

>PRK12377 putative replication protein; Provisional

Probab=97.45  E-value=0.00055  Score=61.08  Aligned_cols=73  Identities=15%  Similarity=0.007  Sum_probs=44.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      ...+.++|.+|+|||+||..+.+.  +......+.++++      .+++..|-.......      ...  .+    .+.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~------~~l~~~l~~~~~~~~------~~~--~~----l~~  160 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTV------PDVMSRLHESYDNGQ------SGE--KF----LQE  160 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEH------HHHHHHHHHHHhccc------hHH--HH----HHH
Confidence            457899999999999999999984  3333334466644      345555544332110      111  22    222


Q ss_pred             cCCCeEEEEEeCCC
Q 038944          259 LMTKRYLNVIDDVW  272 (334)
Q Consensus       259 L~~kr~LlVlDdvw  272 (334)
                      + .+-=||||||+-
T Consensus       161 l-~~~dLLiIDDlg  173 (248)
T PRK12377        161 L-CKVDLLVLDEIG  173 (248)
T ss_pred             h-cCCCEEEEcCCC
Confidence            2 355699999993

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

Probab=97.45  E-value=0.0012  Score=63.19  Aligned_cols=95  Identities=15%  Similarity=0.081  Sum_probs=61.3

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL  259 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L  259 (334)
                      ++.|+|+.++|||||++.+...  ..+.   .+++..-... +-.++ .                     +....+.+.-
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~~~~d~~~~~~~l-~---------------------d~~~~~~~~~   91 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKG--LLEE---IIYINFDDLRLDRIEL-L---------------------DLLRAYIELK   91 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhh--CCcc---eEEEEecchhcchhhH-H---------------------HHHHHHHHhh
Confidence            9999999999999999777663  2222   3444322211 10000 0                     1111121111


Q ss_pred             CCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHH
Q 038944          260 MTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMF  303 (334)
Q Consensus       260 ~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va  303 (334)
                      ..++.+|+||.|-....|......+.+..+. +|++|+.+..+-
T Consensus        92 ~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll  134 (398)
T COG1373          92 EREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLL  134 (398)
T ss_pred             ccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhh
Confidence            2278899999999999999999988876666 899998876543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.45  E-value=0.0019  Score=61.66  Aligned_cols=46  Identities=15%  Similarity=0.081  Sum_probs=36.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCC--------CceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPP--------QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~--------~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++++|.+..++.|.+++..+..        -..-+-++|+.|+||||+|..+..
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~   58 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAA   58 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            3578999999999999876531        245677999999999999998865

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

Probab=97.44  E-value=0.002  Score=58.54  Aligned_cols=116  Identities=15%  Similarity=0.136  Sum_probs=74.5

Q ss_pred             CCCCeeechh---hHHHHHHHHhcCC-CCceEEEEEccCCccHHHHHHHHHccCCC-----CCceeeEEEEEcCCCCCHH
Q 038944          154 KSRDTVGLDD---RMEELLDLLIEGP-PQLSVVVILDSIGLDKAAFAGEAYNSSYV-----KHYFDCHAWVPGTYPYDAD  224 (334)
Q Consensus       154 ~~~~~vGr~~---~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-----~~~F~~~~wv~vs~~~~~~  224 (334)
                      ..+..+|...   ..+.|.++|..+. ...+-+.|||.+|.|||++++......-.     ...+ ++..|.....++..
T Consensus        32 ~~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~-PVv~vq~P~~p~~~  110 (302)
T PF05621_consen   32 RADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERI-PVVYVQMPPEPDER  110 (302)
T ss_pred             hcCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccc-cEEEEecCCCCChH
Confidence            3445667543   3345555555443 46678999999999999999998853111     1122 56677888899999


Q ss_pred             HHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 038944          225 QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       225 ~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~  273 (334)
                      .++..|+.+++........... +......+.+.+  +--+||+|.+-+
T Consensus       111 ~~Y~~IL~~lgaP~~~~~~~~~-~~~~~~~llr~~--~vrmLIIDE~H~  156 (302)
T PF05621_consen  111 RFYSAILEALGAPYRPRDRVAK-LEQQVLRLLRRL--GVRMLIIDEFHN  156 (302)
T ss_pred             HHHHHHHHHhCcccCCCCCHHH-HHHHHHHHHHHc--CCcEEEeechHH
Confidence            9999999999987653222111 112222333333  334899999965

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

>PRK08181 transposase; Validated

Probab=97.43  E-value=0.00025  Score=64.06  Aligned_cols=98  Identities=13%  Similarity=0.112  Sum_probs=51.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL  259 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L  259 (334)
                      .-+.++|.+|+|||.||..+.+.  .......+.|++      ..+++..+......       ....  .....+    
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~~------~~~L~~~l~~a~~~-------~~~~--~~l~~l----  165 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTR------TTDLVQKLQVARRE-------LQLE--SAIAKL----  165 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHH--HHHcCCceeeee------HHHHHHHHHHHHhC-------CcHH--HHHHHH----
Confidence            35899999999999999999873  222222344543      44566655433211       0111  222222    


Q ss_pred             CCCeEEEEEeCCCCh---hHHH-HHHhhCCC-CCCCeEEEEecCCh
Q 038944          260 MTKRYLNVIDDVWNI---EVCD-IIREILPD-NQNRSRVLITLTEI  300 (334)
Q Consensus       260 ~~kr~LlVlDdvw~~---~~w~-~l~~~l~~-~~~gsrIivTTr~~  300 (334)
                       .+-=||||||+-..   ..|. .+...+.. ...+ .+||||...
T Consensus       166 -~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~-s~IiTSN~~  209 (269)
T PRK08181        166 -DKFDLLILDDLAYVTKDQAETSVLFELISARYERR-SILITANQP  209 (269)
T ss_pred             -hcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCC-CEEEEcCCC
Confidence             13349999999532   2222 22222221 1124 488887754

>PRK10536 hypothetical protein; Provisional

Probab=97.43  E-value=0.0014  Score=58.41  Aligned_cols=44  Identities=7%  Similarity=0.110  Sum_probs=35.7

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+.++......++.+|.+.    .++.+.|..|+|||+||..+..+
T Consensus        54 ~~~i~p~n~~Q~~~l~al~~~----~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         54 TSPILARNEAQAHYLKAIESK----QLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             CccccCCCHHHHHHHHHHhcC----CeEEEECCCCCCHHHHHHHHHHH
Confidence            344667888888888888663    48999999999999999887764

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.43  E-value=0.00092  Score=67.21  Aligned_cols=137  Identities=12%  Similarity=0.120  Sum_probs=74.6

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      -.+++|.+..++.|..++..+. -...+-++|..|+||||+|+.+.+.-.      |..+-.....|+.....+.|....
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~------c~~~~~~~~~c~~c~~c~~i~~~~   87 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVN------CTTNDPKGRPCGTCEMCRAIAEGS   87 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhc------CCCCCCCCCCCccCHHHHHHhcCC
Confidence            3468999999999988887653 234567899999999999999986321      111100111223233334443322


Q ss_pred             CCCCC---ccccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCC--ChhHHHHHHhhCCCCCCCeEEEEecC
Q 038944          235 MPSSR---LSEIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVW--NIEVCDIIREILPDNQNRSRVLITLT  298 (334)
Q Consensus       235 ~~~~~---~~~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw--~~~~w~~l~~~l~~~~~gsrIivTTr  298 (334)
                      .....   .......+ ..++...+... ..+++-++|+|++.  +....+.|...+......+.+|++|.
T Consensus        88 ~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~  158 (585)
T PRK14950         88 AVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATT  158 (585)
T ss_pred             CCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeC
Confidence            11100   00001111 11222222221 23567789999985  44667778777655445566666554

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.41  E-value=0.00065  Score=63.67  Aligned_cols=105  Identities=10%  Similarity=-0.075  Sum_probs=63.9

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceee-EEEEEcCCC-CCHHHHHHHHHHHhCCCCCcccc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDC-HAWVPGTYP-YDADQMLDIVIKFLMPSSRLSEI  243 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~-~~~~~il~~il~~~~~~~~~~~~  243 (334)
                      .++++.+..=..+ .-..|+|.+|+|||||++.+.+... .++=+. ++|+.+.+. .++.++++.+...+.........
T Consensus       121 ~RvID~l~PiGkG-QR~LIvG~pGtGKTTLl~~la~~i~-~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~  198 (380)
T PRK12608        121 MRVVDLVAPIGKG-QRGLIVAPPRAGKTVLLQQIAAAVA-ANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPP  198 (380)
T ss_pred             HhhhhheeecCCC-ceEEEECCCCCCHHHHHHHHHHHHH-hcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCH
Confidence            4577777642222 2459999999999999999877321 112233 477777754 57889999998877654421111


Q ss_pred             chhh-HHHHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          244 MDKN-YEMKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       244 ~~~~-~~~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      .... .-.....+-+++  +|++.+||+|++-
T Consensus       199 ~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        199 DEHIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence            1100 001222222333  6999999999994

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.40  E-value=0.0019  Score=65.05  Aligned_cols=45  Identities=22%  Similarity=0.267  Sum_probs=37.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..+..|.+++..+. -..-+-++|..|+||||+|+.+.+
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk   60 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAK   60 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHH
Confidence            468999999999999988653 234678999999999999998876

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.40  E-value=0.00091  Score=59.51  Aligned_cols=114  Identities=12%  Similarity=0.064  Sum_probs=59.8

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIM  244 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~  244 (334)
                      +..+.++..........+.++|.+|+|||+|+..+.+..  ...-...+++      +..+++..+-......     ..
T Consensus        85 l~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l--~~~g~~v~~i------t~~~l~~~l~~~~~~~-----~~  151 (244)
T PRK07952         85 LSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNEL--LLRGKSVLII------TVADIMSAMKDTFSNS-----ET  151 (244)
T ss_pred             HHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHH--HhcCCeEEEE------EHHHHHHHHHHHHhhc-----cc
Confidence            334444443322334578899999999999999999842  2222234455      3455665555443211     11


Q ss_pred             hhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--hHHHH--HHhhCC--CCCCCeEEEEecCC
Q 038944          245 DKNYEMKKIILHEYLMTKRYLNVIDDVWNI--EVCDI--IREILP--DNQNRSRVLITLTE  299 (334)
Q Consensus       245 ~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~~w~~--l~~~l~--~~~~gsrIivTTr~  299 (334)
                      ...  .+.    +.+. +.=||||||+-..  ..|..  +...+.  .....+ +||||..
T Consensus       152 ~~~--~~l----~~l~-~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~-tiitSNl  204 (244)
T PRK07952        152 SEE--QLL----NDLS-NVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRP-TGMLTNS  204 (244)
T ss_pred             cHH--HHH----HHhc-cCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCC-EEEeCCC
Confidence            111  222    2343 3448899999543  44542  222332  122333 6667664

>PRK07261 topology modulation protein; Provisional

Probab=97.39  E-value=0.00057  Score=57.49  Aligned_cols=54  Identities=20%  Similarity=0.251  Sum_probs=32.0

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCC-CceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVK-HYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      .|.|+|++|+||||||+.+....... -+.|...|-......+..++...+..-+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~   56 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPNWQERDDDDMIADISNFL   56 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccccccCCHHHHHHHHHHHH
Confidence            48999999999999999997643221 1344455533222333344444443333

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.0017  Score=63.34  Aligned_cols=45  Identities=18%  Similarity=0.177  Sum_probs=35.8

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+.-++.|.+.+..+. -..-+-++|+.|+||||+|+.+..
T Consensus        13 ~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk   57 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISL   57 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHH
Confidence            468999888888887776553 234688999999999999988865

>PRK05642 DNA replication initiation factor; Validated

Probab=97.39  E-value=0.00069  Score=60.04  Aligned_cols=23  Identities=13%  Similarity=0.174  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+.|+|..|+|||+|++.+.+
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~   67 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACL   67 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999999987

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.39  E-value=0.0012  Score=66.40  Aligned_cols=153  Identities=15%  Similarity=0.130  Sum_probs=81.5

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH-
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF-  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~-  233 (334)
                      -.+++|.+..+..|.+.+..+. -...+-++|..|+||||+|+.+.+..      .|..++ .+.+|.....-+.|... 
T Consensus        15 f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L------~c~~~~-~~~pCg~C~~C~~i~~g~   86 (647)
T PRK07994         15 FAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGL------NCETGI-TATPCGECDNCREIEQGR   86 (647)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhh------hhccCC-CCCCCCCCHHHHHHHcCC
Confidence            3468999999999988887654 22346789999999999999987631      111110 01112111222222110 


Q ss_pred             ------hCCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCC--ChhHHHHHHhhCCCCCCCeEEEE-ecCChHHH
Q 038944          234 ------LMPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVW--NIEVCDIIREILPDNQNRSRVLI-TLTEIKMF  303 (334)
Q Consensus       234 ------~~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw--~~~~w~~l~~~l~~~~~gsrIiv-TTr~~~va  303 (334)
                            +...... ...+..  ++...+... ..+++-++|||++.  +...++.|+..+-.-....++|+ ||....+.
T Consensus        87 ~~D~ieidaas~~-~VddiR--~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl  163 (647)
T PRK07994         87 FVDLIEIDAASRT-KVEDTR--ELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLP  163 (647)
T ss_pred             CCCceeecccccC-CHHHHH--HHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccc
Confidence                  0000000 011111  333333222 35677799999996  44678888777755444555554 55555554


Q ss_pred             hhccc-cCcccccccC
Q 038944          304 TFLLE-TLFSLLICVS  318 (334)
Q Consensus       304 ~~~~~-~~~~~l~~l~  318 (334)
                      ..+-+ ...+++..++
T Consensus       164 ~TI~SRC~~~~f~~Ls  179 (647)
T PRK07994        164 VTILSRCLQFHLKALD  179 (647)
T ss_pred             hHHHhhheEeeCCCCC
Confidence            33332 2344555554

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.36  E-value=0.00097  Score=64.67  Aligned_cols=99  Identities=16%  Similarity=0.218  Sum_probs=55.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCce-e-eEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYF-D-CHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~-~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      ..-+.|+|.+|+|||+|++.+.+.  +...+ . ...|++      ..+++..+...+....     .  .  .    +.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~--l~~~~~~~~v~yi~------~~~f~~~~~~~~~~~~-----~--~--~----f~  188 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYIT------SEKFLNDLVDSMKEGK-----L--N--E----FR  188 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEE------HHHHHHHHHHHHhccc-----H--H--H----HH
Confidence            456999999999999999999984  33322 2 244553      3456666666554221     0  1  2    22


Q ss_pred             HHcCCCeEEEEEeCCCCh---hHH-HHHHhhCCC-CCCCeEEEEecC
Q 038944          257 EYLMTKRYLNVIDDVWNI---EVC-DIIREILPD-NQNRSRVLITLT  298 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~---~~w-~~l~~~l~~-~~~gsrIivTTr  298 (334)
                      +.+..+.-+|+|||+...   ..+ +.+...+.. ...|..||+||.
T Consensus       189 ~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd  235 (440)
T PRK14088        189 EKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSD  235 (440)
T ss_pred             HHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECC
Confidence            222234558999999632   111 122222211 123456888774

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.35  E-value=0.00087  Score=70.34  Aligned_cols=134  Identities=12%  Similarity=0.160  Sum_probs=73.3

Q ss_pred             CCCeeechhhHHHHHHHHhcC-------CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQML  227 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il  227 (334)
                      ...++|.+..++.+.+.+...       +.+..++.++|+.|+|||++|+.+...  ....-...+.+..|.-.+ ....
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~--l~~~~~~~i~~d~s~~~~-~~~~  640 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEF--LFDDEDAMVRIDMSEYME-KHSV  640 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhhcc-cchH
Confidence            346899999999999888642       123567889999999999999999873  211111222233332111 1111


Q ss_pred             HHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCC-----------CCeEEE
Q 038944          228 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREILPDNQ-----------NRSRVL  294 (334)
Q Consensus       228 ~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~-----------~gsrIi  294 (334)
                      ..+   ++....-.+.....  .+...++.   ....+|+||++..  .+.++.+...|..+.           ..+-||
T Consensus       641 ~~l---~g~~~g~~g~~~~g--~l~~~v~~---~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI  712 (852)
T TIGR03346       641 ARL---IGAPPGYVGYEEGG--QLTEAVRR---KPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVII  712 (852)
T ss_pred             HHh---cCCCCCccCccccc--HHHHHHHc---CCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEE
Confidence            111   11110000011111  33333332   2234899999974  468888887775431           223377


Q ss_pred             EecCC
Q 038944          295 ITLTE  299 (334)
Q Consensus       295 vTTr~  299 (334)
                      +||..
T Consensus       713 ~TSn~  717 (852)
T TIGR03346       713 MTSNL  717 (852)
T ss_pred             EeCCc
Confidence            77765

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

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.35  E-value=0.0009  Score=65.59  Aligned_cols=47  Identities=26%  Similarity=0.253  Sum_probs=36.8

Q ss_pred             CCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|.+..++++.+.+.-.           -...+-+.++|++|+|||++|+.+++.
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            45778999999888876421           123456889999999999999999994

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.

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

Probab=97.35  E-value=0.001  Score=63.47  Aligned_cols=49  Identities=18%  Similarity=0.137  Sum_probs=37.6

Q ss_pred             CCCCeeechhhHHHHHHHHhc----C-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIE----G-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.++.|.+..+++|.+.+.-    .       -...+-+.++|++|+|||+||+.+.+.
T Consensus       143 ~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        143 TYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             CHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            344688999888888776631    1       124567889999999999999999983

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.34  E-value=0.00057  Score=71.41  Aligned_cols=47  Identities=17%  Similarity=0.270  Sum_probs=38.2

Q ss_pred             CCCeeechhhHHHHHHHHhc-------CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIE-------GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++|.+..++.+.+.+..       +..+..++.++|+.|+|||.||+.+..
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~  618 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAE  618 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            35689999999999888853       234566899999999999999987765

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.33  E-value=0.0011  Score=61.74  Aligned_cols=23  Identities=9%  Similarity=0.124  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-+.++|..|+|||+||..+.+.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~  206 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKE  206 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH
Confidence            67999999999999999999884

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.33  E-value=0.00084  Score=70.17  Aligned_cols=47  Identities=9%  Similarity=0.196  Sum_probs=37.2

Q ss_pred             CCCeeechhhHHHHHHHHhc-------CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIE-------GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++|.+..++.+.+.+..       .+.+...+.++|+.|+|||+||+.+.+
T Consensus       508 ~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~  561 (821)
T CHL00095        508 HKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALAS  561 (821)
T ss_pred             cCcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHH
Confidence            35689999999999888753       223345677899999999999998876

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.31  E-value=0.0026  Score=66.07  Aligned_cols=151  Identities=11%  Similarity=0.003  Sum_probs=78.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH--
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF--  233 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~--  233 (334)
                      .+++|.+..++.|..++..+. -...+-++|..|+||||+|+.+.+...-.+.+.       ...|+...--+.|...  
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~-------~~pCg~C~sC~~~~~g~~   86 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILARSLNCVEGPT-------STPCGECDSCVALAPGGP   86 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHhCcccCCC-------CCCCcccHHHHHHHcCCC
Confidence            468999999999999987654 224578999999999999999876321111100       0001110001111100  


Q ss_pred             -------hCCCCCccccchhhHHHHHHHHHH-HcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEec-CChHH
Q 038944          234 -------LMPSSRLSEIMDKNYEMKKIILHE-YLMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITL-TEIKM  302 (334)
Q Consensus       234 -------~~~~~~~~~~~~~~~~~l~~~l~~-~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTT-r~~~v  302 (334)
                             +...... ...+..  ++...+.. -..+++-++|||++..  ...++.|+..+-+-...+.+|++| ....+
T Consensus        87 ~~~dv~eidaas~~-~Vd~iR--~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kL  163 (824)
T PRK07764         87 GSLDVTEIDAASHG-GVDDAR--ELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKV  163 (824)
T ss_pred             CCCcEEEecccccC-CHHHHH--HHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhh
Confidence                   0000000 000111  22222211 1345666888999864  478888888886655566665554 44445


Q ss_pred             Hhhcccc-Cccccccc
Q 038944          303 FTFLLET-LFSLLICV  317 (334)
Q Consensus       303 a~~~~~~-~~~~l~~l  317 (334)
                      -..+... ..+.+..+
T Consensus       164 l~TIrSRc~~v~F~~l  179 (824)
T PRK07764        164 IGTIRSRTHHYPFRLV  179 (824)
T ss_pred             hHHHHhheeEEEeeCC
Confidence            5444333 33444444

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.30  E-value=0.00075  Score=64.84  Aligned_cols=99  Identities=16%  Similarity=0.184  Sum_probs=53.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCce--eeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYF--DCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      ...+.|+|..|+|||+|++.+++.  +....  ...++++      ..++...+...+....         .+.....+.
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~--l~~~~~~~~v~yi~------~~~~~~~~~~~~~~~~---------~~~~~~~~~  198 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNE--ILENNPNAKVVYVS------SEKFTNDFVNALRNNK---------MEEFKEKYR  198 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HHHhCCCCcEEEEE------HHHHHHHHHHHHHcCC---------HHHHHHHHH
Confidence            456899999999999999999984  32222  1234553      3445555555543221         113322222


Q ss_pred             HHcCCCeEEEEEeCCCCh---hHH-HHHHhhCCC-CCCCeEEEEecCC
Q 038944          257 EYLMTKRYLNVIDDVWNI---EVC-DIIREILPD-NQNRSRVLITLTE  299 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~---~~w-~~l~~~l~~-~~~gsrIivTTr~  299 (334)
                          + .-+|+|||+...   +.+ +.+...+.. ...|..+|+||..
T Consensus       199 ----~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~  241 (405)
T TIGR00362       199 ----S-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDR  241 (405)
T ss_pred             ----h-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCC
Confidence                2 238899999642   111 222222211 1234567777754

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).

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.29  E-value=0.0017  Score=62.89  Aligned_cols=157  Identities=13%  Similarity=0.026  Sum_probs=81.2

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      -.+++|.+..+..|..++..+. -...+-++|+.|+||||+|+.+.+...-.....   ........+...+...+...+
T Consensus        17 f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~---~~pCg~C~sC~~i~~g~~~dv   92 (484)
T PRK14956         17 FRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLNCENPIG---NEPCNECTSCLEITKGISSDV   92 (484)
T ss_pred             HHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcCcccccC---ccccCCCcHHHHHHccCCccc
Confidence            3468999999998888887654 224578999999999999999987321110000   000000011111111110000


Q ss_pred             ---CCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEE-EecCChHHHhhcc
Q 038944          235 ---MPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVL-ITLTEIKMFTFLL  307 (334)
Q Consensus       235 ---~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIi-vTTr~~~va~~~~  307 (334)
                         ...... ...+..  ++.+.+... ..++.-++|+|++..  ...++.++..+-.-......| .||....+...+-
T Consensus        93 iEIdaas~~-gVd~IR--eL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~  169 (484)
T PRK14956         93 LEIDAASNR-GIENIR--ELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETIL  169 (484)
T ss_pred             eeechhhcc-cHHHHH--HHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHH
Confidence               000000 011111  333333322 245666999999964  467888887775433345544 4555555654444


Q ss_pred             ccC-cccccccC
Q 038944          308 ETL-FSLLICVS  318 (334)
Q Consensus       308 ~~~-~~~l~~l~  318 (334)
                      +.+ .+.+..++
T Consensus       170 SRCq~~~f~~ls  181 (484)
T PRK14956        170 SRCQDFIFKKVP  181 (484)
T ss_pred             hhhheeeecCCC
Confidence            433 24444444

>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=97.29  E-value=0.00041  Score=60.81  Aligned_cols=111  Identities=13%  Similarity=0.120  Sum_probs=62.5

Q ss_pred             HHHHHHhcC-CCCceEEEEEccCCccHHHHHHHHHccCCCCCcee--eEEEEEcCCCCCHHHHHHHHHHHhCCCCCcccc
Q 038944          167 ELLDLLIEG-PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD--CHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEI  243 (334)
Q Consensus       167 ~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~  243 (334)
                      .....+..+ +.....+.|+|..|+|||.|.+.+++.  ..+..+  .++++      +..++...+...+....     
T Consensus        21 ~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~--~~~~~~~~~v~y~------~~~~f~~~~~~~~~~~~-----   87 (219)
T PF00308_consen   21 AAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANE--AQKQHPGKRVVYL------SAEEFIREFADALRDGE-----   87 (219)
T ss_dssp             HHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHH--HHHHCTTS-EEEE------EHHHHHHHHHHHHHTTS-----
T ss_pred             HHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHH--HHhccccccceee------cHHHHHHHHHHHHHccc-----
Confidence            344444443 334566899999999999999999983  322211  23444      45566666665554421     


Q ss_pred             chhhHHHHHHHHHHHcCCCeEEEEEeCCCCh---hHHHHHHhhCCC--CCCCeEEEEecCC
Q 038944          244 MDKNYEMKKIILHEYLMTKRYLNVIDDVWNI---EVCDIIREILPD--NQNRSRVLITLTE  299 (334)
Q Consensus       244 ~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~---~~w~~l~~~l~~--~~~gsrIivTTr~  299 (334)
                              ...+.+.+. .-=+|+|||+...   ..|......+-+  ...|.+||+|+..
T Consensus        88 --------~~~~~~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~  139 (219)
T PF00308_consen   88 --------IEEFKDRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDR  139 (219)
T ss_dssp             --------HHHHHHHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS
T ss_pred             --------chhhhhhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCC
Confidence                    112333333 2347899999643   334333222211  1346789999853

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.

>TIGR00763 lon ATP-dependent protease La

Probab=97.29  E-value=0.0021  Score=66.78  Aligned_cols=53  Identities=19%  Similarity=0.343  Sum_probs=41.0

Q ss_pred             CCCeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          155 SRDTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      ..+++|.++.++.+.+++..    ...+.+++.++|++|+|||++|+.+.+  ....+|
T Consensus       319 ~~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~--~l~~~~  375 (775)
T TIGR00763       319 DEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAK--ALNRKF  375 (775)
T ss_pred             hhhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHH--HhcCCe
Confidence            44588999999999987752    223345899999999999999999998  444444

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.27  E-value=0.003  Score=59.83  Aligned_cols=45  Identities=18%  Similarity=0.203  Sum_probs=37.8

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+...+.+.+.+..+. -.+.+-++|++|+||||+|+.+.+
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~-~~~~~L~~G~~G~GKt~~a~~la~   61 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNH-LAQALLFCGPRGVGKTTCARILAR   61 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999987643 345788999999999999999876

>PHA00729 NTP-binding motif containing protein

Probab=97.27  E-value=0.0016  Score=56.99  Aligned_cols=23  Identities=22%  Similarity=0.281  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...|.|.|.+|+||||||..+.+
T Consensus        17 f~nIlItG~pGvGKT~LA~aLa~   39 (226)
T PHA00729         17 FVSAVIFGKQGSGKTTYALKVAR   39 (226)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHH
Confidence            45788999999999999999987

>PRK09183 transposase/IS protein; Provisional

Probab=97.26  E-value=0.00067  Score=61.06  Aligned_cols=22  Identities=23%  Similarity=0.226  Sum_probs=19.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+.|+|.+|+|||+||..+.+
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~  124 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGY  124 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHH
Confidence            4677999999999999999976

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.25  E-value=0.0023  Score=67.12  Aligned_cols=47  Identities=13%  Similarity=0.276  Sum_probs=37.7

Q ss_pred             CCCeeechhhHHHHHHHHhc-------CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIE-------GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++|.+..++.+...+..       .+.+..++.++|+.|+|||+||+.+.+
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~  620 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALAN  620 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            44688999998888888763       123345788999999999999999987

>PRK06526 transposase; Provisional

Probab=97.25  E-value=0.00046  Score=61.90  Aligned_cols=24  Identities=25%  Similarity=0.070  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-+.++|++|+|||+||..+.+.
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHH
Confidence            346899999999999999998763

>PRK06921 hypothetical protein; Provisional

Probab=97.25  E-value=0.0011  Score=59.86  Aligned_cols=37  Identities=16%  Similarity=0.075  Sum_probs=27.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCc-eeeEEEEEc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHY-FDCHAWVPG  217 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~v  217 (334)
                      ..-+.++|..|+|||+|+..+.+.  +... -..++|++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEEH
Confidence            467899999999999999999983  3332 234566653

>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=97.23  E-value=0.00025  Score=55.71  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=20.3

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ||.|.|++|+||||+|+.+.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999873

...

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0046  Score=61.84  Aligned_cols=152  Identities=12%  Similarity=0.021  Sum_probs=80.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH--
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF--  233 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~--  233 (334)
                      .+++|.+..++.|.+++..+. -...+-++|+.|+||||+|+.+.+...-.....       ..+|+.-..-+.|...  
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~-------~~pCg~C~~C~~i~~~~~   84 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR-INHAYLFSGPRGCGKTSSARILARSLNCAQGPT-------ATPCGVCESCVALAPNGP   84 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhccccCCC-------CCcccccHHHHHhhcccC
Confidence            468999999999999987653 234568899999999999998886321111000       0011111111111100  


Q ss_pred             -------hCCCCCccccchhhHHHHHHHHHHH-cCCCeEEEEEeCCC--ChhHHHHHHhhCCCCCCCeEEE-EecCChHH
Q 038944          234 -------LMPSSRLSEIMDKNYEMKKIILHEY-LMTKRYLNVIDDVW--NIEVCDIIREILPDNQNRSRVL-ITLTEIKM  302 (334)
Q Consensus       234 -------~~~~~~~~~~~~~~~~~l~~~l~~~-L~~kr~LlVlDdvw--~~~~w~~l~~~l~~~~~gsrIi-vTTr~~~v  302 (334)
                             +...... ...+..  ++.+.+... ..+++-++|+|++.  +....+.|+..+..-.....+| +||....+
T Consensus        85 ~~~dvieidaas~~-gvd~iR--el~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kl  161 (584)
T PRK14952         85 GSIDVVELDAASHG-GVDDTR--ELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKV  161 (584)
T ss_pred             CCceEEEecccccc-CHHHHH--HHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhh
Confidence                   0000000 011111  333333221 23566688999986  4468888888876544456555 45555555


Q ss_pred             Hhhcccc-CcccccccC
Q 038944          303 FTFLLET-LFSLLICVS  318 (334)
Q Consensus       303 a~~~~~~-~~~~l~~l~  318 (334)
                      -..+.+. ..+.+..++
T Consensus       162 l~TI~SRc~~~~F~~l~  178 (584)
T PRK14952        162 LPTIRSRTHHYPFRLLP  178 (584)
T ss_pred             HHHHHHhceEEEeeCCC
Confidence            5443332 334444443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.22  E-value=0.0012  Score=64.24  Aligned_cols=120  Identities=14%  Similarity=0.140  Sum_probs=61.5

Q ss_pred             eeechhh--HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee--eEEEEEcCCCCCHHHHHHHHHHH
Q 038944          158 TVGLDDR--MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD--CHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       158 ~vGr~~~--~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      ++|....  ......+....+....-+.|+|.+|+|||+|++.+.+.  +...+.  ...+++      ...+...+...
T Consensus       125 v~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~v~yi~------~~~~~~~~~~~  196 (450)
T PRK00149        125 VVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNY--ILEKNPNAKVVYVT------SEKFTNDFVNA  196 (450)
T ss_pred             ccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEEE------HHHHHHHHHHH
Confidence            4564433  22333333332333456899999999999999999984  333332  234443      33445555554


Q ss_pred             hCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh---hHH-HHHHhhCCC-CCCCeEEEEecCC
Q 038944          234 LMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI---EVC-DIIREILPD-NQNRSRVLITLTE  299 (334)
Q Consensus       234 ~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~---~~w-~~l~~~l~~-~~~gsrIivTTr~  299 (334)
                      +....       ..  .+..    .++ +--+|+|||+...   ..+ +.+...|.. ...|..||+||..
T Consensus       197 ~~~~~-------~~--~~~~----~~~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~  253 (450)
T PRK00149        197 LRNNT-------ME--EFKE----KYR-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDR  253 (450)
T ss_pred             HHcCc-------HH--HHHH----HHh-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCC
Confidence            43211       01  2322    332 2348999999532   111 223322211 1234557777764

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.22  E-value=0.0012  Score=64.14  Aligned_cols=102  Identities=16%  Similarity=0.239  Sum_probs=57.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCce--eeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF--DCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIIL  255 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l  255 (334)
                      ...-+.|+|..|+|||+|++.+.+.  +....  ...+++      +..+++..+...+....           .....+
T Consensus       140 ~~npl~i~G~~G~GKTHLl~Ai~~~--l~~~~~~~~v~yv------~~~~f~~~~~~~l~~~~-----------~~~~~~  200 (450)
T PRK14087        140 SYNPLFIYGESGMGKTHLLKAAKNY--IESNFSDLKVSYM------SGDEFARKAVDILQKTH-----------KEIEQF  200 (450)
T ss_pred             ccCceEEECCCCCcHHHHHHHHHHH--HHHhCCCCeEEEE------EHHHHHHHHHHHHHHhh-----------hHHHHH
Confidence            3456899999999999999999883  22111  122344      34567777766654311           112233


Q ss_pred             HHHcCCCeEEEEEeCCCCh---hHH-HHHHhhCCC-CCCCeEEEEecCC
Q 038944          256 HEYLMTKRYLNVIDDVWNI---EVC-DIIREILPD-NQNRSRVLITLTE  299 (334)
Q Consensus       256 ~~~L~~kr~LlVlDdvw~~---~~w-~~l~~~l~~-~~~gsrIivTTr~  299 (334)
                      .+.+. +.-+|+|||+-..   ..| +.+...+.. ...|..||+|+..
T Consensus       201 ~~~~~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~  248 (450)
T PRK14087        201 KNEIC-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDK  248 (450)
T ss_pred             HHHhc-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCC
Confidence            34343 3348899999532   222 233333321 1235568888654

>PRK06620 hypothetical protein; Validated

Probab=97.21  E-value=0.00072  Score=59.07  Aligned_cols=23  Identities=13%  Similarity=-0.047  Sum_probs=20.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+.|+|++|+|||+|++.+.+.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhc
Confidence            56899999999999999998874

>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=97.21  E-value=0.00097  Score=53.87  Aligned_cols=21  Identities=14%  Similarity=0.284  Sum_probs=19.5

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ||.++|++|+||||+|+.+..
T Consensus         1 lii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            678999999999999999986

...

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.21  E-value=0.0091  Score=50.84  Aligned_cols=40  Identities=10%  Similarity=0.163  Sum_probs=28.0

Q ss_pred             CCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          261 TKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       261 ~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      +.+-++|+|++..  .+.++.+...+......+.+|++|++.
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~  136 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSP  136 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            5667899999854  456788888876655566677766543

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.20  E-value=0.0015  Score=57.44  Aligned_cols=97  Identities=11%  Similarity=-0.004  Sum_probs=54.8

Q ss_pred             HHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH----hCCCCCccccchh
Q 038944          171 LLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF----LMPSSRLSEIMDK  246 (334)
Q Consensus       171 ~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~----~~~~~~~~~~~~~  246 (334)
                      +|..+=+.-.++.|+|.+|+|||+++.++....  ...-..++|++.. .++...+. ++...    +.....-....+.
T Consensus        15 ~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~--~~~~~~v~yi~~e-~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~   90 (225)
T PRK09361         15 LLGGGFERGTITQIYGPPGSGKTNICLQLAVEA--AKNGKKVIYIDTE-GLSPERFK-QIAGEDFEELLSNIIIFEPSSF   90 (225)
T ss_pred             HhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHH--HHCCCeEEEEECC-CCCHHHHH-HHHhhChHhHhhCeEEEeCCCH
Confidence            333333456799999999999999998887632  1223567888876 66665543 23322    1000000001111


Q ss_pred             -hHHHHHHHHHHHcCCCeEEEEEeCC
Q 038944          247 -NYEMKKIILHEYLMTKRYLNVIDDV  271 (334)
Q Consensus       247 -~~~~l~~~l~~~L~~kr~LlVlDdv  271 (334)
                       .+......+...+..+--++|+|.+
T Consensus        91 ~~~~~~i~~~~~~~~~~~~lvVIDsi  116 (225)
T PRK09361         91 EEQSEAIRKAEKLAKENVGLIVLDSA  116 (225)
T ss_pred             HHHHHHHHHHHHHHHhcccEEEEeCc
Confidence             1113444455555466679999998

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.19  E-value=0.0023  Score=53.91  Aligned_cols=36  Identities=19%  Similarity=0.216  Sum_probs=27.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEE
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWV  215 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv  215 (334)
                      +..+|.+.|+.|+||||+|+.+++  ....++....++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~--~l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYE--RLKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH--HHHHcCCcEEEE
Confidence            456999999999999999999998  444444444444

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.18  E-value=0.0025  Score=56.27  Aligned_cols=95  Identities=9%  Similarity=0.058  Sum_probs=57.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCc----eeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc-------ccch
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY----FDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS-------EIMD  245 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~-------~~~~  245 (334)
                      +.-.++.|+|.+|+|||+|+.++.-.......    ...++|++....++..++.+ +++..+......       ...+
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~-~~~~~~~~~~~~~~~i~~~~~~~   95 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQ-IAERFGLDPEEVLDNIYVARAYN   95 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHH-HHHHhccChHhHhcCEEEEecCC
Confidence            45679999999999999999988643222221    35788999888887665543 334433221100       0011


Q ss_pred             -hhHHHHHHHHHHHc-CC-CeEEEEEeCCC
Q 038944          246 -KNYEMKKIILHEYL-MT-KRYLNVIDDVW  272 (334)
Q Consensus       246 -~~~~~l~~~l~~~L-~~-kr~LlVlDdvw  272 (334)
                       ..+..+...+.+.+ +. +--|||+|.+.
T Consensus        96 ~~~l~~~l~~l~~~l~~~~~~~liVIDSis  125 (235)
T cd01123          96 SDHQLQLLEELEAILIESSRIKLVIVDSVT  125 (235)
T ss_pred             HHHHHHHHHHHHHHHhhcCCeeEEEEeCcH
Confidence             11124445555555 33 66799999995

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 .

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.18  E-value=0.0048  Score=61.92  Aligned_cols=47  Identities=15%  Similarity=0.166  Sum_probs=38.5

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|.+..++.|.+++..+. -..-+-++|+.|+||||+|+.+.+
T Consensus        22 ~f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk   68 (598)
T PRK09111         22 TFDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILAR   68 (598)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            34568999999999999887653 234677899999999999999976

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.17  E-value=0.012  Score=57.89  Aligned_cols=45  Identities=11%  Similarity=0.082  Sum_probs=36.6

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+.-+..|.+++..+. -....-++|+.|+||||+|+.+..
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk   60 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAK   60 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468899999999999887653 234566799999999999998876

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.17  E-value=0.0023  Score=67.06  Aligned_cols=45  Identities=16%  Similarity=0.279  Sum_probs=37.6

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++||+.+++++++.|.....+  -+-++|.+|+|||++|+.+...
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~~~--n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRTKN--NPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCCcC--ceEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999999876532  3458999999999999988873

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

Probab=97.16  E-value=0.0024  Score=63.63  Aligned_cols=104  Identities=19%  Similarity=0.181  Sum_probs=66.5

Q ss_pred             CCCCCeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLD  228 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~  228 (334)
                      .-+.+-+|+++-+++|++++.-    ++.+-+++..+|++|+|||.+|+.|..  .....|-.   ++|+.-.|+.+|  
T Consensus       408 iLdeDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~--ALnRkFfR---fSvGG~tDvAeI--  480 (906)
T KOG2004|consen  408 ILDEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIAR--ALNRKFFR---FSVGGMTDVAEI--  480 (906)
T ss_pred             hhcccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHH--HhCCceEE---EeccccccHHhh--
Confidence            4455668999999999999864    345678999999999999999999998  55555522   344544444332  


Q ss_pred             HHHHHhCCCCCc-cccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 038944          229 IVIKFLMPSSRL-SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       229 ~il~~~~~~~~~-~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~  273 (334)
                            .+.... .+.|.-   .+...|+ ..+...-|+.||.|..
T Consensus       481 ------kGHRRTYVGAMPG---kiIq~LK-~v~t~NPliLiDEvDK  516 (906)
T KOG2004|consen  481 ------KGHRRTYVGAMPG---KIIQCLK-KVKTENPLILIDEVDK  516 (906)
T ss_pred             ------cccceeeeccCCh---HHHHHHH-hhCCCCceEEeehhhh
Confidence                  121110 012221   2333332 3355667889999864

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.15  E-value=0.0012  Score=64.03  Aligned_cols=99  Identities=8%  Similarity=0.096  Sum_probs=53.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      ..-+.|+|..|+|||+|++.+.+.  +.......++++      ...+...+...+...            . ...++..
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~--l~~~~~~v~yi~------~~~f~~~~~~~l~~~------------~-~~~f~~~  199 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHA--LRESGGKILYVR------SELFTEHLVSAIRSG------------E-MQRFRQF  199 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHH--HHHcCCCEEEee------HHHHHHHHHHHHhcc------------h-HHHHHHH
Confidence            456889999999999999999984  222212234443      344555555544321            1 1123333


Q ss_pred             cCCCeEEEEEeCCCChh---H-HHHHHhhCCC-CCCCeEEEEecCC
Q 038944          259 LMTKRYLNVIDDVWNIE---V-CDIIREILPD-NQNRSRVLITLTE  299 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~~---~-w~~l~~~l~~-~~~gsrIivTTr~  299 (334)
                      +. +.-+|++||+-...   . -+.+...+.. ...|..||+||..
T Consensus       200 ~~-~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~  244 (445)
T PRK12422        200 YR-NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTC  244 (445)
T ss_pred             cc-cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCC
Confidence            33 33488899984321   1 1222222210 1135568888754

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

Probab=97.15  E-value=0.0023  Score=63.89  Aligned_cols=55  Identities=16%  Similarity=0.277  Sum_probs=45.1

Q ss_pred             CCCCCeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .-+.+-+|.++.+++|++.|.-    +.-.-+++..||++|+|||.|++.|.+  .....|
T Consensus       320 iLd~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~--al~Rkf  378 (782)
T COG0466         320 ILDKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAK--ALGRKF  378 (782)
T ss_pred             HhcccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHH--HhCCCE
Confidence            4455668999999999999963    233457999999999999999999998  666666

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.15  E-value=0.0013  Score=60.59  Aligned_cols=118  Identities=12%  Similarity=0.077  Sum_probs=65.4

Q ss_pred             echhhHHHHHHHHhcCC--CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCC
Q 038944          160 GLDDRMEELLDLLIEGP--PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPS  237 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~~--~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~  237 (334)
                      ++........+++..-.  ...+-+.++|..|+|||.||..+.+... ...+ .+.++++      ..++.++-......
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~-~v~~~~~------~~l~~~lk~~~~~~  206 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELA-KKGV-SSTLLHF------PEFIRELKNSISDG  206 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHH-HcCC-CEEEEEH------HHHHHHHHHHHhcC
Confidence            34444445555655321  2346789999999999999999998432 2223 3455544      35666665544221


Q ss_pred             CCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--hHHH--HHHhhC-CCC-CCCeEEEEecCC
Q 038944          238 SRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI--EVCD--IIREIL-PDN-QNRSRVLITLTE  299 (334)
Q Consensus       238 ~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~~w~--~l~~~l-~~~-~~gsrIivTTr~  299 (334)
                                  .+...+.. + .+-=||||||+-.+  ..|.  .+...+ ... ..+-..|+||-.
T Consensus       207 ------------~~~~~l~~-l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        207 ------------SVKEKIDA-V-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             ------------cHHHHHHH-h-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence                        11122222 2 24569999999643  4564  344433 221 134447777764

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

Probab=97.14  E-value=0.0022  Score=57.98  Aligned_cols=148  Identities=12%  Similarity=0.131  Sum_probs=84.8

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEE-EEcCCCCCHHHHHHHHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAW-VPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~w-v~vs~~~~~~~il~~il~  232 (334)
                      .-.+++|.+..+.-|.+.+..  ...++.-.+|++|.|||+-|......---.+.|.|++- .++|..-... +-+.   
T Consensus        34 t~de~~gQe~vV~~L~~a~~~--~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGis-vvr~---  107 (346)
T KOG0989|consen   34 TFDELAGQEHVVQVLKNALLR--RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGIS-VVRE---  107 (346)
T ss_pred             cHHhhcchHHHHHHHHHHHhh--cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhccccccccc-chhh---
Confidence            345688999889999888887  34778899999999999988777653222456777653 3444433211 0000   


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHc--CCCeE-EEEEeCCCC--hhHHHHHHhhCCCCCCCeEE-EEecCChHHHhhc
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRY-LNVIDDVWN--IEVCDIIREILPDNQNRSRV-LITLTEIKMFTFL  306 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~-LlVlDdvw~--~~~w~~l~~~l~~~~~gsrI-ivTTr~~~va~~~  306 (334)
                               ...+..  .+........  ..+.| .+|||++..  .+.|..++..+-+-...+|. +||+.-..+....
T Consensus       108 ---------Kik~fa--kl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi  176 (346)
T KOG0989|consen  108 ---------KIKNFA--KLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPL  176 (346)
T ss_pred             ---------hhcCHH--HHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHH
Confidence                     000000  1111111111  12333 677999875  48999999888765556664 4555444433333


Q ss_pred             ccc-CcccccccC
Q 038944          307 LET-LFSLLICVS  318 (334)
Q Consensus       307 ~~~-~~~~l~~l~  318 (334)
                      .+. ..+++..|.
T Consensus       177 ~SRC~KfrFk~L~  189 (346)
T KOG0989|consen  177 VSRCQKFRFKKLK  189 (346)
T ss_pred             HhhHHHhcCCCcc
Confidence            222 234444555

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

Probab=97.14  E-value=0.0028  Score=65.51  Aligned_cols=45  Identities=18%  Similarity=0.268  Sum_probs=37.4

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++||+++.+++++.|.....  .-+-++|.+|+|||++|+.+...
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~--~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKK--NNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCC--CceEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999977542  23468999999999999999873

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.13  E-value=0.0017  Score=65.27  Aligned_cols=50  Identities=12%  Similarity=0.104  Sum_probs=40.7

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCC---CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGP---PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~---~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-.+++|.++.++++..||....   ..-.++.++|++|+||||+++.+.+.
T Consensus        81 ~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        81 ETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            345678999999999999987532   23467999999999999999999973

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

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.12  E-value=0.0019  Score=55.96  Aligned_cols=92  Identities=10%  Similarity=0.021  Sum_probs=54.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCC-Ccc---ccch-hhHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSS-RLS---EIMD-KNYEMK  251 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~-~~~---~~~~-~~~~~l  251 (334)
                      +.-.++-|+|.+|+|||+++..+...  .......++|++... ++...+.+. .+...... ...   ...+ .++...
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~   85 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGVA   85 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHHH
Confidence            45689999999999999999887653  222345788998865 776665543 33221000 000   0011 111134


Q ss_pred             HHHHHHHcCC-CeEEEEEeCCC
Q 038944          252 KIILHEYLMT-KRYLNVIDDVW  272 (334)
Q Consensus       252 ~~~l~~~L~~-kr~LlVlDdvw  272 (334)
                      ...+.+.+.. +--+||+|.+-
T Consensus        86 ~~~l~~~~~~~~~~lvVIDSis  107 (209)
T TIGR02237        86 IQKTSKFIDRDSASLVVVDSFT  107 (209)
T ss_pred             HHHHHHHHhhcCccEEEEeCcH
Confidence            5555555543 45589999984

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

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

Probab=97.11  E-value=0.0016  Score=58.64  Aligned_cols=101  Identities=11%  Similarity=0.161  Sum_probs=59.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh----hH--H
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK----NY--E  249 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~----~~--~  249 (334)
                      .-++|+|..|+|||||++.+++  .++.+|. .++++.+.+.. .+.++..++.+.-..+....  ...+.    .+  -
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~--~i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~  147 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELIN--NIAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVA  147 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHH--HHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            3589999999999999999999  4444453 45667777654 45566666654321110000  00000    00  0


Q ss_pred             HHHHHHHHHc--C-CCeEEEEEeCCCCh-hHHHHHHh
Q 038944          250 MKKIILHEYL--M-TKRYLNVIDDVWNI-EVCDIIRE  282 (334)
Q Consensus       250 ~l~~~l~~~L--~-~kr~LlVlDdvw~~-~~w~~l~~  282 (334)
                      ...-.+-+++  + |+..|+++||+-.- ..+.++..
T Consensus       148 ~~a~~~AEyfr~~~g~~Vl~~~Dsltr~a~A~reis~  184 (274)
T cd01133         148 LTGLTMAEYFRDEEGQDVLLFIDNIFRFTQAGSEVSA  184 (274)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEeChhHHHHHHHHHHH
Confidence            2233445555  3 89999999999432 44444443

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.10  E-value=0.00054  Score=63.92  Aligned_cols=47  Identities=13%  Similarity=0.333  Sum_probs=40.5

Q ss_pred             CCeeechhhHHHHHHHHhcC----CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG----PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.++.++++++++...    +...+++.++|++|+||||||+.+.+.
T Consensus        51 ~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       51 HDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             hhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            36999999999999999752    335689999999999999999999874

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

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.10  E-value=0.0017  Score=67.97  Aligned_cols=45  Identities=16%  Similarity=0.298  Sum_probs=37.6

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++||+++.++++++|.....+  -+.++|.+|+|||++|+.+...
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~--n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKN--NPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccC--CeEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999999876432  3459999999999999988763

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.08  E-value=0.0017  Score=56.03  Aligned_cols=112  Identities=11%  Similarity=0.058  Sum_probs=62.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcC-CCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGT-YPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      .++.|+|+.|+||||++..+...  ...+...++++--. .++.... ...++.+-..      ..+..  .....+...
T Consensus         2 GlilI~GptGSGKTTll~~ll~~--~~~~~~~~i~t~e~~~E~~~~~-~~~~i~q~~v------g~~~~--~~~~~i~~a   70 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY--INKNKTHHILTIEDPIEFVHES-KRSLINQREV------GLDTL--SFENALKAA   70 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--hhhcCCcEEEEEcCCccccccC-ccceeeeccc------CCCcc--CHHHHHHHH
Confidence            47899999999999999987763  32233334433211 1111000 0011111000      01112  445566666


Q ss_pred             cCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          259 LMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      |....=++++|++.+.+.+..+....   ..|-.++.|+...+++..
T Consensus        71 Lr~~pd~ii~gEird~e~~~~~l~~a---~~G~~v~~t~Ha~~~~~~  114 (198)
T cd01131          71 LRQDPDVILVGEMRDLETIRLALTAA---ETGHLVMSTLHTNSAAKT  114 (198)
T ss_pred             hcCCcCEEEEcCCCCHHHHHHHHHHH---HcCCEEEEEecCCcHHHH
Confidence            76556699999998887666544443   235558888887776554

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.

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

Probab=97.06  E-value=0.0018  Score=61.37  Aligned_cols=120  Identities=18%  Similarity=0.086  Sum_probs=66.2

Q ss_pred             CCeeechhhHHHHH-HHHhc-CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          156 RDTVGLDDRMEELL-DLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       156 ~~~vGr~~~~~~l~-~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      +-++|-......-. ..+.. .......+.|+|..|.|||.|++.+.+  ....+......++++.    .......+..
T Consensus        88 nFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign--~~~~~~~~a~v~y~~s----e~f~~~~v~a  161 (408)
T COG0593          88 NFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGN--EALANGPNARVVYLTS----EDFTNDFVKA  161 (408)
T ss_pred             heeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHH--HHHhhCCCceEEeccH----HHHHHHHHHH
Confidence            33556554443322 22222 223578999999999999999999999  4444554333444432    3333333333


Q ss_pred             hCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecC
Q 038944          234 LMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLT  298 (334)
Q Consensus       234 ~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr  298 (334)
                      +..             .-+..+++..  .-=++++||++--       +.+..+...+..  .|..||+|++
T Consensus       162 ~~~-------------~~~~~Fk~~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~--~~kqIvltsd  216 (408)
T COG0593         162 LRD-------------NEMEKFKEKY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLE--NGKQIVLTSD  216 (408)
T ss_pred             HHh-------------hhHHHHHHhh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHh--cCCEEEEEcC
Confidence            222             2233444544  3348899999642       222233333333  3448999985

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.06  E-value=0.0021  Score=64.09  Aligned_cols=99  Identities=10%  Similarity=0.159  Sum_probs=53.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCce--eeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYF--DCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      ...+.|+|..|+|||.|++.+.+.  ....+  ....++      +..+++.++...+...             ....+.
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~~--a~~~~~g~~V~Yi------taeef~~el~~al~~~-------------~~~~f~  372 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGHY--ARRLYPGTRVRYV------SSEEFTNEFINSIRDG-------------KGDSFR  372 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEe------eHHHHHHHHHHHHHhc-------------cHHHHH
Confidence            445899999999999999999984  32221  123444      3445555555443321             111222


Q ss_pred             HHcCCCeEEEEEeCCCCh---hHHHH-HHhhCCC-CCCCeEEEEecCC
Q 038944          257 EYLMTKRYLNVIDDVWNI---EVCDI-IREILPD-NQNRSRVLITLTE  299 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~---~~w~~-l~~~l~~-~~~gsrIivTTr~  299 (334)
                      +.+.. -=+|+|||+...   +.|.. +...|.. ..+|..|||||..
T Consensus       373 ~~y~~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~  419 (617)
T PRK14086        373 RRYRE-MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDR  419 (617)
T ss_pred             HHhhc-CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCC
Confidence            33322 247899999643   23322 2222211 1235568888875

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.05  E-value=0.0062  Score=61.32  Aligned_cols=46  Identities=11%  Similarity=-0.044  Sum_probs=36.5

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|.+.-+..|.+++..+. -..-+-++|+.|+||||+|+.+.+
T Consensus        15 f~eivGQe~i~~~L~~~i~~~r-i~ha~Lf~Gp~GvGKttlA~~lAk   60 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMDR-VGHGYIFSGLRGVGKTTAARVFAK   60 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHH
Confidence            3468899988888888886543 234577999999999999988876

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

Probab=97.04  E-value=0.016  Score=60.23  Aligned_cols=55  Identities=13%  Similarity=0.235  Sum_probs=43.3

Q ss_pred             CCCCCeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .-+.+.+|.++.+++|+++|..    +..+-.++.++|++|+||||+++.+..  .....|
T Consensus       319 ~l~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~--~l~~~~  377 (784)
T PRK10787        319 ILDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAK--ATGRKY  377 (784)
T ss_pred             HhhhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHH--HhCCCE
Confidence            4455689999999999999873    223456899999999999999999997  444444

>PRK13695 putative NTPase; Provisional

Probab=97.03  E-value=0.00069  Score=57.06  Aligned_cols=34  Identities=9%  Similarity=0.040  Sum_probs=24.2

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEE
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWV  215 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv  215 (334)
                      .++|+|.+|+|||||++.+++.... ..|....|+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~-~G~~~~g~~   35 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKE-EGYKVGGFY   35 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEE
Confidence            4789999999999999998874221 224444454

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=97.02  E-value=0.0052  Score=51.95  Aligned_cols=116  Identities=11%  Similarity=0.062  Sum_probs=61.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccC-CC--C---Cceee--EEEEEcCCCCCHHHHHHHHHHHhCCCCC--c--cccchh
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSS-YV--K---HYFDC--HAWVPGTYPYDADQMLDIVIKFLMPSSR--L--SEIMDK  246 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~-~~--~---~~F~~--~~wv~vs~~~~~~~il~~il~~~~~~~~--~--~~~~~~  246 (334)
                      -.+++|+|..|+|||||.+.+..+. .+  .   ..|..  ..|+  .+        .+.++.++....  .  ....+.
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~--~q--------~~~l~~~~L~~~~~~~~~~~LSg   90 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFI--DQ--------LQFLIDVGLGYLTLGQKLSTLSG   90 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEE--hH--------HHHHHHcCCCccccCCCcCcCCH
Confidence            4589999999999999999986421 11  1   11111  2232  22        355666654321  1  011111


Q ss_pred             hHHHHHHHHHHHcCCC--eEEEEEeCCCC---hhHHHHHHhhCCC-CCCCeEEEEecCChHHHhh
Q 038944          247 NYEMKKIILHEYLMTK--RYLNVIDDVWN---IEVCDIIREILPD-NQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       247 ~~~~l~~~l~~~L~~k--r~LlVlDdvw~---~~~w~~l~~~l~~-~~~gsrIivTTr~~~va~~  305 (334)
                      ...+... +-..+-.+  .-+++||+.-.   ....+.+...+.. ...|..||++|.+.+.+..
T Consensus        91 Gq~qrl~-laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~~  154 (176)
T cd03238          91 GELQRVK-LASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLSS  154 (176)
T ss_pred             HHHHHHH-HHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHh
Confidence            1012333 33444445  56788898743   3333444333322 1246668899998887653

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.02  E-value=0.0061  Score=54.94  Aligned_cols=54  Identities=15%  Similarity=0.149  Sum_probs=33.5

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHH
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQML  227 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il  227 (334)
                      ++++..++..+    .-+-+.|.+|+|||+||+.+..  .....|   ..++.+...+..+++
T Consensus        11 ~~~~l~~l~~g----~~vLL~G~~GtGKT~lA~~la~--~lg~~~---~~i~~~~~~~~~dll   64 (262)
T TIGR02640        11 TSRALRYLKSG----YPVHLRGPAGTGKTTLAMHVAR--KRDRPV---MLINGDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHhcC----CeEEEEcCCCCCHHHHHHHHHH--HhCCCE---EEEeCCccCCHHHHh
Confidence            34445555443    2455899999999999999987  333333   345555555554443

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).

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

Probab=97.02  E-value=0.0017  Score=58.25  Aligned_cols=75  Identities=21%  Similarity=0.138  Sum_probs=46.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  257 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~  257 (334)
                      +..-+.++|.+|+|||.||..+-+..- +..+. +.++      +..+++.++.......            .....|.+
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~s-v~f~------~~~el~~~Lk~~~~~~------------~~~~~l~~  163 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KAGIS-VLFI------TAPDLLSKLKAAFDEG------------RLEEKLLR  163 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCe-EEEE------EHHHHHHHHHHHHhcC------------chHHHHHH
Confidence            456789999999999999999998533 22233 3444      3456667766555431            12222222


Q ss_pred             HcCCCeEEEEEeCCCC
Q 038944          258 YLMTKRYLNVIDDVWN  273 (334)
Q Consensus       258 ~L~~kr~LlVlDdvw~  273 (334)
                      .+ .+-=||||||+-.
T Consensus       164 ~l-~~~dlLIiDDlG~  178 (254)
T COG1484         164 EL-KKVDLLIIDDIGY  178 (254)
T ss_pred             Hh-hcCCEEEEecccC
Confidence            22 1234999999954

>PRK06696 uridine kinase; Validated

Probab=97.01  E-value=0.001  Score=58.51  Aligned_cols=41  Identities=20%  Similarity=0.176  Sum_probs=33.6

Q ss_pred             chhhHHHHHHHHhc-CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          161 LDDRMEELLDLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       161 r~~~~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      |..-+++|.+.+.. ......+|+|.|.+|+||||||+.+..
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~   44 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAE   44 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            55667777777765 345678999999999999999999987

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.98  E-value=0.0044  Score=50.67  Aligned_cols=40  Identities=10%  Similarity=0.072  Sum_probs=28.6

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCC
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYD  222 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  222 (334)
                      ++.|+|.+|+||||++..+...  ...+-.+.+|+.....+.
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECCcchH
Confidence            4679999999999999999773  222334567777665543

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.

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

Probab=96.98  E-value=0.0046  Score=63.74  Aligned_cols=48  Identities=13%  Similarity=0.165  Sum_probs=39.0

Q ss_pred             CCCeeechhhHHHHHHHHhc-------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE-------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|.+..++.|.+.+..       .+.+...+.++|++|+|||+||+.+...
T Consensus       457 ~~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~  511 (758)
T PRK11034        457 KMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_pred             cceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHH
Confidence            44689999999999988873       1234567899999999999999999873

>CHL00176 ftsH cell division protein; Validated

Probab=96.98  E-value=0.0023  Score=64.74  Aligned_cols=49  Identities=18%  Similarity=0.255  Sum_probs=34.9

Q ss_pred             CCCCeeechhhHHHHHHHH---hcCC-------CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLL---IEGP-------PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L---~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.++.|.++.++++.+.+   ....       ...+-+.++|++|+|||+||+.+.+.
T Consensus       181 ~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e  239 (638)
T CHL00176        181 TFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE  239 (638)
T ss_pred             CHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3456888877776665543   3221       22456889999999999999999884

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.98  E-value=0.012  Score=59.18  Aligned_cols=46  Identities=15%  Similarity=0.135  Sum_probs=37.2

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|.+.-++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 f~~iiGq~~v~~~L~~~i~~~~-~~hayLf~Gp~G~GKtt~A~~lak   60 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNAIDTGR-VAHAFLFTGARGVGKTSTARILAK   60 (576)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3468999999999999887653 234567899999999999998876

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

Probab=96.98  E-value=0.00037  Score=59.06  Aligned_cols=24  Identities=17%  Similarity=0.137  Sum_probs=20.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.-+.++|..|+|||.||..+.+.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~   70 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANE   70 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHH
Confidence            356999999999999999999873

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.

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

Probab=96.97  E-value=0.0081  Score=52.61  Aligned_cols=94  Identities=12%  Similarity=0.057  Sum_probs=55.3

Q ss_pred             cCCCCceEEEEEccCCccHHHHHHHHHccCCCCCce------eeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc----c--
Q 038944          174 EGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF------DCHAWVPGTYPYDADQMLDIVIKFLMPSSRL----S--  241 (334)
Q Consensus       174 ~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F------~~~~wv~vs~~~~~~~il~~il~~~~~~~~~----~--  241 (334)
                      .+=+.-.++.|+|.+|+|||+|+..+.....  ..-      ..++|+.....++...+. .+.+........    .  
T Consensus        14 GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~--~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~   90 (226)
T cd01393          14 GGIPTGRITEIFGEFGSGKTQLCLQLAVEAQ--LPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYV   90 (226)
T ss_pred             CCCcCCcEEEEeCCCCCChhHHHHHHHHHhh--cccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEE
Confidence            3334567999999999999999988865321  122      456888888778776554 333333221110    0  


Q ss_pred             -ccchhhHHHHHHHHHHHc----CCCeEEEEEeCCC
Q 038944          242 -EIMDKNYEMKKIILHEYL----MTKRYLNVIDDVW  272 (334)
Q Consensus       242 -~~~~~~~~~l~~~l~~~L----~~kr~LlVlDdvw  272 (334)
                       ...+..  ++...+...+    ..+--|+|+|.+.
T Consensus        91 ~~~~~~~--~~~~~l~~~~~~~~~~~~~lvVIDsis  124 (226)
T cd01393          91 ARPYNGE--QQLEIVEELERIMSSGRVDLVVVDSVA  124 (226)
T ss_pred             EeCCCHH--HHHHHHHHHHHHhhcCCeeEEEEcCcc
Confidence             111222  4444444443    2345599999984

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.

>PRK07667 uridine kinase; Provisional

Probab=96.94  E-value=0.0013  Score=56.44  Aligned_cols=37  Identities=14%  Similarity=0.147  Sum_probs=31.5

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.+.+.+........+|+|-|.+|+||||+|+.+..
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4667777776666678999999999999999999987

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

Probab=96.94  E-value=0.0062  Score=62.14  Aligned_cols=117  Identities=16%  Similarity=0.288  Sum_probs=71.8

Q ss_pred             CCCeeechhhHHHHHHHHhc-------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce---eeEEEEEcCCCCCHH
Q 038944          155 SRDTVGLDDRMEELLDLLIE-------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF---DCHAWVPGTYPYDAD  224 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~~~~~  224 (334)
                      ...++|.+..+..+.+.+..       ++.+..+...+|+.|||||.||+.+...     -|   +.-+-+      |+.
T Consensus       490 ~~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~-----Lfg~e~aliR~------DMS  558 (786)
T COG0542         490 KKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA-----LFGDEQALIRI------DMS  558 (786)
T ss_pred             hcceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHH-----hcCCCccceee------chH
Confidence            44689999999999888763       2356778888999999999999988762     23   222222      333


Q ss_pred             HHHHH-HHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeE-EEEEeCCCC--hhHHHHHHhhCCCC
Q 038944          225 QMLDI-VIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRY-LNVIDDVWN--IEVCDIIREILPDN  287 (334)
Q Consensus       225 ~il~~-il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~-LlVlDdvw~--~~~w~~l~~~l~~~  287 (334)
                      +.... -.+.+-+..+.  -...+  + -..|-+.++.|.| +|.||+|..  ++.++.+...|.++
T Consensus       559 Ey~EkHsVSrLIGaPPG--YVGye--e-GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         559 EYMEKHSVSRLIGAPPG--YVGYE--E-GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             HHHHHHHHHHHhCCCCC--Cceec--c-ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCC
Confidence            33211 12223222221  11111  2 2344455666777 777899974  57888888888654

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.94  E-value=0.0044  Score=52.35  Aligned_cols=24  Identities=13%  Similarity=0.093  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||++.+..-
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            358999999999999999999864

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.94  E-value=0.0031  Score=66.06  Aligned_cols=45  Identities=18%  Similarity=0.337  Sum_probs=37.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++||+.++.++++.|.....+  -+-++|.+|+||||+|+.+...
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~~~--n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRRQN--NPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCCcC--ceeEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999876422  3459999999999999998873

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.93  E-value=0.016  Score=57.84  Aligned_cols=50  Identities=18%  Similarity=0.138  Sum_probs=40.2

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .....++|....+.++.+.+..-...-.-|.|+|..|+|||++|+.+++.
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHh
Confidence            44567999999999998888653323345679999999999999999985

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.91  E-value=0.021  Score=57.63  Aligned_cols=46  Identities=13%  Similarity=0.096  Sum_probs=37.2

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|.+...+.|..++..+. -...+-++|..|+||||+|+.+..
T Consensus        16 f~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk   61 (614)
T PRK14971         16 FESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAK   61 (614)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHH
Confidence            3468999999999999987653 234578999999999999988765

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

Probab=96.90  E-value=0.0044  Score=63.89  Aligned_cols=44  Identities=16%  Similarity=0.244  Sum_probs=36.8

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++||+++++++++.|.....  .-+-++|.+|+|||++|+.+..
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~--~n~LLvGppGvGKT~lae~la~  229 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRK--NNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCC--CCeEEECCCCCCHHHHHHHHHH
Confidence            4589999999999999987532  2235799999999999999886

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.86  E-value=0.0028  Score=62.53  Aligned_cols=48  Identities=21%  Similarity=0.322  Sum_probs=33.9

Q ss_pred             CCCeeechhhHHHHHHHHh---cC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLI---EG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++++.+++.   ..       ....+-+-++|++|+|||+||+.+.+.
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~  111 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE  111 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            3457888877766655443   21       122345788999999999999999984

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.

>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=96.84  E-value=0.0032  Score=54.34  Aligned_cols=52  Identities=17%  Similarity=0.106  Sum_probs=31.8

Q ss_pred             echhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEE
Q 038944          160 GLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWV  215 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv  215 (334)
                      .+..+-...++.|..    ..++.+.|++|.|||.||-...-+.-...+|+..+++
T Consensus         4 p~~~~Q~~~~~al~~----~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~   55 (205)
T PF02562_consen    4 PKNEEQKFALDALLN----NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIIT   55 (205)
T ss_dssp             --SHHHHHHHHHHHH-----SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE
T ss_pred             CCCHHHHHHHHHHHh----CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            345556667777773    4599999999999999997665432223556665555

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

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.83  E-value=0.016  Score=58.04  Aligned_cols=46  Identities=13%  Similarity=0.081  Sum_probs=36.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..+..|.+.+..+. -...+-++|+.|+||||+|+.+.+.
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r-i~ha~Lf~GPpG~GKTtiArilAk~   61 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR-VAPAYLFSGTRGVGKTTIARIFAKA   61 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHh
Confidence            457898888888888776542 2356778999999999999988873

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

Probab=96.82  E-value=0.0015  Score=58.47  Aligned_cols=47  Identities=21%  Similarity=0.273  Sum_probs=38.5

Q ss_pred             CCeeechhhHHHHHHHHhc---CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIE---GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.++-++++-=++..   .+..+.-+-++|++|.||||||..+.+.
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~E   75 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANE   75 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHH
Confidence            4689988888887666653   3456888999999999999999999993

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=96.82  E-value=0.022  Score=52.70  Aligned_cols=145  Identities=14%  Similarity=0.074  Sum_probs=86.9

Q ss_pred             hhhHHHHHHHHhcCC-CCceEEEEEccCCccHHHHHHHHHccCCCC--Cc---eeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          162 DDRMEELLDLLIEGP-PQLSVVVILDSIGLDKAAFAGEAYNSSYVK--HY---FDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       162 ~~~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~--~~---F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      +.-.+.|.+.+.+.+ ....+|+|.|.=|+||||+.+.+.+..+-.  ..   +..-+|-.-..+--...++..|..++.
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~~~~~~~~i~fn~w~~~~~~~~~~~~~~~l~~~l~   81 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELKEDNKEKYIFIYFNAWEYDGEDDLWASFLEELFDQLE   81 (325)
T ss_pred             hHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccceeeEEEccccCCCcchHHHHHHHHHHHHHH
Confidence            344567778887754 677899999999999999999998743322  11   233456554433334566666666554


Q ss_pred             CCCCcc---------------------------c-c--------------------------------ch--hhHHHHHH
Q 038944          236 PSSRLS---------------------------E-I--------------------------------MD--KNYEMKKI  253 (334)
Q Consensus       236 ~~~~~~---------------------------~-~--------------------------------~~--~~~~~l~~  253 (334)
                      ......                           . .                                ..  ...+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (325)
T PF07693_consen   82 KHFGSKKIKLYAKKKLKSLKIKFKIKINLSKAIPLALIGLPALILAVAIAKLKAELKNAFKSLEEKFLKKLKKEVEELIS  161 (325)
T ss_pred             HhcCccchhHHHhhhhhhhhceeeeeeecceeehHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHhhhhhHHHHHHHH
Confidence            321110                           0 0                                00  01112344


Q ss_pred             HHHHHc--CCCeEEEEEeCCCC--h----hHHHHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          254 ILHEYL--MTKRYLNVIDDVWN--I----EVCDIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       254 ~l~~~L--~~kr~LlVlDdvw~--~----~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      .+.+.|  .++|.++++||+..  +    +.|+.+...+..  ++..+|+..-.+.++.....
T Consensus       162 ~~~~~l~~~~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~--~~i~~Il~~D~~~l~~ai~~  222 (325)
T PF07693_consen  162 KIKKKLKESKKRIVIIIDDLDRCSPEEIVELLEAIKLLLDF--PNIIFILAFDPEILEKAIEK  222 (325)
T ss_pred             HHHHhhhcCCceEEEEEcchhcCCcHHHHHHHHHHHHhcCC--CCeEEEEEecHHHHHHHHHh
Confidence            555555  35899999999974  2    466666665533  56767766666666665544

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.82  E-value=0.0024  Score=66.99  Aligned_cols=45  Identities=16%  Similarity=0.280  Sum_probs=37.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++||+.++++++..|.....+  -+-++|.+|+|||++|..+...
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~--n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKN--NPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCC--ceEEEcCCCCCHHHHHHHHHHH
Confidence            45899999999999999876533  3347999999999999988773

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

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

Probab=96.81  E-value=0.0091  Score=52.28  Aligned_cols=105  Identities=14%  Similarity=0.103  Sum_probs=65.4

Q ss_pred             CCCCCeeechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~i  230 (334)
                      ++-..++|.+..++.|++--..  ...+..-+-.||..|.||+.|++.+.+  ......-.  -|.|++.          
T Consensus        57 i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~--e~~~~glr--LVEV~k~----------  122 (287)
T COG2607          57 IDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLN--EYADEGLR--LVEVDKE----------  122 (287)
T ss_pred             cCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHH--HHHhcCCe--EEEEcHH----------
Confidence            3445689999988888764332  223345678999999999999999998  33222222  2222221          


Q ss_pred             HHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCC---ChhHHHHHHhhCCC
Q 038944          231 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW---NIEVCDIIREILPD  286 (334)
Q Consensus       231 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw---~~~~w~~l~~~l~~  286 (334)
                                 +..+..  .+.+.|+.  ...||.|..||+-   ..+.++.+..+|..
T Consensus       123 -----------dl~~Lp--~l~~~Lr~--~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG  166 (287)
T COG2607         123 -----------DLATLP--DLVELLRA--RPEKFILFCDDLSFEEGDDAYKALKSALEG  166 (287)
T ss_pred             -----------HHhhHH--HHHHHHhc--CCceEEEEecCCCCCCCchHHHHHHHHhcC
Confidence                       111111  23333222  3579999999995   34689999988864

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.80  E-value=0.00097  Score=54.69  Aligned_cols=23  Identities=13%  Similarity=0.127  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..-|+|.||+|+|||||++.+.+
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e   27 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAE   27 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHH
Confidence            35689999999999999999997

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.79  E-value=0.012  Score=54.56  Aligned_cols=102  Identities=10%  Similarity=0.059  Sum_probs=60.7

Q ss_pred             HHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCc----eeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc----
Q 038944          170 DLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY----FDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS----  241 (334)
Q Consensus       170 ~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~----  241 (334)
                      ++|..+=+.-.++-|+|.+|+|||+|+.++.-.......    =...+|++.-..|++.++.+. ++.++......    
T Consensus        93 ~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~-~~~~g~~~~~~l~~i  171 (317)
T PRK04301         93 ELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQM-AEALGLDPDEVLDNI  171 (317)
T ss_pred             HHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHH-HHHcCCChHhhhccE
Confidence            344333345679999999999999999887653221111    136899999888988876544 44444321110    


Q ss_pred             ---cc-chhhHHHHHHHHHHHcCC--CeEEEEEeCCC
Q 038944          242 ---EI-MDKNYEMKKIILHEYLMT--KRYLNVIDDVW  272 (334)
Q Consensus       242 ---~~-~~~~~~~l~~~l~~~L~~--kr~LlVlDdvw  272 (334)
                         .. .......+...+...+..  +--|||+|-+-
T Consensus       172 ~~~~~~~~~~~~~~~~~l~~~i~~~~~~~lvVIDSis  208 (317)
T PRK04301        172 HVARAYNSDHQMLLAEKAEELIKEGENIKLVIVDSLT  208 (317)
T ss_pred             EEEeCCCHHHHHHHHHHHHHHHhccCceeEEEEECch
Confidence               00 001111345566666643  44499999984

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.78  E-value=0.0015  Score=64.26  Aligned_cols=45  Identities=13%  Similarity=0.320  Sum_probs=39.1

Q ss_pred             CeeechhhHHHHHHHHh----cCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDLLI----EGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~----~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +++|.++.+++|++.|.    .-+..-+++.++|++|+||||||+.+.+
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~  125 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKS  125 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHH
Confidence            58999999999999993    2234567999999999999999999987

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.78  E-value=0.0055  Score=63.43  Aligned_cols=48  Identities=19%  Similarity=0.189  Sum_probs=36.8

Q ss_pred             CCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -+++.|.+..++.+.+++...           -...+-+.++|.+|+||||||+.+.+.
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~  235 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE  235 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHH
Confidence            345789999999888776421           023456889999999999999999983

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.

>PTZ00301 uridine kinase; Provisional

Probab=96.70  E-value=0.0014  Score=57.07  Aligned_cols=24  Identities=17%  Similarity=0.227  Sum_probs=21.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++.+|+|.|.+|+||||||+.+.+
T Consensus         2 ~~~iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          2 PCTVIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             CCEEEEEECCCcCCHHHHHHHHHH
Confidence            357999999999999999998865

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

Probab=96.70  E-value=0.0028  Score=61.14  Aligned_cols=52  Identities=19%  Similarity=0.219  Sum_probs=38.4

Q ss_pred             CCeeechhhHHHHHHHHhc---C--------CCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          156 RDTVGLDDRMEELLDLLIE---G--------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~--------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .++.|.+..+++|.+.+.-   .        -...+-+.++|++|+|||++|+.+.+  .....|
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~--el~~~f  245 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVAN--ETSATF  245 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHH--hhCCCE
Confidence            3567888888888877642   1        12345677899999999999999999  444444

>cd01394 radB RadB

Probab=96.70  E-value=0.0092  Score=52.04  Aligned_cols=92  Identities=14%  Similarity=-0.048  Sum_probs=50.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC----CCCCccccchh-hHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM----PSSRLSEIMDK-NYEMK  251 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~----~~~~~~~~~~~-~~~~l  251 (334)
                      ..-.++.|.|.+|+|||||+.++...  ...+=...+|++....++  .-+++++....    .........+. ++...
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (218)
T cd01394          17 ERGTVTQVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTEGLSS--ERFRQIAGDRPERAASSIIVFEPMDFNEQGRA   92 (218)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCCCCH--HHHHHHHhHChHhhhcCEEEEeCCCHHHHHHH
Confidence            45679999999999999999888753  212223467777655554  33334443211    10000011111 11123


Q ss_pred             HHHHHHHcCCCeEEEEEeCCC
Q 038944          252 KIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       252 ~~~l~~~L~~kr~LlVlDdvw  272 (334)
                      ...+...+..+--++|+|-+-
T Consensus        93 ~~~~~~~~~~~~~lvvIDsi~  113 (218)
T cd01394          93 IQETETFADEKVDLVVVDSAT  113 (218)
T ss_pred             HHHHHHHHhcCCcEEEEechH
Confidence            344555555445689999984

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

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.70  E-value=0.034  Score=55.56  Aligned_cols=46  Identities=15%  Similarity=0.082  Sum_probs=38.3

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..+..|..++..+. -...+-++|+.|+||||+|+.+.+.
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~-i~hayLf~Gp~G~GKTt~Ar~lAk~   61 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK-IANAYIFSGPRGVGKTSSARAFARC   61 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999997653 3456789999999999999998873

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.69  E-value=0.038  Score=54.78  Aligned_cols=49  Identities=20%  Similarity=0.201  Sum_probs=40.3

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....++|....++++.+.+..-...-.-|.|+|..|+|||++|+.+++.
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            3456899999999998888764334456889999999999999999985

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.69  E-value=0.012  Score=54.52  Aligned_cols=101  Identities=9%  Similarity=0.042  Sum_probs=59.5

Q ss_pred             HHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCC----CceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc-----
Q 038944          171 LLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVK----HYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS-----  241 (334)
Q Consensus       171 ~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~-----  241 (334)
                      +|..+=+.-.++-|+|.+|+|||+|+..+.-.....    ..=...+|++.-..|++.++.+ +++.++......     
T Consensus        88 lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~d~~~~l~~i~  166 (313)
T TIGR02238        88 ILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGVDPDAVLDNIL  166 (313)
T ss_pred             HhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCCChHHhcCcEE
Confidence            344333456799999999999999997765321221    1113678999989999888754 566665432210     


Q ss_pred             --ccchhh-HHHHHHHHHHHc-CCCeEEEEEeCCC
Q 038944          242 --EIMDKN-YEMKKIILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       242 --~~~~~~-~~~l~~~l~~~L-~~kr~LlVlDdvw  272 (334)
                        ...+.+ +-++...+...+ .++--|||+|.+-
T Consensus       167 ~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       167 YARAYTSEHQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             EecCCCHHHHHHHHHHHHHHhhccCCCEEEEEcch
Confidence              000111 113334444444 3345589999984

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.68  E-value=0.0024  Score=60.37  Aligned_cols=46  Identities=22%  Similarity=0.176  Sum_probs=37.0

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|.+..++.|.+.+..+. -..-+-++|+.|+||+|+|..+.+
T Consensus        18 ~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~   63 (365)
T PRK07471         18 TTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMAR   63 (365)
T ss_pred             hhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999888763 234688999999999999976654

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

Probab=96.67  E-value=0.026  Score=52.09  Aligned_cols=46  Identities=15%  Similarity=0.147  Sum_probs=35.6

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|-+.....+..+......-..-+-++|++|+||||+|..+.+.
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~   47 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKE   47 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHH
Confidence            4667778888888888854433335899999999999999888763

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.66  E-value=0.31  Score=47.11  Aligned_cols=23  Identities=17%  Similarity=0.218  Sum_probs=19.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -+++.++|++|+||||++..+..
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~  243 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAA  243 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            35999999999999998777654

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.66  E-value=0.031  Score=56.54  Aligned_cols=137  Identities=12%  Similarity=0.025  Sum_probs=72.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|.+..+..|..++..+. -..-+-++|..|+||||+|+.+.+.---...+.     .....|+....-+.+.....
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~-----~~~~~Cg~C~~C~~i~~g~h   89 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDK-----PTPEPCGKCELCRAIAAGNA   89 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhcCCCcCC-----CCCCCCcccHHHHHHhcCCC
Confidence            468899999999988887653 124567899999999999999987321110000     00112222222223322211


Q ss_pred             CCCCcc---ccchhh-HHHHHHHHHHH-cCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecC
Q 038944          236 PSSRLS---EIMDKN-YEMKKIILHEY-LMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLT  298 (334)
Q Consensus       236 ~~~~~~---~~~~~~-~~~l~~~l~~~-L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr  298 (334)
                      ......   .....+ ..++...+... ..+++-++|+|++..  ...++.|...+-.-.....+|++|.
T Consensus        90 ~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~  159 (620)
T PRK14948         90 LDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATT  159 (620)
T ss_pred             ccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeC
Confidence            100000   001111 11222222111 135566889999864  4678888877765444565555544

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

Probab=96.66  E-value=0.026  Score=56.42  Aligned_cols=135  Identities=15%  Similarity=0.085  Sum_probs=85.3

Q ss_pred             CCCeeechhhHHHHHHHHhc---CCCCceEEEEEccCCccHHHHHHHHHccCC------CCCceeeEEEEEcCCCCCHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIE---GPPQLSVVVILDSIGLDKAAFAGEAYNSSY------VKHYFDCHAWVPGTYPYDADQ  225 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~------~~~~F~~~~wv~vs~~~~~~~  225 (334)
                      +..+-+|+.+..+|-.++..   +...-..+.|.|-+|+|||..+..|.+..+      --..|+ .+.|+.-.-..+.+
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l~~~~~  473 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRLASPRE  473 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceeecCHHH
Confidence            44567899999999988864   223344999999999999999999987321      112232 33444444457899


Q ss_pred             HHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc-----CCCeEEEEEeCCCChh--HHHHHHhhCCC-CCCCeEEEEec
Q 038944          226 MLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL-----MTKRYLNVIDDVWNIE--VCDIIREILPD-NQNRSRVLITL  297 (334)
Q Consensus       226 il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L-----~~kr~LlVlDdvw~~~--~w~~l~~~l~~-~~~gsrIivTT  297 (334)
                      ++..|...+.+....   +.    ..+..|..++     +.+..++++|++...-  .-+.+-..|.+ ...+||++|.+
T Consensus       474 ~Y~~I~~~lsg~~~~---~~----~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~  546 (767)
T KOG1514|consen  474 IYEKIWEALSGERVT---WD----AALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIA  546 (767)
T ss_pred             HHHHHHHhcccCccc---HH----HHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEE
Confidence            999999999987643   22    3334444444     2355788888873220  01222233332 45688877764

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.65  E-value=0.013  Score=54.28  Aligned_cols=105  Identities=10%  Similarity=-0.004  Sum_probs=60.5

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCC----CceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc-
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVK----HYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS-  241 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~-  241 (334)
                      .|=.+|..+=+.-.++-|+|.+|+|||||+..+.......    ..-...+|++....|+..++ .++.+.++...... 
T Consensus        84 ~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~~~~~~l  162 (316)
T TIGR02239        84 ELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGLNPEDVL  162 (316)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCCChHHhh
Confidence            3444454443567899999999999999998876422111    11235689988888888774 44555554332110 


Q ss_pred             ------ccchhh-HHHHHHHHHHHcC-CCeEEEEEeCCC
Q 038944          242 ------EIMDKN-YEMKKIILHEYLM-TKRYLNVIDDVW  272 (334)
Q Consensus       242 ------~~~~~~-~~~l~~~l~~~L~-~kr~LlVlDdvw  272 (334)
                            ...+.+ +..+...+...+. .+--|||+|-+-
T Consensus       163 ~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~LvVIDSI~  201 (316)
T TIGR02239       163 DNVAYARAYNTDHQLQLLQQAAAMMSESRFALLIVDSAT  201 (316)
T ss_pred             ccEEEEecCChHHHHHHHHHHHHhhccCCccEEEEECcH
Confidence                  011111 1123333444443 345589999984

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).

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.65  E-value=0.0079  Score=50.83  Aligned_cols=22  Identities=23%  Similarity=0.309  Sum_probs=19.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ||.|+|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999873

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.

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

Probab=96.65  E-value=0.039  Score=45.88  Aligned_cols=124  Identities=12%  Similarity=0.117  Sum_probs=68.0

Q ss_pred             echhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc----CCCC--------------CceeeEEEEEcCCCC
Q 038944          160 GLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS----SYVK--------------HYFDCHAWVPGTYPY  221 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~----~~~~--------------~~F~~~~wv~vs~~~  221 (334)
                      |-+...+.|.+.+..+. -...+-++|..|+||+|+|..+.+.    ....              ....-..|+.-....
T Consensus         1 gq~~~~~~L~~~~~~~~-l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~   79 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR-LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKK   79 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC---SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSS
T ss_pred             CcHHHHHHHHHHHHcCC-cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEeccccc
Confidence            34555666666665543 2346788999999999998877642    1110              111122233222110


Q ss_pred             CHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc-----CCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEE
Q 038944          222 DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL-----MTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVL  294 (334)
Q Consensus       222 ~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L-----~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIi  294 (334)
                                          .....+  +.. .+.+++     .+++=++|+|++..  .+.++.|+..+-.-..++++|
T Consensus        80 --------------------~~i~i~--~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fi  136 (162)
T PF13177_consen   80 --------------------KSIKID--QIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFI  136 (162)
T ss_dssp             --------------------SSBSHH--HHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEE
T ss_pred             --------------------chhhHH--HHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEE
Confidence                                011111  222 333333     24566889999974  478888888886656688888


Q ss_pred             EecCChH-HHhhcc
Q 038944          295 ITLTEIK-MFTFLL  307 (334)
Q Consensus       295 vTTr~~~-va~~~~  307 (334)
                      ++|.+.+ +-.++-
T Consensus       137 L~t~~~~~il~TI~  150 (162)
T PF13177_consen  137 LITNNPSKILPTIR  150 (162)
T ss_dssp             EEES-GGGS-HHHH
T ss_pred             EEECChHHChHHHH
Confidence            8887655 444333

...

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.63  E-value=0.025  Score=55.09  Aligned_cols=46  Identities=15%  Similarity=0.067  Sum_probs=37.3

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|.+..+..|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk   61 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAK   61 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHH
Confidence            3468999999999998887653 235677899999999999998865

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.60  E-value=0.018  Score=52.02  Aligned_cols=130  Identities=10%  Similarity=0.052  Sum_probs=71.0

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEE---cCCCCCHHHHHHHHHHHhCCCCCc
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVP---GTYPYDADQMLDIVIKFLMPSSRL  240 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~---vs~~~~~~~il~~il~~~~~~~~~  240 (334)
                      ..+.++..|... ....-+.|+|..|.|||||.+.+...  +.. ....+++.   +...-..    .++......-...
T Consensus        97 ~~~~~l~~l~~~-~~~~~~~i~g~~g~GKttl~~~l~~~--~~~-~~G~i~~~g~~v~~~d~~----~ei~~~~~~~~q~  168 (270)
T TIGR02858        97 AADKLLPYLVRN-NRVLNTLIISPPQCGKTTLLRDLARI--LST-GISQLGLRGKKVGIVDER----SEIAGCVNGVPQH  168 (270)
T ss_pred             cHHHHHHHHHhC-CCeeEEEEEcCCCCCHHHHHHHHhCc--cCC-CCceEEECCEEeecchhH----HHHHHHhcccccc
Confidence            445555566543 23578999999999999999999873  221 11122221   1100011    2222222111100


Q ss_pred             c-----ccchhhHHHHHHHHHHHc-CCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhc
Q 038944          241 S-----EIMDKNYEMKKIILHEYL-MTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       241 ~-----~~~~~~~~~l~~~l~~~L-~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~  306 (334)
                      .     +..+..  .-...+...+ ....-++++|.+-..+.+..+...+.   .|..||+||...++...+
T Consensus       169 ~~~~r~~v~~~~--~k~~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~~~~~  235 (270)
T TIGR02858       169 DVGIRTDVLDGC--PKAEGMMMLIRSMSPDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDVEDLY  235 (270)
T ss_pred             cccccccccccc--hHHHHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHHHHHH
Confidence            0     111111  1122222222 24677999999988777777776662   477799999988876553

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.60  E-value=0.011  Score=60.69  Aligned_cols=48  Identities=25%  Similarity=0.235  Sum_probs=38.1

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ..++|....+..+.+.+..-...-.-|.|+|..|+|||++|+.+++..
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s  423 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS  423 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            468999999998877776432233468899999999999999999853

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.60  E-value=0.0055  Score=53.11  Aligned_cols=25  Identities=20%  Similarity=0.231  Sum_probs=22.9

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++.+|+|-|.+|+||||+|+.++.
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~   30 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSE   30 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHH
Confidence            3568999999999999999999998

>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=96.60  E-value=0.018  Score=48.71  Aligned_cols=24  Identities=17%  Similarity=0.051  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl   48 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQ   48 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC
Confidence            359999999999999999999863

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.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=96.57  E-value=0.032  Score=45.41  Aligned_cols=97  Identities=12%  Similarity=0.067  Sum_probs=54.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEE-------cCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVP-------GTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMK  251 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-------vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l  251 (334)
                      -.+++|+|..|.|||||++.+..-...   ..-.+|+.       +++              +.        ...   ..
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~---~~G~i~~~~~~~i~~~~~--------------lS--------~G~---~~   77 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELEP---DEGIVTWGSTVKIGYFEQ--------------LS--------GGE---KM   77 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCC---CceEEEECCeEEEEEEcc--------------CC--------HHH---HH
Confidence            358999999999999999999874221   11222221       111              10        011   22


Q ss_pred             HHHHHHHcCCCeEEEEEeCCCC---hhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          252 KIILHEYLMTKRYLNVIDDVWN---IEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       252 ~~~l~~~L~~kr~LlVlDdvw~---~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      .-.+-..+..+.-++++|+.-.   ......+...+...  +.-||++|...+.+..
T Consensus        78 rv~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~~  132 (144)
T cd03221          78 RLALAKLLLENPNLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLDQ  132 (144)
T ss_pred             HHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHHH
Confidence            2223444455667889999753   34444444443322  2358888887766544

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.

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=96.56  E-value=0.0057  Score=55.42  Aligned_cols=89  Identities=18%  Similarity=0.173  Sum_probs=49.3

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIM  244 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~  244 (334)
                      ...+++.+....   +-+-++|+.|+|||++++.......- ..|- ..-++.|...+...+ +.++++--.+... ...
T Consensus        22 ~~~ll~~l~~~~---~pvLl~G~~GtGKT~li~~~l~~l~~-~~~~-~~~~~~s~~Tts~~~-q~~ie~~l~k~~~-~~~   94 (272)
T PF12775_consen   22 YSYLLDLLLSNG---RPVLLVGPSGTGKTSLIQNFLSSLDS-DKYL-VITINFSAQTTSNQL-QKIIESKLEKRRG-RVY   94 (272)
T ss_dssp             HHHHHHHHHHCT---EEEEEESSTTSSHHHHHHHHHHCSTT-CCEE-EEEEES-TTHHHHHH-HHCCCTTECECTT-EEE
T ss_pred             HHHHHHHHHHcC---CcEEEECCCCCchhHHHHhhhccCCc-cccc-eeEeeccCCCCHHHH-HHHHhhcEEcCCC-CCC
Confidence            356677777653   34689999999999999998863221 2222 334455554444433 3333221111110 000


Q ss_pred             hhhHHHHHHHHHHHcCCCeEEEEEeCCC
Q 038944          245 DKNYEMKKIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       245 ~~~~~~l~~~l~~~L~~kr~LlVlDdvw  272 (334)
                      ..            -.+|+.++.+||+-
T Consensus        95 gP------------~~~k~lv~fiDDlN  110 (272)
T PF12775_consen   95 GP------------PGGKKLVLFIDDLN  110 (272)
T ss_dssp             EE------------ESSSEEEEEEETTT
T ss_pred             CC------------CCCcEEEEEecccC
Confidence            00            14789999999995

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.56  E-value=0.0028  Score=54.95  Aligned_cols=123  Identities=12%  Similarity=0.091  Sum_probs=63.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKIIL  255 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~l  255 (334)
                      -.++.|.|..|.||||+.+.+.--.-.   ..+..+|+... .. -.+...|+..++......   .....++.++. .+
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~~l---a~~G~~vpa~~-~~-l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~-~i  102 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLAIM---AQIGCFVPAEY-AT-LPIFNRLLSRLSNDDSMERNLSTFASEMSETA-YI  102 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH---HHcCCCcchhh-cC-ccChhheeEecCCccccchhhhHHHHHHHHHH-HH
Confidence            478999999999999999988642100   11111221111 11 123333444443322110   01111111222 11


Q ss_pred             HHHcCCCeEEEEEeCCCC---hhH----HHHHHhhCCCCCCCeEEEEecCChHHHhhccccC
Q 038944          256 HEYLMTKRYLNVIDDVWN---IEV----CDIIREILPDNQNRSRVLITLTEIKMFTFLLETL  310 (334)
Q Consensus       256 ~~~L~~kr~LlVlDdvw~---~~~----w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~~~  310 (334)
                      .. +..++-|++||..-.   ..+    ...+...+..  .|+.+|++|...+++..+....
T Consensus       103 l~-~~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~~--~~~~~i~~TH~~~l~~~~~~~~  161 (204)
T cd03282         103 LD-YADGDSLVLIDELGRGTSSADGFAISLAILECLIK--KESTVFFATHFRDIAAILGNKS  161 (204)
T ss_pred             HH-hcCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHh--cCCEEEEECChHHHHHHhhcCC
Confidence            12 235678999999843   322    1222333322  3788999999999998776543

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.55  E-value=0.0076  Score=63.12  Aligned_cols=45  Identities=20%  Similarity=0.267  Sum_probs=38.6

Q ss_pred             CeeechhhHHHHHHHHhcC-CCCceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDLLIEG-PPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++||+.+.+.|...+..- .....++.+.|..|+|||+|++.|..
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~   46 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHK   46 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHH
Confidence            3689999999999888752 34456999999999999999999997

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.55  E-value=0.023  Score=53.47  Aligned_cols=47  Identities=19%  Similarity=0.182  Sum_probs=38.4

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-..++|.+...+.+...+..+. -..-+-|+|..|+||||+|..+.+
T Consensus        21 ~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~   67 (351)
T PRK09112         21 ENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLAN   67 (351)
T ss_pred             chhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHH
Confidence            34568999999999999887654 234688899999999999998776

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

Probab=96.55  E-value=0.016  Score=49.00  Aligned_cols=122  Identities=12%  Similarity=0.104  Sum_probs=63.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEE---EcCCCCCHHHHH------HHHHHHhCCCCCc---cccchh
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWV---PGTYPYDADQML------DIVIKFLMPSSRL---SEIMDK  246 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---~vs~~~~~~~il------~~il~~~~~~~~~---~~~~~~  246 (334)
                      -.+++|+|..|.|||||.+.+..-..   ...-.+++   .+. ..+.....      -++++.++.....   ....+.
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~~---~~~G~v~~~g~~~~-~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLLK---PSSGEILLDGKDLA-SLSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC---CCCcEEEECCEECC-cCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            45899999999999999999987321   12222222   121 11222211      1144554432110   011111


Q ss_pred             hHHHHHHHHHHHcCCCeEEEEEeCCCC---hhHHHHHHhhCCC-CCC-CeEEEEecCChHHHhh
Q 038944          247 NYEMKKIILHEYLMTKRYLNVIDDVWN---IEVCDIIREILPD-NQN-RSRVLITLTEIKMFTF  305 (334)
Q Consensus       247 ~~~~l~~~l~~~L~~kr~LlVlDdvw~---~~~w~~l~~~l~~-~~~-gsrIivTTr~~~va~~  305 (334)
                      . +...-.+-..|....-+++||+.-.   ....+.+...+.. ... |.-||++|.+.+....
T Consensus       101 G-~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~~  163 (180)
T cd03214         101 G-ERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAAR  163 (180)
T ss_pred             H-HHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            1 1222334455556778899999853   3334444443332 112 5678888888776543

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.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.54  E-value=0.015  Score=54.34  Aligned_cols=100  Identities=10%  Similarity=0.010  Sum_probs=58.4

Q ss_pred             HhcCCCCceEEEEEccCCccHHHHHHHHHccCCC----CCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc------
Q 038944          172 LIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYV----KHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS------  241 (334)
Q Consensus       172 L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~----~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~------  241 (334)
                      |..+=..-.+.-|+|.+|+|||+|+..+.-....    ...-...+|++.-..|++.++.+ +++.++......      
T Consensus       119 LgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~  197 (344)
T PLN03187        119 LGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIY  197 (344)
T ss_pred             cCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEE
Confidence            3333345678889999999999999877532122    11123679999999999888765 556665432110      


Q ss_pred             -ccchhh-HHHHHHHHHHHc-CCCeEEEEEeCCC
Q 038944          242 -EIMDKN-YEMKKIILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       242 -~~~~~~-~~~l~~~l~~~L-~~kr~LlVlDdvw  272 (334)
                       ...+.+ +-.+...+...+ ..+--|||+|.+-
T Consensus       198 ~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        198 ARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             ecCCCHHHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence             111111 002233333333 2334589999984

>PRK08233 hypothetical protein; Provisional

Probab=96.54  E-value=0.0022  Score=54.10  Aligned_cols=24  Identities=13%  Similarity=0.166  Sum_probs=21.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+|+|.|.+|+||||||+.+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            479999999999999999999874

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.53  E-value=0.0019  Score=50.89  Aligned_cols=21  Identities=24%  Similarity=0.155  Sum_probs=19.2

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|.|.+|+||||+|+.+.+.
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            689999999999999999883

...

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.53  E-value=0.049  Score=53.91  Aligned_cols=45  Identities=13%  Similarity=0.009  Sum_probs=36.5

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|-+..++.|...+..+. -....-++|..|+||||+|+.+.+
T Consensus        14 deiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk   58 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFAR   58 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHH
Confidence            468999998999998887653 334668899999999999997765

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.53  E-value=0.033  Score=56.77  Aligned_cols=45  Identities=20%  Similarity=0.206  Sum_probs=36.5

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..++.|..++..+. -....-++|+.|+||||+|+.+..
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk   62 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFAN   62 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHH
Confidence            458899999999999887653 234567899999999999998875

>PRK04296 thymidine kinase; Provisional

Probab=96.53  E-value=0.0042  Score=53.20  Aligned_cols=113  Identities=12%  Similarity=-0.075  Sum_probs=59.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL  259 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L  259 (334)
                      .++.|+|..|.||||++......  ...+-.....+  .+.++.......++++++............  ++...+.+ .
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~--~~~~g~~v~i~--k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~--~~~~~~~~-~   75 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYN--YEERGMKVLVF--KPAIDDRYGEGKVVSRIGLSREAIPVSSDT--DIFELIEE-E   75 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHH--HHHcCCeEEEE--eccccccccCCcEecCCCCcccceEeCChH--HHHHHHHh-h
Confidence            46788999999999999777663  21222222222  122232232444555655332210011122  45555555 3


Q ss_pred             CCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          260 MTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       260 ~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      .++.-+||+|.+--  .++...+...+  ...|..||+|.++.+
T Consensus        76 ~~~~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~  117 (190)
T PRK04296         76 GEKIDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTD  117 (190)
T ss_pred             CCCCCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCcc
Confidence            34445899999843  23233333332  235778999988833

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.52  E-value=0.0023  Score=55.55  Aligned_cols=25  Identities=20%  Similarity=0.291  Sum_probs=22.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +..+|+|.|.+|+|||||++.++..
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999973

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=96.51  E-value=0.032  Score=55.58  Aligned_cols=137  Identities=16%  Similarity=0.223  Sum_probs=79.0

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHH-HHHHHHccCCCCCceeeEEEEEcCCCCC--HHHHHHHHHHHhCCCCCc
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAA-FAGEAYNSSYVKHYFDCHAWVPGTYPYD--ADQMLDIVIKFLMPSSRL  240 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTt-La~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~il~~il~~~~~~~~~  240 (334)
                      -.++|++.+..+    .||.|||..|+|||| |+|.+|.+-     |-..-.+.+.++-.  ...+.+.+.+.++.....
T Consensus       360 ~R~~ll~~ir~n----~vvvivgETGSGKTTQl~QyL~edG-----Y~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~  430 (1042)
T KOG0924|consen  360 CRDQLLSVIREN----QVVVIVGETGSGKTTQLAQYLYEDG-----YADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGD  430 (1042)
T ss_pred             HHHHHHHHHhhC----cEEEEEecCCCCchhhhHHHHHhcc-----cccCCeeeecCchHHHHHHHHHHHHHHhCCcccc
Confidence            345566666554    499999999999999 999999852     32222445555543  345566777777554332


Q ss_pred             c------------------ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh----h-HHHHHHhhCCCCCCCeEEEEec
Q 038944          241 S------------------EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI----E-VCDIIREILPDNQNRSRVLITL  297 (334)
Q Consensus       241 ~------------------~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~----~-~w~~l~~~l~~~~~gsrIivTT  297 (334)
                      .                  ...+--  -|.+.|....-+|--.||+|..-..    + .+.-+..++.. ...-|+|||+
T Consensus       431 ~VGYsIRFEdvT~~~T~IkymTDGi--LLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~lar-RrdlKliVtS  507 (1042)
T KOG0924|consen  431 TVGYSIRFEDVTSEDTKIKYMTDGI--LLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDLKLIVTS  507 (1042)
T ss_pred             ccceEEEeeecCCCceeEEEeccch--HHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHHh-hccceEEEee
Confidence            1                  111212  3344444444456668889998543    2 23333444433 2367899998


Q ss_pred             CChH---HHhhccccCcc
Q 038944          298 TEIK---MFTFLLETLFS  312 (334)
Q Consensus       298 r~~~---va~~~~~~~~~  312 (334)
                      --.+   .+..++..+.+
T Consensus       508 ATm~a~kf~nfFgn~p~f  525 (1042)
T KOG0924|consen  508 ATMDAQKFSNFFGNCPQF  525 (1042)
T ss_pred             ccccHHHHHHHhCCCcee
Confidence            7655   44445533333

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

Probab=96.49  E-value=0.0021  Score=55.15  Aligned_cols=22  Identities=18%  Similarity=0.193  Sum_probs=20.3

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ||+|.|.+|+||||+|+.+...
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~   22 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQI   22 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            7999999999999999999873

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 ....

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.48  E-value=0.0047  Score=54.49  Aligned_cols=26  Identities=23%  Similarity=0.233  Sum_probs=23.3

Q ss_pred             CCCceEEEEEccCCccHHHHHHHHHc
Q 038944          176 PPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       176 ~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+..+++|.|..|+|||||++.+..
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            35678999999999999999998886

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.47  E-value=0.011  Score=55.01  Aligned_cols=47  Identities=19%  Similarity=0.203  Sum_probs=37.8

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|....+.++.+.+..-...-.-|.|+|..|+||+++|+.++..
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            45899999999998888753333345789999999999999999874

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.45  E-value=0.013  Score=52.30  Aligned_cols=62  Identities=15%  Similarity=0.068  Sum_probs=40.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEE---------EEEcCCCCCHHHH--HHHHHHHhCCCCCc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHA---------WVPGTYPYDADQM--LDIVIKFLMPSSRL  240 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~---------wv~vs~~~~~~~i--l~~il~~~~~~~~~  240 (334)
                      ++..+|-++||+|+||||..|.++.+..-+  +.+--         -|+..-+.|+++.  .++.+++.+....+
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl~~~--~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPNG   89 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHLHAK--KTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPNG   89 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHHhhc--cCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCCc
Confidence            456788999999999999999999853222  21111         1122233466654  67888888766553

>TIGR00235 udk uridine kinase

Probab=96.45  E-value=0.0028  Score=54.93  Aligned_cols=26  Identities=23%  Similarity=0.308  Sum_probs=22.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.-.+|+|+|.+|+|||||++.+...
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999999999873

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

>TIGR01069 mutS2 MutS2 family protein

Probab=96.45  E-value=0.072  Score=55.30  Aligned_cols=121  Identities=13%  Similarity=0.074  Sum_probs=59.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKIIL  255 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~l  255 (334)
                      ..++.|+|+.|.|||||.+.+....   -...+.++|+...... -.++..+...++......   ..-...+..+...+
T Consensus       322 ~~~liItGpNg~GKSTlLK~i~~~~---l~aq~G~~Vpa~~~~~-~~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~il  397 (771)
T TIGR01069       322 KRVLAITGPNTGGKTVTLKTLGLLA---LMFQSGIPIPANEHSE-IPYFEEIFADIGDEQSIEQNLSTFSGHMKNISAIL  397 (771)
T ss_pred             ceEEEEECCCCCCchHHHHHHHHHH---HHHHhCCCccCCcccc-ccchhheeeecChHhHHhhhhhHHHHHHHHHHHHH
Confidence            4799999999999999999886420   0011112222221100 001111111111110000   00010111232222


Q ss_pred             HHHcCCCeEEEEEeCCCCh---hHHHHH----HhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          256 HEYLMTKRYLNVIDDVWNI---EVCDII----REILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       256 ~~~L~~kr~LlVlDdvw~~---~~w~~l----~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      . .+ +++-|++||..-..   ..-..+    ...+.  ..|+.+|+||...++.....
T Consensus       398 ~-~~-~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~--~~g~~viitTH~~eL~~~~~  452 (771)
T TIGR01069       398 S-KT-TENSLVLFDELGAGTDPDEGSALAISILEYLL--KQNAQVLITTHYKELKALMY  452 (771)
T ss_pred             H-hc-CCCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHhc
Confidence            2 22 57899999998753   222222    22332  35788999999999876543

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.43  E-value=0.041  Score=45.89  Aligned_cols=115  Identities=10%  Similarity=0.009  Sum_probs=58.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCC-CCc--eee---EEEEEcCCCC--CHHHHHHHHHHHhCCCCCccccchhhHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYV-KHY--FDC---HAWVPGTYPY--DADQMLDIVIKFLMPSSRLSEIMDKNYEM  250 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~--F~~---~~wv~vs~~~--~~~~il~~il~~~~~~~~~~~~~~~~~~~  250 (334)
                      -.+++|+|..|.|||||++.+..-... ...  |+.   ..+  +++..  ....+...+.-. ....   -+...   .
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~--~~q~~~~~~~tv~~nl~~~-~~~~---LS~G~---~   97 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLF--LPQRPYLPLGTLREQLIYP-WDDV---LSGGE---Q   97 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEE--ECCCCccccccHHHHhhcc-CCCC---CCHHH---H
Confidence            458999999999999999999874221 111  111   222  23332  112333333211 1111   11111   2


Q ss_pred             HHHHHHHHcCCCeEEEEEeCCCCh---hHHHHHHhhCCCCCCCeEEEEecCChHHHh
Q 038944          251 KKIILHEYLMTKRYLNVIDDVWNI---EVCDIIREILPDNQNRSRVLITLTEIKMFT  304 (334)
Q Consensus       251 l~~~l~~~L~~kr~LlVlDdvw~~---~~w~~l~~~l~~~~~gsrIivTTr~~~va~  304 (334)
                      ..-.+-..+..+.=+++||+.-+.   .....+...+...  +.-||++|.+...+.
T Consensus        98 ~rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~~  152 (166)
T cd03223          98 QRLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLWK  152 (166)
T ss_pred             HHHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHHh
Confidence            223334444456667889987533   3333333333221  355888888877654

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

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

Probab=96.41  E-value=0.013  Score=52.56  Aligned_cols=95  Identities=14%  Similarity=0.073  Sum_probs=57.6

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCC----CceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc-------ccch
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVK----HYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS-------EIMD  245 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~-------~~~~  245 (334)
                      ..-.|.=|+|.+|+|||.|+-.+.-...+.    ..=...+|++-...|++.++. +|++.........       ...+
T Consensus        36 ~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~  114 (256)
T PF08423_consen   36 PTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFD  114 (256)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SS
T ss_pred             CCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCC
Confidence            345699999999999999997776432222    112358999999999988875 5677654322110       0111


Q ss_pred             h-hHHHHHHHHHHHc-CCCeEEEEEeCCC
Q 038944          246 K-NYEMKKIILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       246 ~-~~~~l~~~l~~~L-~~kr~LlVlDdvw  272 (334)
                      . .+..+...+...+ ..+--|||+|.+-
T Consensus       115 ~~~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  115 LEELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHHHhhccccceEEEEecchH
Confidence            1 1113444444444 3455699999983

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 ....

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.39  E-value=0.04  Score=46.87  Aligned_cols=47  Identities=15%  Similarity=0.070  Sum_probs=30.3

Q ss_pred             CCeEEEEEeCCCCh---hH----HHHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          261 TKRYLNVIDDVWNI---EV----CDIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       261 ~kr~LlVlDdvw~~---~~----w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      +++-|+++|..-..   ..    ...+...+.. ..|+.+|++|...+++..+..
T Consensus        77 ~~~~llllDEp~~g~d~~~~~~~~~~~l~~l~~-~~~~~iii~TH~~~l~~~~~~  130 (185)
T smart00534       77 TENSLVLLDELGRGTSTYDGVAIAAAVLEYLLE-KIGALTLFATHYHELTKLADE  130 (185)
T ss_pred             CCCeEEEEecCCCCCCHHHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHHHHhhc
Confidence            47889999998643   11    1222222222 236779999999998887654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.39  E-value=0.012  Score=53.59  Aligned_cols=24  Identities=17%  Similarity=0.242  Sum_probs=21.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..++.++|.+|+||||++..+..
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~  216 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAA  216 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999988876

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.37  E-value=0.8  Score=47.80  Aligned_cols=124  Identities=11%  Similarity=0.072  Sum_probs=60.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKII  254 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~  254 (334)
                      ..+++.|.|+.+.||||+.+.+.--.-   ...+.++|+..... .-.++..|+..++......   ......+..+...
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl~~~---maq~G~~vpa~~~~-~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~I  401 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGLAAL---MAKSGLPIPANEPS-EIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRI  401 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHHHHH---HHHhCCCcccCCCc-cccccceEEEecCCccchhhchhHHHHHHHHHHHH
Confidence            357889999999999999988852100   01122222222110 0011111111111111000   0111111122222


Q ss_pred             HHHHcCCCeEEEEEeCCCCh---hHHHHH----HhhCCCCCCCeEEEEecCChHHHhhcccc
Q 038944          255 LHEYLMTKRYLNVIDDVWNI---EVCDII----REILPDNQNRSRVLITLTEIKMFTFLLET  309 (334)
Q Consensus       255 l~~~L~~kr~LlVlDdvw~~---~~w~~l----~~~l~~~~~gsrIivTTr~~~va~~~~~~  309 (334)
                      +.. + +.+-|++||..-..   ..-..+    ...+.  ..|+.+|+||...+++..+...
T Consensus       402 l~~-~-~~~sLvLlDE~~~GtDp~eg~ala~aile~l~--~~~~~vIitTH~~el~~~~~~~  459 (782)
T PRK00409        402 LEK-A-DKNSLVLFDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKALMYNR  459 (782)
T ss_pred             HHh-C-CcCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEEECChHHHHHHHhcC
Confidence            222 2 57789999999743   222222    22332  3478999999999988776543

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.35  E-value=0.021  Score=54.43  Aligned_cols=75  Identities=13%  Similarity=0.199  Sum_probs=48.8

Q ss_pred             eeechhhHHHHHHHHhcC------------CCCceEEEEEccCCccHHHHHHHHHccCCCCCce---eeEEEEEcCC-CC
Q 038944          158 TVGLDDRMEELLDLLIEG------------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF---DCHAWVPGTY-PY  221 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~-~~  221 (334)
                      ++|.++.++.+...+...            +...+-|.++|++|+|||++|+.+..  .....|   +..-++..+. ..
T Consensus        14 IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~--~l~~~fi~vdat~~~e~g~vG~   91 (441)
T TIGR00390        14 IIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAK--LANAPFIKVEATKFTEVGYVGR   91 (441)
T ss_pred             ccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHH--HhCCeEEEeecceeecCCcccC
Confidence            789988888887666531            12346788999999999999999988  444444   2222322222 23


Q ss_pred             CHHHHHHHHHHHh
Q 038944          222 DADQMLDIVIKFL  234 (334)
Q Consensus       222 ~~~~il~~il~~~  234 (334)
                      +...+++.+....
T Consensus        92 dvE~i~r~l~e~A  104 (441)
T TIGR00390        92 DVESMVRDLTDAA  104 (441)
T ss_pred             CHHHHHHHHHHHH
Confidence            5666666665543

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.05  Score=51.62  Aligned_cols=24  Identities=8%  Similarity=0.239  Sum_probs=21.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.++|+++|.+|+||||++..+..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999988864

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.33  E-value=0.016  Score=52.21  Aligned_cols=103  Identities=17%  Similarity=0.098  Sum_probs=61.8

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCC--CCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchhh------HH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYV--KHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDKN------YE  249 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~~------~~  249 (334)
                      -++|.|-.|+|||+|+..+.++...  +.+-+.++++-+.+.. ++.++..++.+.-..+....  ...++.      --
T Consensus        71 R~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a~  150 (276)
T cd01135          71 KIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIITP  150 (276)
T ss_pred             EEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHHH
Confidence            5799999999999999988875331  2234678888888765 56677777665422111100  000100      00


Q ss_pred             HHHHHHHHHc---CCCeEEEEEeCCCCh-hHHHHHHhh
Q 038944          250 MKKIILHEYL---MTKRYLNVIDDVWNI-EVCDIIREI  283 (334)
Q Consensus       250 ~l~~~l~~~L---~~kr~LlVlDdvw~~-~~w~~l~~~  283 (334)
                      ...-.+-+++   ++++.|+++||+-.- +.+.++...
T Consensus       151 ~~a~aiAEyfrd~~g~~VLl~~D~ltr~A~A~rEisl~  188 (276)
T cd01135         151 RMALTTAEYLAYEKGKHVLVILTDMTNYAEALREISAA  188 (276)
T ss_pred             HHHHHHHHHHHhccCCeEEEEEcChhHHHHHHHHHHhc
Confidence            2233344555   379999999999543 555555543

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=96.33  E-value=0.033  Score=47.97  Aligned_cols=24  Identities=17%  Similarity=0.176  Sum_probs=21.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+...
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          26 GEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999874

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.33  E-value=0.0097  Score=57.76  Aligned_cols=41  Identities=17%  Similarity=0.141  Sum_probs=35.9

Q ss_pred             eeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          158 TVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|+++.++.+...+..+.    -+-+.|.+|+|||+||+.+...
T Consensus        22 i~gre~vI~lll~aalag~----hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         22 LYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             ccCcHHHHHHHHHHHccCC----CEEEECCCChhHHHHHHHHHHH
Confidence            8999999999888887654    5789999999999999999974

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.31  E-value=0.03  Score=51.73  Aligned_cols=103  Identities=7%  Similarity=0.068  Sum_probs=59.2

Q ss_pred             HHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc----c
Q 038944          170 DLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL----S  241 (334)
Q Consensus       170 ~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~----~  241 (334)
                      ++|..+=+.-.++-|+|.+|+|||||+.++.-......    .=...+||+.-..|+..++. ++++.++.....    .
T Consensus        86 ~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl~~~~~~~~i  164 (310)
T TIGR02236        86 ELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGLDPDEVLKNI  164 (310)
T ss_pred             HHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhhce
Confidence            33433334567999999999999999988865322210    01268999998889888765 444544432110    0


Q ss_pred             ---ccch-hhHHHHHHHHHHHcCC---CeEEEEEeCCCC
Q 038944          242 ---EIMD-KNYEMKKIILHEYLMT---KRYLNVIDDVWN  273 (334)
Q Consensus       242 ---~~~~-~~~~~l~~~l~~~L~~---kr~LlVlDdvw~  273 (334)
                         ...+ ...-.+...+.+.+..   +--+||+|.+-.
T Consensus       165 ~i~~~~~~~~~~~lld~l~~~i~~~~~~~~lVVIDSisa  203 (310)
T TIGR02236       165 YVARAYNSNHQMLLVEKAEDLIKELNNPVKLLIVDSLTS  203 (310)
T ss_pred             EEEecCCHHHHHHHHHHHHHHHHhcCCCceEEEEecchH
Confidence               0000 0100234445555532   234899998843

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.

>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=96.30  E-value=0.008  Score=51.72  Aligned_cols=23  Identities=13%  Similarity=0.245  Sum_probs=19.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+.+||+.|+||||.+-++..
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa   23 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAA   23 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHH
Confidence            47999999999999997665544

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 ....

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.28  E-value=0.093  Score=52.55  Aligned_cols=46  Identities=17%  Similarity=0.145  Sum_probs=37.5

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|.+...+.|.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 f~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAk   60 (559)
T PRK05563         15 FEDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAK   60 (559)
T ss_pred             HHhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3568999999999999988754 234566799999999999998865

>TIGR00959 ffh signal recognition particle protein

Probab=96.27  E-value=0.019  Score=55.31  Aligned_cols=24  Identities=17%  Similarity=0.252  Sum_probs=19.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.++|.+|+||||.+..+..
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~  121 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAY  121 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH
Confidence            467999999999999998665543

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.27  E-value=0.04  Score=52.72  Aligned_cols=24  Identities=21%  Similarity=0.191  Sum_probs=21.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.++|.+|+||||++..+..
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~  245 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAA  245 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999988865

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.26  E-value=0.033  Score=52.08  Aligned_cols=104  Identities=9%  Similarity=0.024  Sum_probs=61.4

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc--
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS--  241 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~--  241 (334)
                      |=++|..+=+.-.++-|+|.+|+|||+|+..+.-......    .-..++|++.-..|++.++. +|++.++......  
T Consensus       112 LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~~~~~~~l~  190 (342)
T PLN03186        112 LDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFGLNGADVLE  190 (342)
T ss_pred             HHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcCCChhhhcc
Confidence            3344444435567899999999999999987764322211    11268999999999988764 5566665432110  


Q ss_pred             -----ccchhh-HHHHHHHHHHHc-CCCeEEEEEeCCC
Q 038944          242 -----EIMDKN-YEMKKIILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       242 -----~~~~~~-~~~l~~~l~~~L-~~kr~LlVlDdvw  272 (334)
                           ...+.+ +..+...+...+ ..+--|||+|-+-
T Consensus       191 ~i~~~~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~  228 (342)
T PLN03186        191 NVAYARAYNTDHQSELLLEAASMMAETRFALMIVDSAT  228 (342)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcH
Confidence                 111111 112233333333 3455699999984

>PRK06547 hypothetical protein; Provisional

Probab=96.25  E-value=0.007  Score=50.94  Aligned_cols=26  Identities=23%  Similarity=0.230  Sum_probs=23.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....+|+|.|.+|+||||+|+.+.+.
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999874

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.23  E-value=0.02  Score=48.04  Aligned_cols=24  Identities=17%  Similarity=0.138  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~   51 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGL   51 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            358999999999999999999863

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

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.23  E-value=0.014  Score=50.15  Aligned_cols=115  Identities=8%  Similarity=0.018  Sum_probs=55.9

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccch
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMD  245 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~  245 (334)
                      .+.+..+..+.  -++..|.|.+|+||||+.+.+........ + ..+++..+.     +....+.+..+....      
T Consensus         7 ~~a~~~~l~~~--~~~~~l~G~aGtGKT~~l~~~~~~~~~~g-~-~v~~~apT~-----~Aa~~L~~~~~~~a~------   71 (196)
T PF13604_consen    7 REAVRAILTSG--DRVSVLQGPAGTGKTTLLKALAEALEAAG-K-RVIGLAPTN-----KAAKELREKTGIEAQ------   71 (196)
T ss_dssp             HHHHHHHHHCT--CSEEEEEESTTSTHHHHHHHHHHHHHHTT----EEEEESSH-----HHHHHHHHHHTS-EE------
T ss_pred             HHHHHHHHhcC--CeEEEEEECCCCCHHHHHHHHHHHHHhCC-C-eEEEECCcH-----HHHHHHHHhhCcchh------
Confidence            33444443332  35788899999999999998876322111 1 222222221     222223333332111      


Q ss_pred             hhHHHHHHHHHHHc---------CCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          246 KNYEMKKIILHEYL---------MTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       246 ~~~~~l~~~l~~~L---------~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                          .+...+....         ..+.-+||+|+..-.  ..+..+....+.  .|+|+|+.==..+
T Consensus        72 ----Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~~Q  132 (196)
T PF13604_consen   72 ----TIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDPNQ  132 (196)
T ss_dssp             ----EHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-TTS
T ss_pred             ----hHHHHHhcCCcccccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCcch
Confidence                1111111110         123349999999743  578888777755  5788887644333

>PRK06762 hypothetical protein; Provisional

Probab=96.21  E-value=0.0041  Score=51.75  Aligned_cols=23  Identities=17%  Similarity=0.310  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+|.|.|++|+||||+|+.+.+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999873

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.21  E-value=0.021  Score=51.00  Aligned_cols=129  Identities=9%  Similarity=0.067  Sum_probs=72.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCC--CCC-ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc----ccchhhHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSY--VKH-YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS----EIMDKNYEM  250 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~--~~~-~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~----~~~~~~~~~  250 (334)
                      +-.++++||..|.|||||++.+..=.+  -.+ .|+..-+...+ .....+-..++++.++......    ...+-.  +
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~pt~G~i~f~g~~i~~~~-~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGG--Q  114 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLS-KEERRERVLELLEKVGLPEEFLYRYPHELSGG--Q  114 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCCCCceEEEcCcchhhcc-hhHHHHHHHHHHHHhCCCHHHhhcCCcccCch--h
Confidence            346899999999999999999986211  111 12221111111 2223445666777766432110    111212  3


Q ss_pred             HH-HHHHHHcCCCeEEEEEeCCCChh---HHHHHHhhCC--CCCCCeEEEEecCChHHHhhcccc
Q 038944          251 KK-IILHEYLMTKRYLNVIDDVWNIE---VCDIIREILP--DNQNRSRVLITLTEIKMFTFLLET  309 (334)
Q Consensus       251 l~-~~l~~~L~~kr~LlVlDdvw~~~---~w~~l~~~l~--~~~~gsrIivTTr~~~va~~~~~~  309 (334)
                      .+ -.+.+.|.-+.=|+|.|..-+.-   .=.++...|.  ....|--.+..|.+-.|+..++..
T Consensus       115 rQRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~isdr  179 (268)
T COG4608         115 RQRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYISDR  179 (268)
T ss_pred             hhhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhhccc
Confidence            33 23455677888899999975441   1122222222  122366688899999999988753

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.20  E-value=0.027  Score=54.47  Aligned_cols=25  Identities=12%  Similarity=0.145  Sum_probs=21.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +..++.++|.+|+||||++..+...
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~  118 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARY  118 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999999888753

>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide

Probab=96.20  E-value=0.012  Score=53.17  Aligned_cols=103  Identities=21%  Similarity=0.152  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHHHhhhhhccccccchhHhhhHHhHHHhhhccccchHHHHHHHHHHhccc-ccCCchHHHHHHHHHHHHHh
Q 038944            5 FRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHR-EIKNPDLTTVMDEINCFTYE   83 (334)
Q Consensus         5 ~~~~~~kl~~~l~~~e~~l~~~~~~~i~~L~~~l~~l~~~~~~~~~~~~~~~l~~a~~~-~~~~~~v~~Wl~~lr~~ayd   83 (334)
                      +..++++|..+. ..-...+.-++..++-++.+++            .+|.||+..... .........+..++-..||+
T Consensus       298 VdFlL~NLkdfq-~rysdSlaflKnQiqvIQ~ele------------sLqpFLk~V~ee~~nkh~~~ed~a~~ii~kAye  364 (402)
T PF12061_consen  298 VDFLLKNLKDFQ-GRYSDSLAFLKNQIQVIQTELE------------SLQPFLKHVVEEPHNKHDTNEDCATQIIRKAYE  364 (402)
T ss_pred             HHHHHhhHHHHh-ccccchHHHHHHHHHHHHHHHH------------HhhHHHHHHHhccchhhhhhhhHHHHHHHHHhh
Confidence            455666666655 2222233334455555555555            999999998443 33333488999999999999


Q ss_pred             HHHHHHHHHhhhhcccccCCcccchhhhHHHHHHHHHHHHHHHH
Q 038944           84 SEKVIDTFINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQ  127 (334)
Q Consensus        84 ~ED~lD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~i~~~l~  127 (334)
                      +|.++|-+......       .....+.+..+..+|+.++++++
T Consensus       365 vEYVVDaCi~k~~P-------~Wcl~~WL~dIieei~~ik~~i~  401 (402)
T PF12061_consen  365 VEYVVDACISKSVP-------HWCLERWLLDIIEEITCIKAKIQ  401 (402)
T ss_pred             eeeeeehhhcCCCc-------HHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999987543311       11122344555667776666654

The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.

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

Probab=96.19  E-value=0.037  Score=50.12  Aligned_cols=97  Identities=16%  Similarity=0.031  Sum_probs=61.5

Q ss_pred             HhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC---CCCCccccchhhH
Q 038944          172 LIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM---PSSRLSEIMDKNY  248 (334)
Q Consensus       172 L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~---~~~~~~~~~~~~~  248 (334)
                      |-.+=+.-.++=|+|+.|.||||+|-+++-.  ....-...+|+..-+.|++..+..--...+.   ...+. ...... 
T Consensus        53 LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~v~~~~-~~e~q~-  128 (279)
T COG0468          53 LGGGLPRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLVSQPD-TGEQQL-  128 (279)
T ss_pred             hcCCcccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHHHHHHhhhcceeEecCC-CHHHHH-
Confidence            3333356679999999999999999887763  3333347899999999998775433322121   11111 111222 


Q ss_pred             HHHHHHHHHHcCCCeEEEEEeCCCC
Q 038944          249 EMKKIILHEYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       249 ~~l~~~l~~~L~~kr~LlVlDdvw~  273 (334)
                       .+...+......+--|+|+|.+-.
T Consensus       129 -~i~~~~~~~~~~~i~LvVVDSvaa  152 (279)
T COG0468         129 -EIAEKLARSGAEKIDLLVVDSVAA  152 (279)
T ss_pred             -HHHHHHHHhccCCCCEEEEecCcc
Confidence             555666666655567999999853

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=96.19  E-value=0.013  Score=51.23  Aligned_cols=96  Identities=13%  Similarity=0.046  Sum_probs=55.0

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh--------h-H
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK--------N-Y  248 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~--------~-~  248 (334)
                      -++|+|.+|+|||+|+..+.++.. .   +..+++.+.+.. .+.++.+++...-..+....  ...+.        . .
T Consensus        17 r~~I~g~~g~GKt~Ll~~i~~~~~-~---d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~   92 (215)
T PF00006_consen   17 RIGIFGGAGVGKTVLLQEIANNQD-A---DVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYT   92 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHCT-T---TEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHH
T ss_pred             EEEEEcCcccccchhhHHHHhccc-c---cceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhcc
Confidence            589999999999999999988542 1   223777777653 55566666643311110000  00000        0 0


Q ss_pred             -HHHHHHHHHHcCCCeEEEEEeCCCCh-hHHHHHHh
Q 038944          249 -EMKKIILHEYLMTKRYLNVIDDVWNI-EVCDIIRE  282 (334)
Q Consensus       249 -~~l~~~l~~~L~~kr~LlVlDdvw~~-~~w~~l~~  282 (334)
                       =..++.++.  +||..|+++||+-.- +.+..+..
T Consensus        93 a~t~AEyfrd--~G~dVlli~Dsltr~a~A~reis~  126 (215)
T PF00006_consen   93 ALTIAEYFRD--QGKDVLLIIDSLTRWAQAYREISL  126 (215)
T ss_dssp             HHHHHHHHHH--TTSEEEEEEETHHHHHHHHHHHHH
T ss_pred             chhhhHHHhh--cCCceeehhhhhHHHHHHHHhhhc
Confidence             023344444  799999999999332 34444443

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.18  E-value=0.012  Score=54.51  Aligned_cols=37  Identities=24%  Similarity=0.305  Sum_probs=30.1

Q ss_pred             chhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHH
Q 038944          161 LDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEA  199 (334)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v  199 (334)
                      |..+..--+++|++++  .+.+++.|.+|.|||.||-..
T Consensus       229 rn~eQ~~ALdlLld~d--I~lV~L~G~AGtGKTlLALaA  265 (436)
T COG1875         229 RNAEQRVALDLLLDDD--IDLVSLGGKAGTGKTLLALAA  265 (436)
T ss_pred             ccHHHHHHHHHhcCCC--CCeEEeeccCCccHhHHHHHH
Confidence            5666666788888876  889999999999999987543

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.16  E-value=0.021  Score=54.92  Aligned_cols=97  Identities=10%  Similarity=0.042  Sum_probs=55.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchhh------HHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDKN------YEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~~------~~~  250 (334)
                      ..++|+|..|+|||||++.+.+..    ..++.+.+-+.+.. .+.++..+++..-.......  ...+..      --.
T Consensus       163 qrigI~G~sG~GKSTLL~~I~~~~----~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~  238 (444)
T PRK08972        163 QRMGLFAGSGVGKSVLLGMMTRGT----TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCE  238 (444)
T ss_pred             CEEEEECCCCCChhHHHHHhccCC----CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHH
Confidence            578999999999999999998732    12455556676654 44556666554422111000  001110      001


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHH
Q 038944          251 KKIILHEYL--MTKRYLNVIDDVWNI-EVCDII  280 (334)
Q Consensus       251 l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l  280 (334)
                      ..-.+-+++  +|+..|+++||+-.- ..+.++
T Consensus       239 ~A~tiAEyfrd~G~~VLl~~DslTR~A~A~REI  271 (444)
T PRK08972        239 TATTIAEYFRDQGLNVLLLMDSLTRYAQAQREI  271 (444)
T ss_pred             HHHHHHHHHHHcCCCEEEEEcChHHHHHHHHHH
Confidence            222344444  699999999999432 444444

>PRK03839 putative kinase; Provisional

Probab=96.16  E-value=0.0042  Score=52.52  Aligned_cols=22  Identities=14%  Similarity=0.241  Sum_probs=20.2

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .|.|+|++|+||||+++.+.+.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999984

>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=96.15  E-value=0.0041  Score=43.83  Aligned_cols=22  Identities=18%  Similarity=0.267  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +|.|.|..|+||||+++.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998874

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.14  E-value=0.051  Score=44.46  Aligned_cols=21  Identities=19%  Similarity=0.169  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      |+.|+|.+|+||||||+.+..
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~   21 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEE   21 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHH
Confidence            578999999999999999887

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.14  E-value=0.0047  Score=52.30  Aligned_cols=24  Identities=13%  Similarity=0.228  Sum_probs=21.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++|.|+|++|+||||+++.+..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999986

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.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.12  E-value=0.025  Score=47.74  Aligned_cols=25  Identities=12%  Similarity=0.219  Sum_probs=22.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccC
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      -.++.|.|++|+||+||++.++++.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3578899999999999999999954

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.12  E-value=0.1  Score=50.19  Aligned_cols=24  Identities=13%  Similarity=0.147  Sum_probs=20.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|.++|..|+||||++..+..
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~  122 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAY  122 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999998887753

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.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=96.12  E-value=0.037  Score=47.68  Aligned_cols=22  Identities=18%  Similarity=0.030  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++.|+|+.|.|||||.+.+.-
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHH
Confidence            7999999999999999998864

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.11  E-value=0.028  Score=52.46  Aligned_cols=45  Identities=20%  Similarity=0.209  Sum_probs=34.4

Q ss_pred             eeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          158 TVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|....+.++.+.+..-...-.-|.|+|..|+||+++|+.+++.
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHh
Confidence            467777777777777653333345789999999999999999874

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK10867 signal recognition particle protein; Provisional

Probab=96.11  E-value=0.024  Score=54.62  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=18.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ...+|.++|.+|+||||.+..+.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA  121 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLA  121 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHH
Confidence            46899999999999999665553

>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=96.09  E-value=0.018  Score=50.51  Aligned_cols=21  Identities=19%  Similarity=0.200  Sum_probs=19.5

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +|+|.|.+|+||||||+.+..
T Consensus         1 IigI~G~sGSGKTTla~~L~~   21 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQA   21 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHH
Confidence            589999999999999999986

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

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.09  E-value=0.007  Score=52.79  Aligned_cols=123  Identities=16%  Similarity=0.191  Sum_probs=58.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      .+++.|+|..|.|||||.+.+......   .....|+.... .. ...+.++...+.......+..+. +..-...+...
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~~~l---a~~G~~v~a~~-~~-~~~~d~i~~~l~~~~si~~~~S~-f~~el~~l~~~  102 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALIVFL---AHIGSFVPADS-AT-IGLVDKIFTRMSSRESVSSGQSA-FMIDLYQVSKA  102 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHHHHH---HhCCCeeEcCC-cE-EeeeeeeeeeeCCccChhhccch-HHHHHHHHHHH
Confidence            478999999999999999988632110   00111111110 00 00111222222221110000000 00111122222


Q ss_pred             --cCCCeEEEEEeCCCChh---H-----HHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          259 --LMTKRYLNVIDDVWNIE---V-----CDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       259 --L~~kr~LlVlDdvw~~~---~-----w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                        +..++-|++||..-...   +     +..+......+..+..+|+||...+++....
T Consensus       103 l~~~~~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~~~~  161 (213)
T cd03281         103 LRLATRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRSL  161 (213)
T ss_pred             HHhCCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHHhhh
Confidence              24678999999986531   1     2222222222233467999999999988764

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.09  E-value=0.042  Score=56.95  Aligned_cols=48  Identities=21%  Similarity=0.200  Sum_probs=35.4

Q ss_pred             CCCeeechhhHHHHHHHHhc-----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE-----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.++.|.+..++.|.+.+.-           +-...+-+.++|++|+|||+||+.+.+.
T Consensus       452 ~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e  510 (733)
T TIGR01243       452 WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE  510 (733)
T ss_pred             hhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            34577888888877776542           1123345788999999999999999983

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.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.08  E-value=0.095  Score=42.60  Aligned_cols=22  Identities=14%  Similarity=0.291  Sum_probs=19.5

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++.++|++|+||||+|+.+...
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            4678999999999999999873

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>TIGR02012 tigrfam_recA protein RecA

Probab=96.08  E-value=0.018  Score=53.29  Aligned_cols=87  Identities=14%  Similarity=0.025  Sum_probs=52.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-+++-|+|.+|+||||||.++...  ....-..++|+..-+.++..     .+++++......   .....+  +...
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~e--q~l~  123 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGE--QALE  123 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHH--HHHH
Confidence            55679999999999999999876653  22223456788776666543     344454332110   111112  4455


Q ss_pred             HHHHHc-CCCeEEEEEeCCC
Q 038944          254 ILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L-~~kr~LlVlDdvw  272 (334)
                      .+...+ .+.--+||+|.|-
T Consensus       124 ~~~~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       124 IAETLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             HHHHHhhccCCcEEEEcchh
Confidence            554444 3456689999974

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=96.07  E-value=0.097  Score=44.22  Aligned_cols=21  Identities=14%  Similarity=0.265  Sum_probs=18.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|+|++|+||||+++ +..
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~   22 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IAR   22 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHH
Confidence            589999999999999987 444

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.06  E-value=0.01  Score=47.56  Aligned_cols=41  Identities=12%  Similarity=0.148  Sum_probs=29.7

Q ss_pred             hhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          163 DRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ++..++.+.|...-..-.+|.+.|.-|.|||||++.+.+..
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            34445555554432334699999999999999999999853

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.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.05  E-value=0.044  Score=45.94  Aligned_cols=24  Identities=13%  Similarity=0.055  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~   49 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGL   49 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999873

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.

>PRK04040 adenylate kinase; Provisional

Probab=96.03  E-value=0.0055  Score=52.36  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|+|++|+||||+++.+.+
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH
Confidence            46899999999999999999988

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=96.01  E-value=0.016  Score=55.25  Aligned_cols=77  Identities=13%  Similarity=0.220  Sum_probs=48.8

Q ss_pred             CCeeechhhHHHHHHHHhcC------------CCCceEEEEEccCCccHHHHHHHHHccCCCCCce---eeEEEEEcCC-
Q 038944          156 RDTVGLDDRMEELLDLLIEG------------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF---DCHAWVPGTY-  219 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~-  219 (334)
                      ..++|.+..++.+..++...            +...+-|.++|++|+||||||+.+...  ....|   +..-|...+. 
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~--l~~~fi~vD~t~f~e~Gyv   92 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKL--ANAPFIKVEATKFTEVGYV   92 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHH--hCChheeecchhhccCCcc
Confidence            34899999999998887541            112467899999999999999999873  33333   2222222211 


Q ss_pred             CCCHHHHHHHHHHHh
Q 038944          220 PYDADQMLDIVIKFL  234 (334)
Q Consensus       220 ~~~~~~il~~il~~~  234 (334)
                      ..+...+++.+....
T Consensus        93 G~d~e~~ir~L~~~A  107 (443)
T PRK05201         93 GRDVESIIRDLVEIA  107 (443)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            225555555555444

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

Probab=96.01  E-value=0.022  Score=56.18  Aligned_cols=94  Identities=18%  Similarity=0.220  Sum_probs=60.5

Q ss_pred             CCeeechhhHHHHHHHHhc---CC-------CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHH
Q 038944          156 RDTVGLDDRMEELLDLLIE---GP-------PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQ  225 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  225 (334)
                      .++-|.+....++.+++..   .+       .+.+=+-++|++|.|||.||+.+.++  ..-.|     ..++.+     
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAge--l~vPf-----~~isAp-----  257 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGE--LGVPF-----LSISAP-----  257 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhh--cCCce-----Eeecch-----
Confidence            4577899888888888753   11       24556788999999999999999994  44344     222221     


Q ss_pred             HHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 038944          226 MLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       226 il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~  273 (334)
                         +|+....+..       ++  .+.+-+.+.-..-.+++++|++.-
T Consensus       258 ---eivSGvSGES-------Ek--kiRelF~~A~~~aPcivFiDeIDA  293 (802)
T KOG0733|consen  258 ---EIVSGVSGES-------EK--KIRELFDQAKSNAPCIVFIDEIDA  293 (802)
T ss_pred             ---hhhcccCccc-------HH--HHHHHHHHHhccCCeEEEeecccc
Confidence               2333333322       22  344444455567789999999963

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.00  E-value=0.077  Score=47.28  Aligned_cols=122  Identities=11%  Similarity=0.097  Sum_probs=70.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc--CCCCC---------ce---eeEEEEEcCC----CC--CHH---------------
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS--SYVKH---------YF---DCHAWVPGTY----PY--DAD---------------  224 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~--~~~~~---------~F---~~~~wv~vs~----~~--~~~---------------  224 (334)
                      .+++|+|+.|.|||||.+.+..=  +....         .+   ...+||+=..    .|  ++.               
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~~  110 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWFR  110 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCcccccccc
Confidence            68999999999999999999861  11110         11   2345553211    11  122               


Q ss_pred             -------HHHHHHHHHhCCCCCc---cccchhhHHHHHH-HHHHHcCCCeEEEEEeCCCCh------hHHHHHHhhCCCC
Q 038944          225 -------QMLDIVIKFLMPSSRL---SEIMDKNYEMKKI-ILHEYLMTKRYLNVIDDVWNI------EVCDIIREILPDN  287 (334)
Q Consensus       225 -------~il~~il~~~~~~~~~---~~~~~~~~~~l~~-~l~~~L~~kr~LlVlDdvw~~------~~w~~l~~~l~~~  287 (334)
                             +...+.|+.++.....   ....+-.  +.+. .|-+.|..+.=|++||.--..      ...-.+...+...
T Consensus       111 ~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGG--Q~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e  188 (254)
T COG1121         111 RLNKKDKEKVDEALERVGMEDLRDRQIGELSGG--QKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE  188 (254)
T ss_pred             cccHHHHHHHHHHHHHcCchhhhCCcccccCcH--HHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC
Confidence                   3344445555443211   0222222  4443 344567888889999986532      3555555555443


Q ss_pred             CCCeEEEEecCChHHHhh
Q 038944          288 QNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       288 ~~gsrIivTTr~~~va~~  305 (334)
                        |.-|+++|.+-+....
T Consensus       189 --g~tIl~vtHDL~~v~~  204 (254)
T COG1121         189 --GKTVLMVTHDLGLVMA  204 (254)
T ss_pred             --CCEEEEEeCCcHHhHh
Confidence              7889999998775554

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.00  E-value=0.0044  Score=53.24  Aligned_cols=21  Identities=24%  Similarity=0.289  Sum_probs=19.6

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +|+|.|.+|+|||||++.+..
T Consensus         1 iigi~G~~GsGKSTl~~~l~~   21 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIE   21 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999976

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=96.00  E-value=0.032  Score=53.71  Aligned_cols=99  Identities=13%  Similarity=0.014  Sum_probs=55.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh---h---HH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK---N---YE  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~---~---~~  249 (334)
                      -..++|+|..|+|||||++.+.+...    -+..+.+-+.... .+.++..+.+..-+......  ...+.   .   --
T Consensus       158 Gqri~I~G~sG~GKTtLL~~I~~~~~----~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~  233 (442)
T PRK08927        158 GQRMGIFAGSGVGKSVLLSMLARNAD----ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAA  233 (442)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccC----CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHH
Confidence            45789999999999999999997432    1344556666554 44455555554422111000  00111   0   00


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCCC-hhHHHHHH
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVWN-IEVCDIIR  281 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw~-~~~w~~l~  281 (334)
                      ...-.+-+++  +|+..|+++||+-. ...+.++.
T Consensus       234 ~~a~tiAEyfrd~G~~Vll~~DslTr~A~A~REis  268 (442)
T PRK08927        234 YLTLAIAEYFRDQGKDVLCLMDSVTRFAMAQREIG  268 (442)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCcHHHHhhhhHHH
Confidence            2223344444  69999999999943 23444433

>PRK08149 ATP synthase SpaL; Validated

Probab=95.99  E-value=0.03  Score=53.76  Aligned_cols=87  Identities=14%  Similarity=0.096  Sum_probs=51.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCCcc-----cc-----chhhH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSRLS-----EI-----MDKNY  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~~~-----~~-----~~~~~  248 (334)
                      ..++|+|..|+|||||.+.+.+....    +..+...+.. .-++..+..+.+..........     +.     .... 
T Consensus       152 q~i~I~G~sG~GKTTLl~~i~~~~~~----dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~-  226 (428)
T PRK08149        152 QRMGIFASAGCGKTSLMNMLIEHSEA----DVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAA-  226 (428)
T ss_pred             CEEEEECCCCCChhHHHHHHhcCCCC----CeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHH-
Confidence            47899999999999999999874322    2223333433 3356666666665432211100     00     0001 


Q ss_pred             HHHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          249 EMKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       249 ~~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                       .....+-+++  +||..||++||+-
T Consensus       227 -~~a~tiAE~fr~~G~~Vll~~DslT  251 (428)
T PRK08149        227 -LVATTVAEYFRDQGKRVVLFIDSMT  251 (428)
T ss_pred             -HHHHHHHHHHHHcCCCEEEEccchH
Confidence             2233344444  6999999999994

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=95.97  E-value=0.056  Score=45.85  Aligned_cols=58  Identities=10%  Similarity=0.146  Sum_probs=39.8

Q ss_pred             HHHHHHHHcCCCeEEEEEeCC----CChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          251 KKIILHEYLMTKRYLNVIDDV----WNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       251 l~~~l~~~L~~kr~LlVlDdv----w~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      -.-.+-+.+-++.-+++=|.-    .....|+-+...-.-+..|.-||+.|.+.++...+..
T Consensus       144 QRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~~  205 (223)
T COG2884         144 QRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMRH  205 (223)
T ss_pred             HHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhccC
Confidence            334455556677778888864    3335677665443346789999999999998887743

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

Probab=95.96  E-value=0.029  Score=47.03  Aligned_cols=46  Identities=22%  Similarity=0.194  Sum_probs=33.0

Q ss_pred             eeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          158 TVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ++|....+.++++.+..-.....-|-|+|..|+||+.+|+.+++..
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            4688888888888876522222345599999999999999999953

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

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.95  E-value=0.0069  Score=52.53  Aligned_cols=32  Identities=25%  Similarity=0.315  Sum_probs=26.3

Q ss_pred             HHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          171 LLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       171 ~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+..+....+.+.|+|++|+|||||++.+.+.
T Consensus         5 ~~~~~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          5 WLFNKPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             cccCCCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            44555567789999999999999999999763

>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=95.95  E-value=0.044  Score=45.85  Aligned_cols=21  Identities=19%  Similarity=0.278  Sum_probs=19.1

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++.++|++|+||||++..+..
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~   22 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLAL   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999988876

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.95  E-value=0.012  Score=51.77  Aligned_cols=25  Identities=4%  Similarity=0.024  Sum_probs=21.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....+.|+|..|+|||+||+.+++.
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3467889999999999999999984

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.94  E-value=0.0068  Score=50.52  Aligned_cols=24  Identities=13%  Similarity=0.155  Sum_probs=21.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|.++|++|+||||+|+.+...
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999999999883

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.93  E-value=0.038  Score=46.26  Aligned_cols=24  Identities=17%  Similarity=0.079  Sum_probs=21.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC
Confidence            458999999999999999999873

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=95.93  E-value=0.022  Score=49.71  Aligned_cols=45  Identities=24%  Similarity=0.242  Sum_probs=36.0

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.++||-++-++++--.-.+++  .+-+-|.||+|+||||-+..+.+
T Consensus        26 l~dIVGNe~tv~rl~via~~gn--mP~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAKEGN--MPNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHHcCC--CCceEeeCCCCCchhhHHHHHHH
Confidence            3568999998888876666654  77788999999999997776665

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.93  E-value=0.038  Score=49.79  Aligned_cols=97  Identities=12%  Similarity=-0.008  Sum_probs=56.9

Q ss_pred             eEEEEEccCCccHHHHH-HHHHccCCCCCceee-EEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc-----cc-chh----
Q 038944          180 SVVVILDSIGLDKAAFA-GEAYNSSYVKHYFDC-HAWVPGTYPY-DADQMLDIVIKFLMPSSRLS-----EI-MDK----  246 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~il~~il~~~~~~~~~~-----~~-~~~----  246 (334)
                      .-++|.|..|+|||+|+ ..+.+.  .  +-+. ++++-+.+.. .+.++..++.+.-.......     +. ...    
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~--~--~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a  145 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQ--K--GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLA  145 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHh--c--CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHH
Confidence            36899999999999995 667663  1  1233 3666676654 45566666664321111000     00 000    


Q ss_pred             ----hHHHHHHHHHHHcCCCeEEEEEeCCCCh-hHHHHHHhhC
Q 038944          247 ----NYEMKKIILHEYLMTKRYLNVIDDVWNI-EVCDIIREIL  284 (334)
Q Consensus       247 ----~~~~l~~~l~~~L~~kr~LlVlDdvw~~-~~w~~l~~~l  284 (334)
                          .  ..++.++.  +|+..|+++||+-.- +.|.++...+
T Consensus       146 ~~~a~--aiAE~fr~--~G~~Vlvl~DslTr~A~A~rEisl~~  184 (274)
T cd01132         146 PYTGC--AMGEYFMD--NGKHALIIYDDLSKQAVAYRQMSLLL  184 (274)
T ss_pred             HHHHH--HHHHHHHH--CCCCEEEEEcChHHHHHHHHHHHHhc
Confidence                1  23333333  689999999999543 6777776554

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.93  E-value=0.042  Score=53.04  Aligned_cols=89  Identities=13%  Similarity=0.118  Sum_probs=48.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CCcccc--chhhHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPS-------SRLSEI--MDKNYE  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~-------~~~~~~--~~~~~~  249 (334)
                      -..++|+|..|+|||||++.+.....   .....++..--+.-++..+....+......       .+.+..  ....  
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~---pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~--  239 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADA---FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAP--  239 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC---CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHH--
Confidence            34799999999999999998886322   223344433223345555555444433111       010000  0001  


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      ...-.+-+++  +|+..|+++||+-
T Consensus       240 ~~a~~iAEyfrd~G~~Vll~~DslT  264 (450)
T PRK06002        240 LTATAIAEYFRDRGENVLLIVDSVT  264 (450)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchH
Confidence            1222333444  6899999999994

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

Probab=95.92  E-value=0.021  Score=52.95  Aligned_cols=87  Identities=16%  Similarity=0.034  Sum_probs=52.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-+++-|+|++|+||||||.++.-.  ....-..++|+..-..+++.     .+++++......   ...+.+  ++..
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~e--q~l~  123 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGE--QALE  123 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHH--HHHH
Confidence            45678999999999999999887652  11223457788877766653     334444321110   111122  4555


Q ss_pred             HHHHHcC-CCeEEEEEeCCC
Q 038944          254 ILHEYLM-TKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L~-~kr~LlVlDdvw  272 (334)
                      .+...++ +.--+||+|-|-
T Consensus       124 i~~~li~s~~~~lIVIDSva  143 (325)
T cd00983         124 IADSLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             HHHHHHhccCCCEEEEcchH
Confidence            5544443 455689999974

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09354 recA recombinase A; Provisional

Probab=95.91  E-value=0.026  Score=52.74  Aligned_cols=87  Identities=17%  Similarity=0.037  Sum_probs=53.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-+++-|+|++|+|||||+-++....  ...-..++|+..-..++..     .+++++......   .....+  +...
T Consensus        58 p~G~IteI~G~~GsGKTtLal~~~~~~--~~~G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~E--q~l~  128 (349)
T PRK09354         58 PRGRIVEIYGPESSGKTTLALHAIAEA--QKAGGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGE--QALE  128 (349)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHH--HHHH
Confidence            556799999999999999998876532  2223567888877777653     345554432110   111122  4444


Q ss_pred             HHHHHc-CCCeEEEEEeCCC
Q 038944          254 ILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L-~~kr~LlVlDdvw  272 (334)
                      .+...+ .++--+||+|-|-
T Consensus       129 i~~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        129 IADTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             HHHHHhhcCCCCEEEEeChh
Confidence            555444 3456689999984

>PRK00625 shikimate kinase; Provisional

Probab=95.91  E-value=0.0061  Score=51.37  Aligned_cols=21  Identities=10%  Similarity=0.128  Sum_probs=19.4

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.++||+|+||||+++.+.+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~   22 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAK   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999987

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=95.91  E-value=0.022  Score=55.27  Aligned_cols=90  Identities=11%  Similarity=0.113  Sum_probs=56.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccch--------hhH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMD--------KNY  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~--------~~~  248 (334)
                      .-++|.|.+|+|||||+..+.+.... .+-++++++-+.... .+.++..+++..-.......  ...+        .. 
T Consensus       144 QR~gIfa~~G~GKt~Ll~~~~~~~~~-~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~-  221 (461)
T PRK12597        144 GKTGLFGGAGVGKTVLMMELIFNISK-QHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVV-  221 (461)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHh-hCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHH-
Confidence            36899999999999999888774322 256778888877654 55666666665322111000  0001        11 


Q ss_pred             HHHHHHHHHHc---CCCeEEEEEeCCC
Q 038944          249 EMKKIILHEYL---MTKRYLNVIDDVW  272 (334)
Q Consensus       249 ~~l~~~l~~~L---~~kr~LlVlDdvw  272 (334)
                       .....+-+++   +|+..|+++||+-
T Consensus       222 -~~a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        222 -LTGLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             -HHHHHHHHHHHHhcCCceEEEeccch
Confidence             2344455665   4899999999993

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

Probab=95.90  E-value=0.036  Score=52.01  Aligned_cols=26  Identities=12%  Similarity=0.058  Sum_probs=23.6

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .....+.|+|++|.|||.+|+.+++.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            45679999999999999999999994

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.90  E-value=0.0084  Score=50.39  Aligned_cols=25  Identities=12%  Similarity=0.166  Sum_probs=22.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++++|+|..|+|||||++.+...
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~   29 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPA   29 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHH
Confidence            4679999999999999999999873

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=95.90  E-value=0.012  Score=47.28  Aligned_cols=86  Identities=13%  Similarity=0.086  Sum_probs=48.3

Q ss_pred             EEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCC
Q 038944          182 VVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT  261 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~  261 (334)
                      |-++|.+|+|||+||+.+..  .....   ..-+.++...+..+++...--. ....    .....  .+...+.     
T Consensus         2 vlL~G~~G~GKt~l~~~la~--~~~~~---~~~i~~~~~~~~~dl~g~~~~~-~~~~----~~~~~--~l~~a~~-----   64 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAA--LLGRP---VIRINCSSDTTEEDLIGSYDPS-NGQF----EFKDG--PLVRAMR-----   64 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHH--HHTCE---EEEEE-TTTSTHHHHHCEEET--TTTT----CEEE---CCCTTHH-----
T ss_pred             EEEECCCCCCHHHHHHHHHH--Hhhcc---eEEEEeccccccccceeeeeec-cccc----ccccc--ccccccc-----
Confidence            56899999999999999987  32222   2235677777777665433211 1110    11101  1111111     


Q ss_pred             CeEEEEEeCCCC--hhHHHHHHhhC
Q 038944          262 KRYLNVIDDVWN--IEVCDIIREIL  284 (334)
Q Consensus       262 kr~LlVlDdvw~--~~~w~~l~~~l  284 (334)
                      +..++|||++..  ...+..|...+
T Consensus        65 ~~~il~lDEin~a~~~v~~~L~~ll   89 (139)
T PF07728_consen   65 KGGILVLDEINRAPPEVLESLLSLL   89 (139)
T ss_dssp             EEEEEEESSCGG--HHHHHTTHHHH
T ss_pred             ceeEEEECCcccCCHHHHHHHHHHH
Confidence            789999999973  45555554443

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.

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.89  E-value=0.058  Score=52.69  Aligned_cols=101  Identities=12%  Similarity=0.079  Sum_probs=56.1

Q ss_pred             EEEEEccCCccHHHHH-HHHHccCCC-----CCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhh--HH
Q 038944          181 VVVILDSIGLDKAAFA-GEAYNSSYV-----KHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKN--YE  249 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa-~~v~~~~~~-----~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~--~~  249 (334)
                      -++|.|-.|+|||+|| ..+.|...+     .++-..++++.+.+..+.-.-+.+.++.-+.-....   ...++.  ++
T Consensus       191 R~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~r  270 (574)
T PTZ00185        191 RELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGLQ  270 (574)
T ss_pred             EEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHHH
Confidence            5789999999999996 666664322     124456788889887643333444444443111110   000000  00


Q ss_pred             ----HHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHH
Q 038944          250 ----MKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       250 ----~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                          -..-.+-+++  +|+..|+|+||+-.. ..+.++.
T Consensus       271 ~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr~A~A~REIS  309 (574)
T PTZ00185        271 YLAPYSGVTMGEYFMNRGRHCLCVYDDLSKQAVAYRQIS  309 (574)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEEcCchHHHHHHHHHH
Confidence                1122233333  689999999999543 4454443

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

Probab=95.88  E-value=0.0071  Score=49.08  Aligned_cols=39  Identities=10%  Similarity=0.062  Sum_probs=26.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY  219 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  219 (334)
                      ++|.|+|..|+|||||++.+.+.. .+..+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l-~~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINEL-KRRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHH-HHTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-hHcCCceEEEEEccC
Confidence            589999999999999999999842 124455555555544

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=95.88  E-value=0.015  Score=50.99  Aligned_cols=122  Identities=14%  Similarity=0.083  Sum_probs=58.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKII  254 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~  254 (334)
                      +..++.|.|..|.||||+.+.+.--.-   .+.+..+|+...  ..-.+...++..++......   ..-..++.++...
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~~~~---la~~g~~vpa~~--~~~~~~~~il~~~~l~d~~~~~lS~~~~e~~~~a~i  103 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGVIVL---MAQIGCFVPCDS--ADIPIVDCILARVGASDSQLKGVSTFMAEMLETAAI  103 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHH---HHHhCCCcCccc--EEEeccceeEeeeccccchhcCcChHHHHHHHHHHH
Confidence            457999999999999999887652100   001111111111  00011222222222211100   0000000022222


Q ss_pred             HHHHcCCCeEEEEEeCC---CChh-----HHHHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          255 LHEYLMTKRYLNVIDDV---WNIE-----VCDIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       255 l~~~L~~kr~LlVlDdv---w~~~-----~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      ++.  .+++-|++||..   -+..     .|..+ ..+.. ..|+.+|+||...++...+..
T Consensus       104 l~~--~~~~sLvLLDEp~~gT~~lD~~~~~~~il-~~l~~-~~~~~vlisTH~~el~~~~~~  161 (222)
T cd03285         104 LKS--ATENSLIIIDELGRGTSTYDGFGLAWAIA-EYIAT-QIKCFCLFATHFHELTALADE  161 (222)
T ss_pred             HHh--CCCCeEEEEecCcCCCChHHHHHHHHHHH-HHHHh-cCCCeEEEEechHHHHHHhhc
Confidence            222  356789999999   4332     33322 22222 347889999998888876653

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.87  E-value=0.047  Score=53.58  Aligned_cols=47  Identities=23%  Similarity=0.216  Sum_probs=31.9

Q ss_pred             CCeeechhhHHHHHHHHhc--------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIE--------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~--------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|.+.-++.+.+....        +-...+-|-++|++|+|||.+|+.+.+.
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e  282 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAND  282 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            4567776665555432211        1133466889999999999999999983

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

Probab=95.81  E-value=0.0074  Score=50.88  Aligned_cols=23  Identities=13%  Similarity=0.212  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|+|+.|+|||||++.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999999998764

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.

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

Probab=95.80  E-value=0.041  Score=45.56  Aligned_cols=120  Identities=11%  Similarity=0.094  Sum_probs=59.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEE--EEEcCCCCCHHHHHHHHHHHh-----CCCCC-ccccchh---hH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHA--WVPGTYPYDADQMLDIVIKFL-----MPSSR-LSEIMDK---NY  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~--wv~vs~~~~~~~il~~il~~~-----~~~~~-~~~~~~~---~~  248 (334)
                      ..|-|++-.|.||||+|--+.-. ....-+.+.+  |+.-........++..+ ..+     +.... .......   ..
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~r-a~~~g~~v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~a   80 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALR-ALGHGYRVGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAAA   80 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH-HHHCCCeEEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHHH
Confidence            46788888899999998766531 1112222222  23322233443433333 000     00000 0000000   00


Q ss_pred             HHHHHHHHHHcCC-CeEEEEEeCCCCh-----hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          249 EMKKIILHEYLMT-KRYLNVIDDVWNI-----EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       249 ~~l~~~l~~~L~~-kr~LlVlDdvw~~-----~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      .......++.+.. +-=|+|||++-..     -..+.+...+.....+.-||+|.|+..
T Consensus        81 ~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          81 AEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            1334444555544 4459999998543     244555555544444567999999753

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.80  E-value=0.0091  Score=50.19  Aligned_cols=25  Identities=16%  Similarity=0.039  Sum_probs=22.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.+|.|+|.+|+||||+|+.+...
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4569999999999999999999873

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.79  E-value=0.012  Score=48.35  Aligned_cols=44  Identities=20%  Similarity=0.102  Sum_probs=33.8

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCC
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPS  237 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~  237 (334)
                      +|.|-|.+|+||||+|+.+.++....  |           .+...++++|++..+..
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~--~-----------vsaG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK--L-----------VSAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc--e-----------eeccHHHHHHHHHcCCC
Confidence            68999999999999999999853321  1           13457888888887764

>PRK14974 cell division protein FtsY; Provisional

Probab=95.78  E-value=0.12  Score=48.23  Aligned_cols=24  Identities=17%  Similarity=0.153  Sum_probs=20.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..++.++|++|+||||++..+..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~  162 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAY  162 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH
Confidence            468999999999999997776664

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.78  E-value=0.046  Score=52.66  Aligned_cols=90  Identities=14%  Similarity=0.077  Sum_probs=52.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchhh-H-----H
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDKN-Y-----E  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~~-~-----~  249 (334)
                      -..++|.|..|+|||||.+.+++...    -++++++-+.+.. .+.++....+..-..+....  ...+.. .     -
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAG  237 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHH
Confidence            35789999999999999999998432    2466777777654 44455544443211110000  011110 0     0


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      ...-.+-+++  +||..|+++||+-
T Consensus       238 ~~a~tiAEyfrd~G~~Vll~~DslT  262 (439)
T PRK06936        238 FVATSIAEYFRDQGKRVLLLMDSVT  262 (439)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchh
Confidence            1122234444  6999999999994

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

Probab=95.77  E-value=0.059  Score=52.39  Aligned_cols=109  Identities=17%  Similarity=0.116  Sum_probs=61.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      .++.-+.+.|++|+|||+||-.+..+    ..|+..--+  |.    +++       ++..    +...-.  .+...+.
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKii--Sp----e~m-------iG~s----EsaKc~--~i~k~F~  592 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKII--SP----EDM-------IGLS----ESAKCA--HIKKIFE  592 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEe--Ch----HHc-------cCcc----HHHHHH--HHHHHHH
Confidence            45667778899999999999999873    346543222  11    110       0000    011111  2333333


Q ss_pred             HHcCCCeEEEEEeCCCChhHHHHH------------HhhCCCC-CCCeE--EEEecCChHHHhhccc
Q 038944          257 EYLMTKRYLNVIDDVWNIEVCDII------------REILPDN-QNRSR--VLITLTEIKMFTFLLE  308 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~~~w~~l------------~~~l~~~-~~gsr--IivTTr~~~va~~~~~  308 (334)
                      ..-+..=-.||+||+...-+|-.|            ...|... .+|-|  |+-||....|.+.|+-
T Consensus       593 DAYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i  659 (744)
T KOG0741|consen  593 DAYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGI  659 (744)
T ss_pred             HhhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCH
Confidence            344566679999999655444322            2233221 23444  5558888889888874

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.77  E-value=0.06  Score=52.42  Aligned_cols=52  Identities=21%  Similarity=0.314  Sum_probs=37.6

Q ss_pred             CCCCeeechhh---HHHHHHHHhcCC-------CCceEEEEEccCCccHHHHHHHHHccCCC
Q 038944          154 KSRDTVGLDDR---MEELLDLLIEGP-------PQLSVVVILDSIGLDKAAFAGEAYNSSYV  205 (334)
Q Consensus       154 ~~~~~vGr~~~---~~~l~~~L~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~  205 (334)
                      .-+++-|.|+.   +++++++|.++.       .=.+=|-.+|++|.|||-||+.|.....+
T Consensus       302 ~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~V  363 (752)
T KOG0734|consen  302 TFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGV  363 (752)
T ss_pred             ccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCC
Confidence            34566777654   566777887652       22456788999999999999999985443

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

Probab=95.77  E-value=0.013  Score=53.05  Aligned_cols=63  Identities=17%  Similarity=0.105  Sum_probs=42.9

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHH
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQML  227 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il  227 (334)
                      -.+|+..+.....+..||+|.|.||+||+||.-.+-....-+.|=-.++=|.-|++|+-..||
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiL   99 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSIL   99 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCcccc
Confidence            456777777766778899999999999999998776643223332334445556666544444

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.77  E-value=0.0078  Score=50.70  Aligned_cols=22  Identities=18%  Similarity=0.318  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +++.|+|+.|+|||||++.+.+
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHc
Confidence            4799999999999999999998

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.

>PTZ00035 Rad51 protein; Provisional

Probab=95.76  E-value=0.12  Score=48.45  Aligned_cols=105  Identities=8%  Similarity=-0.028  Sum_probs=59.1

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCC----CceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc--
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVK----HYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS--  241 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~--  241 (334)
                      |=++|..+=+.-.++.|+|.+|+|||||+..+.-.....    ..=...+|+.....|++.++ .++.+.++......  
T Consensus       107 LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~~~~~~l~  185 (337)
T PTZ00035        107 LDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGLDPEDVLD  185 (337)
T ss_pred             HHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCCChHhHhh
Confidence            333444443566899999999999999998886432211    01124568888787888774 44455554432110  


Q ss_pred             -----ccchhh-HHHHHHHHHHHc-CCCeEEEEEeCCCC
Q 038944          242 -----EIMDKN-YEMKKIILHEYL-MTKRYLNVIDDVWN  273 (334)
Q Consensus       242 -----~~~~~~-~~~l~~~l~~~L-~~kr~LlVlDdvw~  273 (334)
                           ...+.+ +-.+...+...+ .++--|||+|-+-.
T Consensus       186 nI~~~~~~~~e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        186 NIAYARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             ceEEEccCCHHHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence                 011111 012223333333 34456999999853

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.75  E-value=0.16  Score=48.84  Aligned_cols=45  Identities=9%  Similarity=-0.007  Sum_probs=28.8

Q ss_pred             HHHHHHHHc---CCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEe
Q 038944          251 KKIILHEYL---MTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT  296 (334)
Q Consensus       251 l~~~l~~~L---~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivT  296 (334)
                      +...+..+.   ..-+.+||||=-...++..++...|...+ =+.+|+|
T Consensus       287 ~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~~~f~~~~-~~~~I~T  334 (420)
T PRK14721        287 LAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVISAYQGHG-IHGCIIT  334 (420)
T ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHHHHhcCCC-CCEEEEE
Confidence            444444432   23367888888888888888887775433 3457776

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.74  E-value=0.033  Score=52.67  Aligned_cols=23  Identities=13%  Similarity=0.211  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.++.++|+.|+||||++.++..
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~  159 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAA  159 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999988876

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.73  E-value=0.026  Score=53.00  Aligned_cols=114  Identities=12%  Similarity=0.094  Sum_probs=65.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      -..+.|.|..|+||||+.+.+.+  .+..+...+++. +..+..  -..... ..+-....  ...+..  .....++..
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~--~i~~~~~~~i~t-iEdp~E--~~~~~~-~~~i~q~e--vg~~~~--~~~~~l~~~  191 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMID--YINKNAAGHIIT-IEDPIE--YVHRNK-RSLINQRE--VGLDTL--SFANALRAA  191 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH--hhCcCCCCEEEE-EcCChh--hhccCc-cceEEccc--cCCCCc--CHHHHHHHh
Confidence            46899999999999999999887  343344445543 222211  000000 00000000  011112  455567777


Q ss_pred             cCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          259 LMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      |....=.|++|.+.+.+.+.....+   ...|--|+.|+.-.+++..
T Consensus       192 lr~~pd~i~vgEird~~~~~~~l~a---a~tGh~v~~T~Ha~~~~~~  235 (343)
T TIGR01420       192 LREDPDVILIGEMRDLETVELALTA---AETGHLVFGTLHTNSAAQT  235 (343)
T ss_pred             hccCCCEEEEeCCCCHHHHHHHHHH---HHcCCcEEEEEcCCCHHHH
Confidence            8778889999999988877654433   2345557777776665543

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.72  E-value=0.022  Score=56.19  Aligned_cols=89  Identities=15%  Similarity=0.062  Sum_probs=48.2

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEE-EEEcCCCC-CHHHHHHHHHHHhCCCCC-cc--ccchhhHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHA-WVPGTYPY-DADQMLDIVIKFLMPSSR-LS--EIMDKNYEMKKIIL  255 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~-wv~vs~~~-~~~~il~~il~~~~~~~~-~~--~~~~~~~~~l~~~l  255 (334)
                      -..|+|.+|+|||||++.|.+... ..+=++.+ .+-|.+.. .+..+.+.+-..+-.... .+  ......  .+.-.+
T Consensus       418 R~LIvgpp~aGKTtLL~~IAn~i~-~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a--~~ai~~  494 (672)
T PRK12678        418 RGLIVSPPKAGKTTILQNIANAIT-TNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVA--ELAIER  494 (672)
T ss_pred             EeEEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHH--HHHHHH
Confidence            578999999999999999988321 12333443 44555543 233333332000100111 00  111112  334445


Q ss_pred             HHHc--CCCeEEEEEeCCC
Q 038944          256 HEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       256 ~~~L--~~kr~LlVlDdvw  272 (334)
                      -++|  .|+..||++|++-
T Consensus       495 Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        495 AKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHcCCCEEEEEeCch
Confidence            5555  7899999999994

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

Probab=95.71  E-value=0.021  Score=48.31  Aligned_cols=22  Identities=23%  Similarity=0.323  Sum_probs=20.1

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .|.|+|.+|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999985

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.71  E-value=0.0071  Score=52.21  Aligned_cols=22  Identities=9%  Similarity=-0.028  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++.|+|..|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6999999999999999999983

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=95.70  E-value=0.013  Score=46.47  Aligned_cols=28  Identities=18%  Similarity=0.182  Sum_probs=19.4

Q ss_pred             EEEEccCCccHHHHHHHHHccCCCCCceee
Q 038944          182 VVILDSIGLDKAAFAGEAYNSSYVKHYFDC  211 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~~~~~~~F~~  211 (334)
                      +-++|.+|+||||+|+.+..  .+...|..
T Consensus         2 vLleg~PG~GKT~la~~lA~--~~~~~f~R   29 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALAR--SLGLSFKR   29 (131)
T ss_dssp             EEEES---HHHHHHHHHHHH--HTT--EEE
T ss_pred             EeeECCCccHHHHHHHHHHH--HcCCceeE
Confidence            56899999999999999998  66677754

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.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.67  E-value=0.023  Score=54.83  Aligned_cols=99  Identities=8%  Similarity=0.128  Sum_probs=59.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc-----cc-----chhhH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS-----EI-----MDKNY  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~-----~~-----~~~~~  248 (334)
                      .-++|.|.+|+|||+|+..+..+.. +.+-++++++-+.... .+.+++.++...-..+....     +.     .... 
T Consensus       139 Qr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~-  216 (449)
T TIGR03305       139 GKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVG-  216 (449)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHH-
Confidence            3689999999999999998876532 2334678888887665 45666776665321111000     00     0011 


Q ss_pred             HHHHHHHHHHc---CCCeEEEEEeCCCCh-hHHHHHH
Q 038944          249 EMKKIILHEYL---MTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       249 ~~l~~~l~~~L---~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                       ...-.+-+++   +|+..|+++||+-.- ..+.++.
T Consensus       217 -~~a~tiAEyfrd~~G~~VLl~~DslTR~A~A~REis  252 (449)
T TIGR03305       217 -HTALTMAEYFRDDEKQDVLLLIDNIFRFIQAGSEVS  252 (449)
T ss_pred             -HHHHHHHHHHHHhcCCceEEEecChHHHHHHHHHHH
Confidence             2334455555   579999999999432 3444443

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.67  E-value=0.0073  Score=51.51  Aligned_cols=22  Identities=18%  Similarity=0.040  Sum_probs=20.2

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999884

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.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.67  E-value=0.014  Score=57.81  Aligned_cols=35  Identities=20%  Similarity=0.244  Sum_probs=28.5

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|.....+..+|+|.|..|+||||||+.+...
T Consensus        54 a~qlL~~~~~~riIIGIaGpSGSGKTTLAk~Lagl   88 (656)
T PLN02318         54 ACQLLAQKNDGIILVGVAGPSGAGKTVFTEKVLNF   88 (656)
T ss_pred             HHHHHHhcCCCeEEEEEECCCCCcHHHHHHHHHhh
Confidence            44555555567899999999999999999999873

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.66  E-value=0.0077  Score=51.02  Aligned_cols=22  Identities=36%  Similarity=0.371  Sum_probs=20.1

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999874

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK13947 shikimate kinase; Provisional

Probab=95.66  E-value=0.0088  Score=49.93  Aligned_cols=21  Identities=14%  Similarity=0.284  Sum_probs=19.6

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -|.|+|++|+||||+|+.+.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~   23 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVAT   23 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHH
Confidence            488999999999999999988

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=95.65  E-value=0.034  Score=53.88  Aligned_cols=92  Identities=12%  Similarity=0.166  Sum_probs=53.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh---h---HHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK---N---YEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~---~---~~~  250 (334)
                      .-++|.|..|+|||||+..+........ =+.++++-+.... .+.+++.+++..-..+....  ...+.   .   --.
T Consensus       145 QR~gIfa~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~  223 (463)
T PRK09280        145 GKIGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVAL  223 (463)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            3689999999999999988765322111 1356777776654 56677777765422111000  00000   0   002


Q ss_pred             HHHHHHHHc---CCCeEEEEEeCCC
Q 038944          251 KKIILHEYL---MTKRYLNVIDDVW  272 (334)
Q Consensus       251 l~~~l~~~L---~~kr~LlVlDdvw  272 (334)
                      ..-.+-+++   +||..||++||+-
T Consensus       224 ~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        224 TGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHhcCCceEEEecchH
Confidence            233455555   7899999999994

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.65  E-value=0.075  Score=52.82  Aligned_cols=48  Identities=13%  Similarity=0.074  Sum_probs=36.0

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|....+.++++.+..-...-.-|.|+|..|+||+++|+.++..
T Consensus       203 f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~  250 (520)
T PRK10820        203 FSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLR  250 (520)
T ss_pred             ccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHh
Confidence            346899998888888777532111223779999999999999999864

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

Probab=95.64  E-value=0.017  Score=48.94  Aligned_cols=37  Identities=14%  Similarity=0.087  Sum_probs=29.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPG  217 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~v  217 (334)
                      .+++.|+|+.|+|||||++.+..  .....|...++.+-
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~--~~~~~~~~~v~~TT   38 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQ--EFPDKFGRVVSHTT   38 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHH--HSTTTEEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--hcccccccceeecc
Confidence            46889999999999999999998  55667865555544

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 ....

>cd01878 HflX HflX subfamily

Probab=95.64  E-value=0.044  Score=47.09  Aligned_cols=26  Identities=8%  Similarity=0.144  Sum_probs=22.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccC
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ....|+|+|.+|+|||||...+.+..
T Consensus        40 ~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          40 GIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHhcch
Confidence            45789999999999999999998753

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.

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=95.64  E-value=0.06  Score=49.56  Aligned_cols=112  Identities=15%  Similarity=0.103  Sum_probs=65.7

Q ss_pred             CCeeechhhHHHHHHHHhcC--CCCceEEEEEccCCccHHHHHHHHHcc-CCCCCceeeEEEEEcCCCCCH-HHHHHHHH
Q 038944          156 RDTVGLDDRMEELLDLLIEG--PPQLSVVVILDSIGLDKAAFAGEAYNS-SYVKHYFDCHAWVPGTYPYDA-DQMLDIVI  231 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~-~~~~~~F~~~~wv~vs~~~~~-~~il~~il  231 (334)
                      ..++|..++..++-.||...  .....-+.|+|+.|.|||+|.-.+..+ ++.+++|-   -|...+..-. +-.++.|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l---~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFL---LVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEE---EEEECccchhhHHHHHHHH
Confidence            35899999999999998753  123456789999999999999888775 34455553   2334444322 22356666


Q ss_pred             HHhCCCCCcc--ccchhhHHHHHHHHHHHcC------CCeEEEEEeCCC
Q 038944          232 KFLMPSSRLS--EIMDKNYEMKKIILHEYLM------TKRYLNVIDDVW  272 (334)
Q Consensus       232 ~~~~~~~~~~--~~~~~~~~~l~~~l~~~L~------~kr~LlVlDdvw  272 (334)
                      .|+..+....  ...+..  +...++-..|+      +-+.++|+|...
T Consensus       101 rql~~e~~~~~k~~gsft--e~l~~lL~~L~~~~~~t~~~ViFIldEfD  147 (408)
T KOG2228|consen  101 RQLALELNRIVKSFGSFT--ENLSKLLEALKKGDETTSGKVIFILDEFD  147 (408)
T ss_pred             HHHHHHHhhhheeecccc--hhHHHHHHHHhcCCCCCCceEEEEeehhh
Confidence            6554432211  111112  33333434442      234777887764

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=95.64  E-value=0.078  Score=50.17  Aligned_cols=24  Identities=25%  Similarity=0.354  Sum_probs=19.9

Q ss_pred             CceEEEEEccCCccHHH-HHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAA-FAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTt-La~~v~~  201 (334)
                      +-+|+++||+.|+|||| ||+....
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar  226 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAAR  226 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHH
Confidence            36899999999999987 7776654

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.63  E-value=0.0078  Score=48.65  Aligned_cols=21  Identities=19%  Similarity=0.185  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ||.|.|.+|+||||+|+.+..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999987

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

Probab=95.63  E-value=0.076  Score=53.38  Aligned_cols=96  Identities=11%  Similarity=0.081  Sum_probs=54.6

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC--CHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY--DADQMLDIVIK  232 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~il~~il~  232 (334)
                      +.+++-....+++..+.....-....-|-+.|..|+|||+||+.+++... +.+.-....|+.|.-.  ....+++    
T Consensus       407 e~d~i~~~s~kke~~n~~~spv~~~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk----  481 (952)
T KOG0735|consen  407 EHDFIQVPSYKKENANQELSPVFRHGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQK----  481 (952)
T ss_pred             CCceeecchhhhhhhhhhcccccccccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHH----
Confidence            33444333333333333333322345688999999999999999998644 3443344455544321  1111111    


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCC
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw  272 (334)
                                       .+...+.+.+....-+|||||+.
T Consensus       482 -----------------~l~~vfse~~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  482 -----------------FLNNVFSEALWYAPSIIVLDDLD  504 (952)
T ss_pred             -----------------HHHHHHHHHHhhCCcEEEEcchh
Confidence                             23344445566678899999995

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.62  E-value=0.011  Score=45.96  Aligned_cols=22  Identities=18%  Similarity=0.391  Sum_probs=19.8

Q ss_pred             EEEEccCCccHHHHHHHHHccC
Q 038944          182 VVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      |.|+|..|+|||||.+.+.+..
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999998754

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=95.62  E-value=0.16  Score=44.30  Aligned_cols=21  Identities=10%  Similarity=0.162  Sum_probs=19.5

Q ss_pred             eEEEEEccCCccHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .++.|.|+.|.||||+.+.+.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~   51 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVA   51 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            789999999999999999984

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.62  E-value=0.01  Score=50.92  Aligned_cols=26  Identities=27%  Similarity=0.210  Sum_probs=22.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCC
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSY  204 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~  204 (334)
                      ..+|+|=||-|+||||||+.+.++..
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhC
Confidence            56899999999999999999988533

>PRK05439 pantothenate kinase; Provisional

Probab=95.62  E-value=0.076  Score=48.94  Aligned_cols=25  Identities=16%  Similarity=0.061  Sum_probs=22.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...-+|+|.|.+|+||||+|+.+..
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~  108 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQA  108 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999998876

>PRK06217 hypothetical protein; Validated

Probab=95.61  E-value=0.01  Score=50.30  Aligned_cols=24  Identities=8%  Similarity=0.057  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHccC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ..|.|.|++|+||||||+.+....
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            358999999999999999999853

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=95.60  E-value=0.049  Score=44.79  Aligned_cols=115  Identities=10%  Similarity=0.110  Sum_probs=58.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC--CCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY--PYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  257 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~  257 (334)
                      .+++|+|..|.|||||.+.+..-..   ...-.+++.-..  ........    ..+..-..  -+..+   ...-.+..
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~~---~~~G~i~~~~~~~~~~~~~~~~----~~i~~~~q--lS~G~---~~r~~l~~   93 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLLK---PTSGEILIDGKDIAKLPLEELR----RRIGYVPQ--LSGGQ---RQRVALAR   93 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC---CCccEEEECCEEcccCCHHHHH----hceEEEee--CCHHH---HHHHHHHH
Confidence            6899999999999999999987321   223333332111  11111111    11110000  00111   22223444


Q ss_pred             HcCCCeEEEEEeCCCC---hhHHHHHHhhCCC-CCCCeEEEEecCChHHHhhc
Q 038944          258 YLMTKRYLNVIDDVWN---IEVCDIIREILPD-NQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       258 ~L~~kr~LlVlDdvw~---~~~w~~l~~~l~~-~~~gsrIivTTr~~~va~~~  306 (334)
                      .+....-+++||+.-.   ......+...+.. ...+.-+|++|.+.+....+
T Consensus        94 ~l~~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~~  146 (157)
T cd00267          94 ALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAELA  146 (157)
T ss_pred             HHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHh
Confidence            4545567889999853   3333333333321 11245688888888776654

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.

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

Probab=95.60  E-value=0.013  Score=52.13  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=29.3

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++++.+.....+..+|+|.|.+|+||+||...+..
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~   51 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIR   51 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHH
Confidence            45667777776666788999999999999999987765

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.

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

Probab=95.59  E-value=0.082  Score=49.06  Aligned_cols=95  Identities=16%  Similarity=0.122  Sum_probs=60.2

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC----C-------CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG----P-------PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY  221 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~----~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  221 (334)
                      +.-.++=|.+++.++|.+...-+    +       .+.+=+-.+|++|.|||-||+.|.+  +....|=     .|..+ 
T Consensus       148 vtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~--~T~AtFI-----rvvgS-  219 (406)
T COG1222         148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVAN--QTDATFI-----RVVGS-  219 (406)
T ss_pred             CChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCceEE-----EeccH-
Confidence            33445678899999988876421    1       3566788999999999999999999  5555552     22221 


Q ss_pred             CHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCC-CeEEEEEeCCC
Q 038944          222 DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT-KRYLNVIDDVW  272 (334)
Q Consensus       222 ~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~-kr~LlVlDdvw  272 (334)
                         ++.+    ..-++.        .  .+...+.+.-+. ..+.|.+|.+.
T Consensus       220 ---ElVq----KYiGEG--------a--RlVRelF~lArekaPsIIFiDEID  254 (406)
T COG1222         220 ---ELVQ----KYIGEG--------A--RLVRELFELAREKAPSIIFIDEID  254 (406)
T ss_pred             ---HHHH----HHhccc--------h--HHHHHHHHHHhhcCCeEEEEechh
Confidence               2211    111111        1  556666666544 46788888885

>PRK13949 shikimate kinase; Provisional

Probab=95.58  E-value=0.01  Score=49.77  Aligned_cols=22  Identities=9%  Similarity=0.228  Sum_probs=20.1

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|++|+||||+++.+.+.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~   24 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARE   24 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999883

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.57  E-value=0.18  Score=47.99  Aligned_cols=24  Identities=13%  Similarity=0.254  Sum_probs=20.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.++|..|+||||.+..+..
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~  196 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAA  196 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999998887765

>COG3903 Predicted ATPase [General function prediction only]

Probab=95.57  E-value=0.011  Score=55.53  Aligned_cols=113  Identities=19%  Similarity=0.145  Sum_probs=73.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceee-EEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDC-HAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      ..+-+.++|.|||||||++-.+-.   +..-|.- +++|...+--|...+.-.....++....+     -+  .....+.
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~-----g~--~~~~~~~   82 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQP-----GD--SAVDTLV   82 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhccccccc-----ch--HHHHHHH
Confidence            467899999999999999988776   4555755 44455555456666666655556554331     11  5566777


Q ss_pred             HHcCCCeEEEEEeCCCCh-hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          257 EYLMTKRYLNVIDDVWNI-EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~-~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      .+..++|-++|+||.-+. +.-..+.-++-.+...-.|+.|+|..
T Consensus        83 ~~~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~  127 (414)
T COG3903          83 RRIGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREA  127 (414)
T ss_pred             HHHhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhh
Confidence            888899999999998654 23333333443444455677787754

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.56  E-value=0.031  Score=56.41  Aligned_cols=75  Identities=11%  Similarity=0.037  Sum_probs=49.9

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCC-ceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKH-YFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      -++++|.++.++.+...+....    -+-++|++|+||||+++.+.+  .+.. .|...+++.-+ ..+...+++.+..+
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~----~~ll~G~pG~GKT~la~~la~--~l~~~~~~~~~~~~n~-~~~~~~~~~~v~~~   89 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKR----NVLLIGEPGVGKSMLAKAMAE--LLPDEELEDILVYPNP-EDPNMPRIVEVPAG   89 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCC----CEEEECCCCCCHHHHHHHHHH--HcCchhheeEEEEeCC-CCCchHHHHHHHHh
Confidence            3457888888877777666542    445899999999999999998  4433 33444444333 23455667777766


Q ss_pred             hCC
Q 038944          234 LMP  236 (334)
Q Consensus       234 ~~~  236 (334)
                      ++.
T Consensus        90 ~g~   92 (608)
T TIGR00764        90 EGR   92 (608)
T ss_pred             hch
Confidence            654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.54  E-value=0.013  Score=50.47  Aligned_cols=25  Identities=20%  Similarity=0.124  Sum_probs=22.7

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++..++.|+|++|+||||||+.+..
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999999987

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.53  E-value=0.033  Score=51.49  Aligned_cols=115  Identities=13%  Similarity=0.085  Sum_probs=60.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      -..+.|+|..|.|||||++.+...  +..... .+.+.-..++....  .....-......  ......  ...+.+...
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~--~~~~~~-iv~ied~~El~~~~--~~~~~l~~~~~~--~~~~~~--~~~~~l~~~  214 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDE--IPKDER-IITIEDTREIFLPH--PNYVHLFYSKGG--QGLAKV--TPKDLLQSC  214 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcc--CCcccc-EEEEcCccccCCCC--CCEEEEEecCCC--CCcCcc--CHHHHHHHH
Confidence            468999999999999999988863  211111 11111111111110  000000000000  001112  344555666


Q ss_pred             cCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          259 LMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      |+...=.|++|.+.+.+.|+-+... ..+..|  ++.|+...+++..
T Consensus       215 Lr~~pd~ii~gE~r~~e~~~~l~a~-~~g~~~--~i~T~Ha~~~~~~  258 (308)
T TIGR02788       215 LRMRPDRIILGELRGDEAFDFIRAV-NTGHPG--SITTLHAGSPEEA  258 (308)
T ss_pred             hcCCCCeEEEeccCCHHHHHHHHHH-hcCCCe--EEEEEeCCCHHHH
Confidence            7777778999999998887654443 233222  5778877776554

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.53  E-value=0.16  Score=52.18  Aligned_cols=23  Identities=13%  Similarity=0.221  Sum_probs=20.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.|++++|+.|+||||.+.++..
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~  207 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAA  207 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHh
Confidence            46999999999999998877765

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.52  E-value=0.012  Score=50.77  Aligned_cols=24  Identities=13%  Similarity=0.170  Sum_probs=21.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+|+|+|+.|+|||||++.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999884

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.51  E-value=0.077  Score=48.08  Aligned_cols=25  Identities=16%  Similarity=0.250  Sum_probs=21.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.+++.++|.+|+||||++..+..
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~   94 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLAN   94 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHH
Confidence            3468999999999999998877764

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.

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.47  E-value=0.069  Score=51.61  Aligned_cols=90  Identities=11%  Similarity=0.030  Sum_probs=50.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC-CCHHHHHHHHHHHhCCCCCcc-----ccchhh---HHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP-YDADQMLDIVIKFLMPSSRLS-----EIMDKN---YEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~il~~il~~~~~~~~~~-----~~~~~~---~~~  250 (334)
                      ..++|+|..|+|||||++.+.+...    .++.+...+... .+..++...++..-.......     +.....   .-.
T Consensus       169 qrigI~G~sG~GKSTLl~~I~g~~~----~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~~  244 (451)
T PRK05688        169 QRLGLFAGTGVGKSVLLGMMTRFTE----ADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAAM  244 (451)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCC----CCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHHH
Confidence            4789999999999999999987321    233333444433 345555555554422211100     010000   001


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCCC
Q 038944          251 KKIILHEYL--MTKRYLNVIDDVWN  273 (334)
Q Consensus       251 l~~~l~~~L--~~kr~LlVlDdvw~  273 (334)
                      ....+-+++  +|+..|+++||+-.
T Consensus       245 ~a~aiAEyfrd~G~~VLl~~DslTR  269 (451)
T PRK05688        245 YCTRIAEYFRDKGKNVLLLMDSLTR  269 (451)
T ss_pred             HHHHHHHHHHHCCCCEEEEecchhH
Confidence            223344444  69999999999943

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.46  E-value=0.022  Score=50.30  Aligned_cols=22  Identities=23%  Similarity=0.376  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|++|+||||+|+.+.+.
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~   29 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKK   29 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3889999999999999999773

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.45  E-value=0.21  Score=48.09  Aligned_cols=124  Identities=10%  Similarity=0.041  Sum_probs=70.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCCcc-----cc-c--hhhHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSRLS-----EI-M--DKNYE  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~~~-----~~-~--~~~~~  249 (334)
                      -..++|+|..|+|||||.+.+....+.    +......+.+ ...+.+++...+..-+......     +. .  ....-
T Consensus       156 Gqri~I~G~sG~GKTtLl~~Ia~~~~~----~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~  231 (432)
T PRK06793        156 GQKIGIFAGSGVGKSTLLGMIAKNAKA----DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAA  231 (432)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCCC----CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHH
Confidence            347899999999999999999874322    1222223333 3667777776665533211100     00 0  00000


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHHhhC---CCCCCCeEEEEecCChHHHhhccc
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIREIL---PDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~~~l---~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      .....+-+++  ++|..||++||+-.- +....+...+   |.  .|--..+.|....+++.++.
T Consensus       232 ~~a~~iAEyfr~~G~~VLlilDslTr~a~A~reisl~~~e~p~--~G~~~~~~s~l~~L~ERag~  294 (432)
T PRK06793        232 KLATSIAEYFRDQGNNVLLMMDSVTRFADARRSVDIAVKELPI--GGKTLLMESYMKKLLERSGK  294 (432)
T ss_pred             HHHHHHHHHHHHcCCcEEEEecchHHHHHHHHHHHHHhcCCCC--CCeeeeeeccchhHHHHhcc
Confidence            2333344444  689999999999543 4555665443   32  25555666666666666553

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.45  E-value=0.12  Score=45.47  Aligned_cols=45  Identities=18%  Similarity=0.162  Sum_probs=30.2

Q ss_pred             CCeEEEEEeCCCCh----h----HHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          261 TKRYLNVIDDVWNI----E----VCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       261 ~kr~LlVlDdvw~~----~----~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      +++-|++||..-..    +    .|. +...|... .++.+|++|...+++....
T Consensus       109 ~~~sLvllDE~~~gT~~~d~~~i~~~-il~~l~~~-~~~~~i~~TH~~~l~~~~~  161 (222)
T cd03287         109 TSRSLVILDELGRGTSTHDGIAIAYA-TLHYLLEE-KKCLVLFVTHYPSLGEILR  161 (222)
T ss_pred             CCCeEEEEccCCCCCChhhHHHHHHH-HHHHHHhc-cCCeEEEEcccHHHHHHHH
Confidence            57899999997432    1    233 33333332 5788999999999987653

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.43  E-value=0.066  Score=50.77  Aligned_cols=98  Identities=20%  Similarity=0.110  Sum_probs=52.1

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccc-h
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIM-D  245 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~-~  245 (334)
                      +|=..|..+=..-.++.|.|.+|+|||||+..+...  ....-...+|++...  +...+.. -++.++......... .
T Consensus        70 eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~EE--s~~qi~~-Ra~rlg~~~~~l~l~~e  144 (372)
T cd01121          70 ELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSGEE--SPEQIKL-RADRLGISTENLYLLAE  144 (372)
T ss_pred             HHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCc--CHHHHHH-HHHHcCCCcccEEEEcc
Confidence            333444333344579999999999999999888763  222223566766543  3344322 234454332211000 1


Q ss_pred             hhHHHHHHHHHHHcCCCeEEEEEeCCC
Q 038944          246 KNYEMKKIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       246 ~~~~~l~~~l~~~L~~kr~LlVlDdvw  272 (334)
                      ..++.+...+.   ..+.-+||+|.+-
T Consensus       145 ~~le~I~~~i~---~~~~~lVVIDSIq  168 (372)
T cd01121         145 TNLEDILASIE---ELKPDLVIIDSIQ  168 (372)
T ss_pred             CcHHHHHHHHH---hcCCcEEEEcchH
Confidence            11224444443   2355689999983

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK05922 type III secretion system ATPase; Validated

Probab=95.42  E-value=0.075  Score=51.14  Aligned_cols=89  Identities=10%  Similarity=0.062  Sum_probs=49.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCCcc--ccchh------hHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSRLS--EIMDK------NYEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~~~--~~~~~------~~~~  250 (334)
                      ..++|+|..|+|||||.+.+.+...    .++...+.++. .-.+...+.+............  ...+.      ..-.
T Consensus       158 qrigI~G~nG~GKSTLL~~Ia~~~~----~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~~  233 (434)
T PRK05922        158 QRIGVFSEPGSGKSSLLSTIAKGSK----STINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAGR  233 (434)
T ss_pred             cEEEEECCCCCChHHHHHHHhccCC----CCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHHH
Confidence            4689999999999999999987421    23333333333 2234455555544332221100  01110      0002


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 038944          251 KKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       251 l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      ..-.+-+++  +|+..|+++||+-
T Consensus       234 ~a~tiAEyfrd~G~~VLl~~DslT  257 (434)
T PRK05922        234 AAMTIAEYFRDQGHRVLFIMDSLS  257 (434)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchh
Confidence            233344555  6899999999994

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.41  E-value=0.041  Score=54.08  Aligned_cols=24  Identities=13%  Similarity=0.203  Sum_probs=20.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++++|.+|+||||++..+..
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            347999999999999999987764

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.41  E-value=0.013  Score=49.89  Aligned_cols=23  Identities=9%  Similarity=0.206  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|+|+.|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            37899999999999999999874

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.38  E-value=0.014  Score=53.27  Aligned_cols=25  Identities=16%  Similarity=0.099  Sum_probs=21.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+|+|.|..|+||||+|+.+..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999987643

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.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.38  E-value=0.16  Score=44.45  Aligned_cols=60  Identities=13%  Similarity=0.180  Sum_probs=38.8

Q ss_pred             HHHHHHcCCCeEEEEEeCCCCh---hHHHHHHhhCCC-CCCCeEEEEecCChHHHhhccccCcc
Q 038944          253 IILHEYLMTKRYLNVIDDVWNI---EVCDIIREILPD-NQNRSRVLITLTEIKMFTFLLETLFS  312 (334)
Q Consensus       253 ~~l~~~L~~kr~LlVlDdvw~~---~~w~~l~~~l~~-~~~gsrIivTTr~~~va~~~~~~~~~  312 (334)
                      ..+.+.+--+.=|.|||...+-   +..+.+...+.. ...|+-++++|..+.++....++..+
T Consensus       153 ~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr~~~~~~liITHy~rll~~i~pD~vh  216 (251)
T COG0396         153 NEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALREEGRGVLIITHYQRLLDYIKPDKVH  216 (251)
T ss_pred             HHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHhcCCCeEEEEecHHHHHhhcCCCEEE
Confidence            3333444445568999999875   444444443321 23477799999999999998766544

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

Probab=95.37  E-value=0.0098  Score=45.81  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=17.8

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |-|+|.+|+|||+||+.+..
T Consensus         1 I~i~G~~G~GKS~l~~~l~~   20 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAK   20 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999776

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

>PRK14530 adenylate kinase; Provisional

Probab=95.37  E-value=0.012  Score=51.21  Aligned_cols=22  Identities=14%  Similarity=0.238  Sum_probs=20.0

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .|.|+|++|+||||+++.+...
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999763

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.36  E-value=0.015  Score=46.94  Aligned_cols=22  Identities=14%  Similarity=0.321  Sum_probs=19.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+.|+|+.|+|||||++.+...
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhc
Confidence            3789999999999999999983

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.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.36  E-value=0.06  Score=51.83  Aligned_cols=90  Identities=16%  Similarity=0.144  Sum_probs=50.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC-CCHHHHHHHHHHHhCCCCCcc--ccchhh-HH-----
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP-YDADQMLDIVIKFLMPSSRLS--EIMDKN-YE-----  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~il~~il~~~~~~~~~~--~~~~~~-~~-----  249 (334)
                      -..++|+|..|+|||||.+.+.+..    +.+...++.+... ..+.+++.+....-.....-.  ...+.. ..     
T Consensus       155 GqrigI~G~sG~GKSTLL~~I~~~~----~~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a~  230 (433)
T PRK07594        155 GQRVGIFSAPGVGKSTLLAMLCNAP----DADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRAL  230 (433)
T ss_pred             CCEEEEECCCCCCccHHHHHhcCCC----CCCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHHH
Confidence            3478999999999999999998732    2344555555543 344455555433110000000  000100 00     


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      ...-.+-+++  +|++.|+++||+-
T Consensus       231 ~~a~tiAEyfrd~G~~VLl~~Dslt  255 (433)
T PRK07594        231 FVATTIAEFFRDNGKRVVLLADSLT  255 (433)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCHH
Confidence            1223344444  6899999999994

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.35  E-value=0.013  Score=49.26  Aligned_cols=23  Identities=9%  Similarity=0.172  Sum_probs=20.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|.+.|++|+||||+|+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999999873

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

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.35  E-value=0.12  Score=43.67  Aligned_cols=24  Identities=17%  Similarity=0.112  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.|.|.+|+||||+|+.+..
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~   40 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEK   40 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999987

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.34  E-value=0.026  Score=48.01  Aligned_cols=23  Identities=13%  Similarity=0.042  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+|.|.|+.|+||||+++.+.+.
T Consensus         1 ~~I~ieG~~GsGKtT~~~~L~~~   23 (200)
T cd01672           1 MFIVFEGIDGAGKTTLIELLAER   23 (200)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            36899999999999999999874

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

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

Probab=95.34  E-value=0.012  Score=48.86  Aligned_cols=20  Identities=15%  Similarity=0.223  Sum_probs=18.6

Q ss_pred             EEEEEccCCccHHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .|+|.|.+|+||||+++.+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999886

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.34  E-value=0.078  Score=51.22  Aligned_cols=91  Identities=12%  Similarity=0.126  Sum_probs=50.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcC-CCCCHHHHHHHHHHHhCCCCCcc--ccchh---h---HH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGT-YPYDADQMLDIVIKFLMPSSRLS--EIMDK---N---YE  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~il~~il~~~~~~~~~~--~~~~~---~---~~  249 (334)
                      -..++|.|..|+|||||.+.+......    +....+-+. +...+.++...+...-.......  ...+.   .   --
T Consensus       163 Gq~~~I~G~sG~GKTtLl~~ia~~~~~----d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~  238 (441)
T PRK09099        163 GQRMGIFAPAGVGKSTLMGMFARGTQC----DVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAA  238 (441)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHH
Confidence            458899999999999999999874322    222333333 33455555555554322111000  01110   0   00


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCCC
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVWN  273 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw~  273 (334)
                      ...-.+-+++  +||..|+++||+-.
T Consensus       239 ~~a~tiAEyfrd~G~~VLl~~DslTr  264 (441)
T PRK09099        239 YVATAIAEYFRDRGLRVLLMMDSLTR  264 (441)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchhH
Confidence            2233344444  68999999999943

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.33  E-value=0.015  Score=50.34  Aligned_cols=26  Identities=19%  Similarity=0.253  Sum_probs=23.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++++|+++|..|+|||||...+...
T Consensus        20 ~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        20 HGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             cCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            56999999999999999999998873

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.31  E-value=0.11  Score=48.17  Aligned_cols=87  Identities=13%  Similarity=0.076  Sum_probs=49.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCC--------Ccc--ccchhhH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSS--------RLS--EIMDKNY  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~--------~~~--~~~~~~~  248 (334)
                      ..++|+|..|.|||||.+.+.+...  .  ++.....+.. .-++..+....+..-....        +.+  ...-.. 
T Consensus        70 qri~I~G~sG~GKTtLl~~Ia~~~~--~--~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~-  144 (326)
T cd01136          70 QRLGIFAGSGVGKSTLLGMIARGTT--A--DVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAA-  144 (326)
T ss_pred             cEEEEECCCCCChHHHHHHHhCCCC--C--CEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHH-
Confidence            4789999999999999999987432  1  2333344442 3355566655554322110        000  000001 


Q ss_pred             HHHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          249 EMKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       249 ~~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                       ...-.+-+++  +||..|+++||+-
T Consensus       145 -~~a~~~AEyfr~~g~~Vll~~Dslt  169 (326)
T cd01136         145 -YTATAIAEYFRDQGKDVLLLMDSLT  169 (326)
T ss_pred             -HHHHHHHHHHHHcCCCeEEEeccch
Confidence             2222333444  6999999999984

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.31  E-value=0.17  Score=45.56  Aligned_cols=54  Identities=7%  Similarity=-0.058  Sum_probs=35.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      -.++.|.|.+|+||||++..+..+.. ..+=..++|++...  +..++...++..+.
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~-~~~g~~vl~iS~E~--~~~~~~~r~~~~~~   83 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLI-TQHGVRVGTISLEE--PVVRTARRLLGQYA   83 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH-HhcCceEEEEEccc--CHHHHHHHHHHHHh
Confidence            45888999999999999988765321 12123567776544  45677777766543

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>COG1084 Predicted GTPase [General function prediction only]

Probab=95.29  E-value=0.25  Score=45.39  Aligned_cols=30  Identities=17%  Similarity=0.292  Sum_probs=24.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc-CCCC
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS-SYVK  206 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~-~~~~  206 (334)
                      +.++.+.|.|++-+|||||++.+-.- +++.
T Consensus       166 p~~pTivVaG~PNVGKSSlv~~lT~AkpEvA  196 (346)
T COG1084         166 PDLPTIVVAGYPNVGKSSLVRKLTTAKPEVA  196 (346)
T ss_pred             CCCCeEEEecCCCCcHHHHHHHHhcCCCccC
Confidence            46788999999999999999999763 4443

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

Probab=95.29  E-value=0.057  Score=54.35  Aligned_cols=74  Identities=15%  Similarity=0.147  Sum_probs=48.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      +.-+++-.+|++|+||||||..|.++.-    | .++=++.|..-+...+-..|...+....                  
T Consensus       324 P~kKilLL~GppGlGKTTLAHViAkqaG----Y-sVvEINASDeRt~~~v~~kI~~avq~~s------------------  380 (877)
T KOG1969|consen  324 PPKKILLLCGPPGLGKTTLAHVIAKQAG----Y-SVVEINASDERTAPMVKEKIENAVQNHS------------------  380 (877)
T ss_pred             CccceEEeecCCCCChhHHHHHHHHhcC----c-eEEEecccccccHHHHHHHHHHHHhhcc------------------
Confidence            4568999999999999999999988421    2 2344566666655555555444333221                  


Q ss_pred             HHcC--CCeEEEEEeCCCCh
Q 038944          257 EYLM--TKRYLNVIDDVWNI  274 (334)
Q Consensus       257 ~~L~--~kr~LlVlDdvw~~  274 (334)
                       .|.  ++.-.||+|.+.-.
T Consensus       381 -~l~adsrP~CLViDEIDGa  399 (877)
T KOG1969|consen  381 -VLDADSRPVCLVIDEIDGA  399 (877)
T ss_pred             -ccccCCCcceEEEecccCC
Confidence             121  45667899999754

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=95.28  E-value=0.12  Score=50.50  Aligned_cols=47  Identities=17%  Similarity=0.167  Sum_probs=36.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|....+..+...+..-...-..+.|.|.+|+|||++|+.++..
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhc
Confidence            45889888888887777543333445789999999999999999985

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.26  E-value=0.051  Score=47.36  Aligned_cols=21  Identities=19%  Similarity=0.162  Sum_probs=19.1

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|+|++|+||||+|+.+..
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~   22 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAE   22 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999876

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.26  E-value=0.22  Score=48.67  Aligned_cols=24  Identities=13%  Similarity=0.199  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.|++++|..|+||||++.++...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~  279 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAAR  279 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHH
Confidence            369999999999999999888763

>PRK13975 thymidylate kinase; Provisional

Probab=95.25  E-value=0.016  Score=49.57  Aligned_cols=23  Identities=17%  Similarity=0.030  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+|.|.|+.|+||||+++.+.+.
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999999983

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=95.25  E-value=0.014  Score=47.58  Aligned_cols=20  Identities=15%  Similarity=0.292  Sum_probs=18.8

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |.++|++|+||||+|+.+..
T Consensus         2 i~l~G~~GsGKstla~~la~   21 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAK   21 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            68999999999999999987

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.

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

Probab=95.22  E-value=0.019  Score=47.33  Aligned_cols=23  Identities=17%  Similarity=0.049  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..||-+.|.+|+||||||+.+..
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~   24 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALER   24 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            35889999999999999999997

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 ....

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.22  E-value=0.032  Score=47.50  Aligned_cols=126  Identities=12%  Similarity=0.011  Sum_probs=62.5

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcccc
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEI  243 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~  243 (334)
                      +...++.+....   -..+.|+|..|.|||||++.+..-  +...- ..+-+.-..++...  ..... ++.........
T Consensus        13 ~~~~~l~~~v~~---g~~i~I~G~tGSGKTTll~aL~~~--i~~~~-~~i~ied~~E~~~~--~~~~~-~~~~~~~~~~~   83 (186)
T cd01130          13 LQAAYLWLAVEA---RKNILISGGTGSGKTTLLNALLAF--IPPDE-RIITIEDTAELQLP--HPNWV-RLVTRPGNVEG   83 (186)
T ss_pred             HHHHHHHHHHhC---CCEEEEECCCCCCHHHHHHHHHhh--cCCCC-CEEEECCccccCCC--CCCEE-EEEEecCCCCC
Confidence            344444444443   358999999999999999988863  21111 11111100011000  00000 00000000000


Q ss_pred             chhhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeE-EEEecCChHHHh
Q 038944          244 MDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSR-VLITLTEIKMFT  304 (334)
Q Consensus       244 ~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsr-IivTTr~~~va~  304 (334)
                      ....  ...+.+...++...=.++++.+.+.+.|.-+..+ .   .|-. ++.|..-.++..
T Consensus        84 ~~~~--~~~~~l~~~lR~~pd~i~igEir~~ea~~~~~a~-~---tGh~g~~~T~Ha~s~~~  139 (186)
T cd01130          84 SGEV--TMADLLRSALRMRPDRIIVGEVRGGEALDLLQAM-N---TGHPGGMTTIHANSAEE  139 (186)
T ss_pred             CCcc--CHHHHHHHHhccCCCEEEEEccCcHHHHHHHHHH-h---cCCCCceeeecCCCHHH
Confidence            1112  3455566666666678889999999888765544 2   3444 555555444444

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.21  E-value=0.018  Score=48.36  Aligned_cols=24  Identities=8%  Similarity=0.230  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|.|+|+.|+||||+++.+.+.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHH
Confidence            346999999999999999999873

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=95.20  E-value=0.16  Score=43.59  Aligned_cols=21  Identities=19%  Similarity=-0.012  Sum_probs=19.9

Q ss_pred             eEEEEEccCCccHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +++.|.|+.|.|||||.+.+.
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            689999999999999999987

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.20  E-value=0.024  Score=48.36  Aligned_cols=25  Identities=12%  Similarity=0.134  Sum_probs=22.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.|+|++|+|||||++.+...
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            4578999999999999999999873

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

Probab=95.17  E-value=0.016  Score=50.86  Aligned_cols=55  Identities=9%  Similarity=0.243  Sum_probs=36.1

Q ss_pred             HHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecCChHHHhhccccCc
Q 038944          255 LHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETLF  311 (334)
Q Consensus       255 l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~~~~  311 (334)
                      +-+.|.-+.=+|++|..=+.       +.|+-+...-  ...+--+|+.|.+..++..+|....
T Consensus       152 IARAL~~~PklLIlDEptSaLD~siQa~IlnlL~~l~--~~~~lt~l~IsHdl~~v~~~cdRi~  213 (252)
T COG1124         152 IARALIPEPKLLILDEPTSALDVSVQAQILNLLLELK--KERGLTYLFISHDLALVEHMCDRIA  213 (252)
T ss_pred             HHHHhccCCCEEEecCchhhhcHHHHHHHHHHHHHHH--HhcCceEEEEeCcHHHHHHHhhhee
Confidence            44556666678999997543       3454443332  2235569999999999999886543

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.17  E-value=0.025  Score=50.79  Aligned_cols=52  Identities=21%  Similarity=0.117  Sum_probs=38.8

Q ss_pred             CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHH
Q 038944          176 PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVI  231 (334)
Q Consensus       176 ~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il  231 (334)
                      =+.-+++.|+|.+|+|||+++.+...  ...++...++||+.....  ..++..+.
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f~~qfl~--~~~~~ge~vlyvs~~e~~--~~l~~~~~   71 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIFALQFLY--EGAREGEPVLYVSTEESP--EELLENAR   71 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHHHHHHHH--HHHhcCCcEEEEEecCCH--HHHHHHHH
Confidence            35678999999999999999977766  344458889999887653  44544443

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.17  E-value=0.058  Score=48.70  Aligned_cols=127  Identities=15%  Similarity=0.112  Sum_probs=65.3

Q ss_pred             eechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCC
Q 038944          159 VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSS  238 (334)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~  238 (334)
                      .|...+..+.+..+....  -.++.|.|..|+||||++..+.+.  +...-...+.+.-+.++....+     .|+....
T Consensus        62 lg~~~~~~~~l~~~~~~~--~GlilisG~tGSGKTT~l~all~~--i~~~~~~iitiEdp~E~~~~~~-----~q~~v~~  132 (264)
T cd01129          62 LGLKPENLEIFRKLLEKP--HGIILVTGPTGSGKTTTLYSALSE--LNTPEKNIITVEDPVEYQIPGI-----NQVQVNE  132 (264)
T ss_pred             cCCCHHHHHHHHHHHhcC--CCEEEEECCCCCcHHHHHHHHHhh--hCCCCCeEEEECCCceecCCCc-----eEEEeCC
Confidence            354444444444444332  358999999999999999988662  2111111222222222221110     1111110


Q ss_pred             CccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHh
Q 038944          239 RLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFT  304 (334)
Q Consensus       239 ~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~  304 (334)
                          . ...  .....++..|+...=.|+++++.+.+....+..+..   .|--++-|..-.++..
T Consensus       133 ----~-~~~--~~~~~l~~~lR~~PD~i~vgEiR~~e~a~~~~~aa~---tGh~v~tTlHa~~~~~  188 (264)
T cd01129         133 ----K-AGL--TFARGLRAILRQDPDIIMVGEIRDAETAEIAVQAAL---TGHLVLSTLHTNDAPG  188 (264)
T ss_pred             ----c-CCc--CHHHHHHHHhccCCCEEEeccCCCHHHHHHHHHHHH---cCCcEEEEeccCCHHH
Confidence                0 011  345566666766677889999999876544433322   3444665655554443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=95.16  E-value=0.15  Score=48.88  Aligned_cols=90  Identities=14%  Similarity=0.094  Sum_probs=48.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh----h--HH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK----N--YE  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~----~--~~  249 (334)
                      -..++|+|..|+|||||.+.+.+....    +......+.... .+.++..+.+.+-+......  ...+.    .  --
T Consensus       137 Gqri~I~G~sG~GKTtLl~~i~~~~~~----~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~~  212 (413)
T TIGR03497       137 GQRVGIFAGSGVGKSTLLGMIARNAKA----DINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKAA  212 (413)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHH
Confidence            458999999999999999988874321    222223344332 44455555444321110000  00000    0  00


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      .....+-+++  +|+..|+++||+-
T Consensus       213 ~~a~tiAEyfr~~G~~Vll~~Dslt  237 (413)
T TIGR03497       213 FTATAIAEYFRDQGKDVLLMMDSVT  237 (413)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEcCcH
Confidence            2223344444  6899999999994

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=95.15  E-value=0.37  Score=44.98  Aligned_cols=43  Identities=12%  Similarity=-0.061  Sum_probs=31.0

Q ss_pred             eee-chhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          158 TVG-LDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       158 ~vG-r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++| .+..++.|.+.+..+. -....-++|+.|+||||+|..+.+
T Consensus         7 i~~~q~~~~~~L~~~~~~~~-l~ha~Lf~G~~G~gk~~~a~~la~   50 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNR-LSHAYLFEGAKGTGKKATALWLAK   50 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            455 5556667766665443 345678999999999999988755

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=95.15  E-value=0.29  Score=45.33  Aligned_cols=45  Identities=11%  Similarity=0.042  Sum_probs=36.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..++.+...+..+. -....-++|..|+||+++|..+.+
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-l~ha~Lf~G~~G~Gk~~~A~~~a~   48 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-IAPAYLFAGPEGVGRKLAALCFIE   48 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999887753 236888999999999998876654

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.15  E-value=0.035  Score=51.05  Aligned_cols=36  Identities=19%  Similarity=0.139  Sum_probs=27.3

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+++-+........+++|+|.+|+|||||+..+..
T Consensus        21 ~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~   56 (300)
T TIGR00750        21 KQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGM   56 (300)
T ss_pred             HHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHH
Confidence            344444444445678999999999999999988775

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.

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.14  E-value=0.027  Score=49.99  Aligned_cols=50  Identities=16%  Similarity=0.165  Sum_probs=39.6

Q ss_pred             CCCCCeeechhhHH---HHHHHHhcC----CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          153 SKSRDTVGLDDRME---ELLDLLIEG----PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       153 ~~~~~~vGr~~~~~---~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-++++|.++.+.   -|++.|.+.    +...+-+..+|++|.|||.+|+.+.+.
T Consensus       118 it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane  174 (368)
T COG1223         118 ITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANE  174 (368)
T ss_pred             ccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcc
Confidence            34457899887765   367777664    356788999999999999999999994

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.11  E-value=0.015  Score=48.04  Aligned_cols=36  Identities=8%  Similarity=0.032  Sum_probs=25.5

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPG  217 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~v  217 (334)
                      |++|+|+.|+|||||+..+...-+ ...+.+.+.-+.
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~-~~G~~V~viK~~   36 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALK-ARGYRVATIKHD   36 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEecc
Confidence            589999999999999999988322 123555444433

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.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=95.11  E-value=0.042  Score=43.48  Aligned_cols=46  Identities=13%  Similarity=0.107  Sum_probs=34.0

Q ss_pred             CeeechhhHHHHHHHHhc-----CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIE-----GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-----~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|..-..+.+++.+.+     .+.+.-|++..|.+|+|||.+++.+.++
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            367876666666666543     2456789999999999999987777653

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=95.11  E-value=0.13  Score=50.07  Aligned_cols=94  Identities=11%  Similarity=-0.005  Sum_probs=54.8

Q ss_pred             EEEEEccCCccHHHHH-HHHHccCCCCCceee-EEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc-----ccch-------
Q 038944          181 VVVILDSIGLDKAAFA-GEAYNSSYVKHYFDC-HAWVPGTYPY-DADQMLDIVIKFLMPSSRLS-----EIMD-------  245 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~il~~il~~~~~~~~~~-----~~~~-------  245 (334)
                      -++|.|-.|+|||||| ..+.+..    .-+. ++++.+.+.. .+.++...+.+.-.......     +...       
T Consensus       143 R~~I~g~~g~GKt~Lal~~I~~q~----~~dv~cV~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r~~ap  218 (485)
T CHL00059        143 RELIIGDRQTGKTAVATDTILNQK----GQNVICVYVAIGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAP  218 (485)
T ss_pred             EEEeecCCCCCHHHHHHHHHHhcc----cCCeEEEEEEecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHHHHHH
Confidence            5899999999999995 5566632    2233 4777887654 55566666654322111100     0000       


Q ss_pred             --hhHHHHHHHHHHHcCCCeEEEEEeCCCC-hhHHHHHHh
Q 038944          246 --KNYEMKKIILHEYLMTKRYLNVIDDVWN-IEVCDIIRE  282 (334)
Q Consensus       246 --~~~~~l~~~l~~~L~~kr~LlVlDdvw~-~~~w~~l~~  282 (334)
                        -.  .+++.++.  +|+..|+|+||+-. ...|.++..
T Consensus       219 ~~a~--aiAEyfr~--~G~~VLlv~DdlTr~A~A~REisl  254 (485)
T CHL00059        219 YTGA--ALAEYFMY--RGRHTLIIYDDLSKQAQAYRQMSL  254 (485)
T ss_pred             HHHh--hHHHHHHH--cCCCEEEEEcChhHHHHHHHHHHH
Confidence              01  23333332  68999999999954 356666554

>PRK13946 shikimate kinase; Provisional

Probab=95.07  E-value=0.019  Score=48.83  Aligned_cols=23  Identities=17%  Similarity=0.250  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.|.++|++|+||||+++.+.+
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~   32 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLAT   32 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999999998

>PRK13948 shikimate kinase; Provisional

Probab=95.05  E-value=0.023  Score=48.28  Aligned_cols=24  Identities=17%  Similarity=0.180  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....|.++||.|+||||+++.+.+
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~   32 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSR   32 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            346788999999999999999987

>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=95.02  E-value=0.02  Score=45.77  Aligned_cols=22  Identities=18%  Similarity=0.252  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|+|||||.+.+..
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g   33 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAG   33 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTT
T ss_pred             CEEEEEccCCCccccceeeecc
Confidence            4899999999999999999986

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 ....

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.01  E-value=0.02  Score=49.13  Aligned_cols=22  Identities=23%  Similarity=0.362  Sum_probs=19.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|-+.|.+|+||||+|+.+..
T Consensus         2 pLiIlTGyPgsGKTtfakeLak   23 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAK   23 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHH
Confidence            4567789999999999998876

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=95.01  E-value=0.019  Score=48.19  Aligned_cols=21  Identities=14%  Similarity=0.289  Sum_probs=18.1

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|.|.+|+|||||++.+.+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~   22 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEE   22 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH
Confidence            689999999999999999874

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.

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=95.00  E-value=0.023  Score=43.77  Aligned_cols=22  Identities=27%  Similarity=0.234  Sum_probs=19.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      -..++|+|..|.|||||+..+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            3689999999999999999976

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

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=95.00  E-value=0.087  Score=50.96  Aligned_cols=92  Identities=11%  Similarity=0.142  Sum_probs=54.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh----hH--HH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK----NY--EM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~----~~--~~  250 (334)
                      .-++|.|..|+|||||+..+..+... .+=.+++++-+.... .+.+++.+++..-.......  ...+.    .+  -.
T Consensus       144 Qr~~If~~~G~GKt~L~~~~~~~~~~-~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~  222 (461)
T TIGR01039       144 GKIGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVAL  222 (461)
T ss_pred             CEEEeecCCCCChHHHHHHHHHHHHh-cCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            36899999999999999988763211 111367777776553 56677777754321111000  00010    00  02


Q ss_pred             HHHHHHHHc---CCCeEEEEEeCCC
Q 038944          251 KKIILHEYL---MTKRYLNVIDDVW  272 (334)
Q Consensus       251 l~~~l~~~L---~~kr~LlVlDdvw  272 (334)
                      ..-.+-+++   +|+..|+++||+-
T Consensus       223 ~a~tiAEyfrd~~G~~VLll~DslT  247 (461)
T TIGR01039       223 TGLTMAEYFRDEQGQDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHhcCCeeEEEecchh
Confidence            344555666   5789999999994

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.00  E-value=0.09  Score=51.05  Aligned_cols=101  Identities=17%  Similarity=0.193  Sum_probs=58.4

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCC---CceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchhh-H-----
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVK---HYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDKN-Y-----  248 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~---~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~~-~-----  248 (334)
                      -++|.|-.|+|||||+..+.+.....   ..| .++++.+.+.. .+.+++.+++..-..+..-.  ...+.. +     
T Consensus       143 R~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~-v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a  221 (458)
T TIGR01041       143 KLPIFSGSGLPHNELAAQIARQATVRGEESEF-AVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVT  221 (458)
T ss_pred             EEEeeCCCCCCHHHHHHHHHHhhcccCCCCce-EEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHH
Confidence            57899999999999999998854332   222 56777777654 55666666664322111100  001100 0     


Q ss_pred             HHHHHHHHHHc---CCCeEEEEEeCCCC-hhHHHHHHh
Q 038944          249 EMKKIILHEYL---MTKRYLNVIDDVWN-IEVCDIIRE  282 (334)
Q Consensus       249 ~~l~~~l~~~L---~~kr~LlVlDdvw~-~~~w~~l~~  282 (334)
                      -.....+-+++   +|++.|+++||+-. .+.+.+|..
T Consensus       222 ~~~a~tiAEyfr~d~G~~VLli~DslTR~A~A~REIsl  259 (458)
T TIGR01041       222 PRMALTAAEYLAFEKDMHVLVILTDMTNYCEALREISA  259 (458)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcChhHHHHHHHHHHH
Confidence            01223344555   58899999999943 245555443

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.00  E-value=0.021  Score=47.19  Aligned_cols=23  Identities=30%  Similarity=0.270  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+.|+|.+|+||||+.+.+-.
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~   26 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALK   26 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHH
Confidence            68999999999999999988776

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=94.99  E-value=0.02  Score=49.33  Aligned_cols=23  Identities=17%  Similarity=0.224  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|+++|+.|+||||+|+.+-+
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            46899999999999999998776

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=94.99  E-value=0.015  Score=48.17  Aligned_cols=21  Identities=19%  Similarity=0.292  Sum_probs=18.7

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|++|+||||+|+.+.+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999873

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.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=94.98  E-value=0.18  Score=47.04  Aligned_cols=101  Identities=17%  Similarity=0.105  Sum_probs=58.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCc-----c------ccchhh
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRL-----S------EIMDKN  247 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~-----~------~~~~~~  247 (334)
                      ..++|.|..|+|||+|++.+.+..    +-++++++-+.+.. .+.+++.++-+........     .      .++...
T Consensus       158 qr~~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~iGERg~Ev~e~l~ef~~l~~~~~~~~~m~rtvlV~nts~~p~~  233 (369)
T cd01134         158 GTAAIPGPFGCGKTVIQQSLSKYS----NSDIVIYVGCGERGNEMTEVLEEFPELTDPVTGEPLMKRTVLIANTSNMPVA  233 (369)
T ss_pred             CEEEEECCCCCChHHHHHHHHhCC----CCCEEEEEEeCCChHHHHHHHHHHHhhccccccCCccceEEEEEECCCCCHH
Confidence            378999999999999999999853    23577888887654 4555666543321111000     0      111100


Q ss_pred             HH----HHHHHHHHHc--CCCeEEEEEeCCCC-hhHHHHHHhhC
Q 038944          248 YE----MKKIILHEYL--MTKRYLNVIDDVWN-IEVCDIIREIL  284 (334)
Q Consensus       248 ~~----~l~~~l~~~L--~~kr~LlVlDdvw~-~~~w~~l~~~l  284 (334)
                      ..    ...-.+-+++  +|+..|+++|++-. .+...++...+
T Consensus       234 ~R~~s~yta~tiAEYfrd~G~dVll~~Ds~tR~A~A~REIs~~l  277 (369)
T cd01134         234 AREASIYTGITIAEYFRDMGYNVALMADSTSRWAEALREISGRL  277 (369)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEcChhHHHHHHHHHHHhc
Confidence            00    1122233444  68999999999932 35555555444

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=94.95  E-value=0.12  Score=50.01  Aligned_cols=100  Identities=11%  Similarity=0.135  Sum_probs=59.7

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCC------------CCceeeEEEEEcCCCCCHHHHHHHHHHHhC-CCCCcc--ccch
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYV------------KHYFDCHAWVPGTYPYDADQMLDIVIKFLM-PSSRLS--EIMD  245 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~------------~~~F~~~~wv~vs~~~~~~~il~~il~~~~-~~~~~~--~~~~  245 (334)
                      -++|.|-.|+|||||+..+.+..+.            .+.| .++++.+.+.....+.+.+.+..-+ ......  ...+
T Consensus       143 RigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~-v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~atsd  221 (466)
T TIGR01040       143 KIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNF-AIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLAN  221 (466)
T ss_pred             eeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCce-EEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECCC
Confidence            5889999999999999998875431            0112 5677788888777777777776655 211100  0001


Q ss_pred             h---h---HHHHHHHHHHHc---CCCeEEEEEeCCCC-hhHHHHHH
Q 038944          246 K---N---YEMKKIILHEYL---MTKRYLNVIDDVWN-IEVCDIIR  281 (334)
Q Consensus       246 ~---~---~~~l~~~l~~~L---~~kr~LlVlDdvw~-~~~w~~l~  281 (334)
                      .   .   .-...-.+-+++   +|+..|+++||+-. ...+.++.
T Consensus       222 ~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslTr~A~A~REis  267 (466)
T TIGR01040       222 DPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMSSYADALREVS  267 (466)
T ss_pred             CCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChHHHHHHHHHHH
Confidence            0   0   002223344555   47999999999943 24444443

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=94.95  E-value=0.096  Score=48.46  Aligned_cols=88  Identities=16%  Similarity=0.060  Sum_probs=51.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-+++-|+|..|+||||||-.+...  ....-..++|+.....+++..     +++++......   .....+  +...
T Consensus        51 p~G~ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e~~ld~~~-----a~~lGvdl~rllv~~P~~~E--~al~  121 (322)
T PF00154_consen   51 PRGRIVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAEHALDPEY-----AESLGVDLDRLLVVQPDTGE--QALW  121 (322)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESSS---HHH-----HHHTT--GGGEEEEE-SSHH--HHHH
T ss_pred             ccCceEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCcccchhhH-----HHhcCccccceEEecCCcHH--HHHH
Confidence            44569999999999999999888863  323345688999888877643     44555443321   111112  4444


Q ss_pred             HHHHHc-CCCeEEEEEeCCCC
Q 038944          254 ILHEYL-MTKRYLNVIDDVWN  273 (334)
Q Consensus       254 ~l~~~L-~~kr~LlVlDdvw~  273 (334)
                      .+...+ .+..-++|+|-|-.
T Consensus       122 ~~e~lirsg~~~lVVvDSv~a  142 (322)
T PF00154_consen  122 IAEQLIRSGAVDLVVVDSVAA  142 (322)
T ss_dssp             HHHHHHHTTSESEEEEE-CTT
T ss_pred             HHHHHhhcccccEEEEecCcc
Confidence            444445 34456899999854

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=94.94  E-value=0.074  Score=54.21  Aligned_cols=27  Identities=22%  Similarity=0.191  Sum_probs=22.3

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      -+.++|++|+||||+|+.+.+  ...-+|
T Consensus       187 gill~G~~G~GKt~~~~~~a~--~~~~~f  213 (644)
T PRK10733        187 GVLMVGPPGTGKTLLAKAIAG--EAKVPF  213 (644)
T ss_pred             cEEEECCCCCCHHHHHHHHHH--HcCCCE
Confidence            488999999999999999988  444444

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=94.94  E-value=0.098  Score=50.26  Aligned_cols=97  Identities=13%  Similarity=0.051  Sum_probs=51.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCCcc--ccchh---h---HHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSRLS--EIMDK---N---YEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~~~--~~~~~---~---~~~  250 (334)
                      ..++|+|..|+|||||.+.+.....  .  +....+.+.. .-.+.++..+.+..-..+....  ...+.   .   .-.
T Consensus       141 q~i~I~G~sG~GKTtLl~~I~~~~~--~--~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~  216 (418)
T TIGR03498       141 QRLGIFAGSGVGKSTLLSMLARNTD--A--DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAY  216 (418)
T ss_pred             cEEEEECCCCCChHHHHHHHhCCCC--C--CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHH
Confidence            5789999999999999999987422  1  2222233333 3345555555544322111100  00010   0   001


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHH
Q 038944          251 KKIILHEYL--MTKRYLNVIDDVWNI-EVCDII  280 (334)
Q Consensus       251 l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l  280 (334)
                      ..-.+-+++  +|+..|+++||+-.- ..+.++
T Consensus       217 ~a~~iAEyfrd~G~~Vll~~DslTr~A~A~REi  249 (418)
T TIGR03498       217 TATAIAEYFRDQGKDVLLLMDSVTRFAMAQREI  249 (418)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchhHHHHHHHHH
Confidence            223344555  689999999999432 344433

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=94.92  E-value=0.025  Score=48.74  Aligned_cols=24  Identities=17%  Similarity=0.174  Sum_probs=21.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+|.|.|.+|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999883

>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=94.92  E-value=0.049  Score=45.15  Aligned_cols=37  Identities=24%  Similarity=0.395  Sum_probs=30.3

Q ss_pred             hhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          162 DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       162 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ....++|.++|..     +++.++|..|+|||||...+..+.
T Consensus        23 ~~g~~~l~~~l~~-----k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   23 GEGIEELKELLKG-----KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTTHHHHHHHHTT-----SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CcCHHHHHHHhcC-----CEEEEECCCCCCHHHHHHHHHhhc
Confidence            3456777777744     589999999999999999999853

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.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=94.91  E-value=0.23  Score=50.66  Aligned_cols=47  Identities=17%  Similarity=0.132  Sum_probs=36.5

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|....+.++.+.+..-...-.-|-|+|..|+||+++|+.+++.
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHh
Confidence            45889988888888877642222233679999999999999999984

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.90  E-value=0.11  Score=46.40  Aligned_cols=20  Identities=20%  Similarity=0.410  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |.++|++|+||||+|+.+..
T Consensus         2 Ivl~G~pGSGKST~a~~La~   21 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAK   21 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            67899999999999999886

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.

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=94.90  E-value=0.025  Score=46.97  Aligned_cols=23  Identities=13%  Similarity=0.161  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++++|+|..|+|||||+..+...
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~   24 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPA   24 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999873

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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=94.89  E-value=0.064  Score=49.94  Aligned_cols=37  Identities=24%  Similarity=0.230  Sum_probs=28.6

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++.+.....+..+|+|.|.+|+|||||+..+..
T Consensus        42 ~~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~   78 (332)
T PRK09435         42 AQELLDALLPHTGNALRIGITGVPGVGKSTFIEALGM   78 (332)
T ss_pred             HHHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3456666654445678999999999999999998765

>PRK14527 adenylate kinase; Provisional

Probab=94.88  E-value=0.024  Score=48.40  Aligned_cols=25  Identities=24%  Similarity=0.243  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+|.|+|.+|+||||+|+.+.+.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999863

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=94.88  E-value=0.021  Score=47.41  Aligned_cols=23  Identities=9%  Similarity=0.130  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|++|+|+.|+|||||...+..
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~   24 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVR   24 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHH
Confidence            57999999999999999999976

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=94.87  E-value=0.049  Score=51.43  Aligned_cols=100  Identities=15%  Similarity=0.086  Sum_probs=55.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCC----CCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYV----KHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKK  252 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~----~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~  252 (334)
                      ...+=+-|||..|.|||.|.-..|+...+    +-||.              ..+.++-+.+..-...  .      ...
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh--------------~Fm~~vh~~l~~~~~~--~------~~l  117 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFH--------------EFMLDVHSRLHQLRGQ--D------DPL  117 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCcccccccccc--------------HHHHHHHHHHHHHhCC--C------ccH
Confidence            34667899999999999999999986433    23442              2333333322221110  0      112


Q ss_pred             HHHHHHcCCCeEEEEEeCCCCh-----hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          253 IILHEYLMTKRYLNVIDDVWNI-----EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       253 ~~l~~~L~~kr~LlVlDdvw~~-----~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      ..+-+.+.++..||+||..--.     --...+...+-  ..|. |+|+|.|..
T Consensus       118 ~~va~~l~~~~~lLcfDEF~V~DiaDAmil~rLf~~l~--~~gv-vlVaTSN~~  168 (362)
T PF03969_consen  118 PQVADELAKESRLLCFDEFQVTDIADAMILKRLFEALF--KRGV-VLVATSNRP  168 (362)
T ss_pred             HHHHHHHHhcCCEEEEeeeeccchhHHHHHHHHHHHHH--HCCC-EEEecCCCC
Confidence            2333444556679999986432     23444444442  2344 666666654

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=94.86  E-value=0.023  Score=51.50  Aligned_cols=23  Identities=13%  Similarity=0.166  Sum_probs=21.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|+|+|.+|+|||||+..+...
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~   24 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDR   24 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999863

>PRK04182 cytidylate kinase; Provisional

Probab=94.86  E-value=0.026  Score=47.29  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=20.4

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +|.|.|+.|+||||+++.+.+.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~   23 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            7899999999999999999873

>cd04159 Arl10_like Arl10-like subfamily

Probab=94.84  E-value=0.21  Score=40.16  Aligned_cols=21  Identities=5%  Similarity=0.082  Sum_probs=19.3

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+|+|.+|+|||||.+.+.+.
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            689999999999999999875

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.

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=94.84  E-value=0.24  Score=48.32  Aligned_cols=47  Identities=17%  Similarity=0.119  Sum_probs=35.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|......++...+..-......+.|.|..|+||+++|+.++..
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~  180 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRH  180 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHh
Confidence            35788887778777776543323345789999999999999999874

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=94.84  E-value=0.23  Score=40.66  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=18.0

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|+|.+|+|||||+..+..
T Consensus         3 i~vvG~~~~GKtsl~~~l~~   22 (164)
T cd04101           3 CAVVGDPAVGKTAFVQMFHS   22 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            78999999999999988864

RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.

>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=94.83  E-value=0.025  Score=43.88  Aligned_cols=21  Identities=14%  Similarity=0.221  Sum_probs=19.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+|+|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999974

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 ....

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=94.81  E-value=0.04  Score=48.16  Aligned_cols=21  Identities=19%  Similarity=0.216  Sum_probs=18.2

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|+|.|-||+||||+|..+..
T Consensus         2 kIaI~GKGG~GKTtiaalll~   22 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLK   22 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHH
Confidence            689999999999999988443

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=94.80  E-value=0.047  Score=50.81  Aligned_cols=47  Identities=15%  Similarity=0.355  Sum_probs=41.1

Q ss_pred             CCCeeechhhHHHHHHHHhcC----CCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG----PPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++|.++..++|++.+...    +..-+|+-.+|+.|.|||||+..+.+
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~  110 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKR  110 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999753    35568999999999999999999987

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.80  E-value=0.025  Score=48.88  Aligned_cols=56  Identities=11%  Similarity=0.203  Sum_probs=34.7

Q ss_pred             HHHHHHcCCCeEEEEEeCCCCh---hHHHHHHhhCCC-CCCCeEEEEecCChHHHhhccc
Q 038944          253 IILHEYLMTKRYLNVIDDVWNI---EVCDIIREILPD-NQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       253 ~~l~~~L~~kr~LlVlDdvw~~---~~w~~l~~~l~~-~~~gsrIivTTr~~~va~~~~~  308 (334)
                      -.|-+.|.=+.-++.+|..=+.   +.-.++...... ...|--+|+.|....-|..+..
T Consensus       145 VAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eGmTMivVTHEM~FAr~Vad  204 (240)
T COG1126         145 VAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGMTMIIVTHEMGFAREVAD  204 (240)
T ss_pred             HHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHcCCeEEEEechhHHHHHhhh
Confidence            3455566666678899998654   333333333221 2346668888888888877654

>PLN02200 adenylate kinase family protein

Probab=94.79  E-value=0.027  Score=49.90  Aligned_cols=24  Identities=13%  Similarity=0.131  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|.|.|++|+||||+|+.+..
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~   65 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVE   65 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999877

>PHA02774 E1; Provisional

Probab=94.79  E-value=0.11  Score=51.45  Aligned_cols=37  Identities=24%  Similarity=0.313  Sum_probs=27.9

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -...|..+|. +.++-..+.|+|++|.|||.+|-.+.+
T Consensus       420 fl~~lk~~l~-~~PKknciv~~GPP~TGKS~fa~sL~~  456 (613)
T PHA02774        420 FLTALKDFLK-GIPKKNCLVIYGPPDTGKSMFCMSLIK  456 (613)
T ss_pred             HHHHHHHHHh-cCCcccEEEEECCCCCCHHHHHHHHHH
Confidence            3445555553 334456899999999999999999988

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=94.79  E-value=0.057  Score=53.28  Aligned_cols=94  Identities=15%  Similarity=0.135  Sum_probs=55.1

Q ss_pred             CCeeechhhHHHHHHHH---hc--------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHH
Q 038944          156 RDTVGLDDRMEELLDLL---IE--------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDAD  224 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L---~~--------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  224 (334)
                      .++.|.+..++.+.+.+   ..        +-...+.+-++|++|.|||.||+.+.+  ..+.+|-...+-.        
T Consensus       242 ~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~--~~~~~fi~v~~~~--------  311 (494)
T COG0464         242 DDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVAL--ESRSRFISVKGSE--------  311 (494)
T ss_pred             ehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHh--hCCCeEEEeeCHH--------
Confidence            34555555555554443   22        114566899999999999999999999  5555664433211        


Q ss_pred             HHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 038944          225 QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       225 ~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~  273 (334)
                           ++...-+       ..+.  .+...+....+...+.|.+|.+..
T Consensus       312 -----l~sk~vG-------esek--~ir~~F~~A~~~~p~iiFiDEiDs  346 (494)
T COG0464         312 -----LLSKWVG-------ESEK--NIRELFEKARKLAPSIIFIDEIDS  346 (494)
T ss_pred             -----Hhccccc-------hHHH--HHHHHHHHHHcCCCcEEEEEchhh
Confidence                 1111111       1112  333444444567889999999853

>PRK15115 response regulator GlrR; Provisional

Probab=94.78  E-value=0.15  Score=49.51  Aligned_cols=47  Identities=23%  Similarity=0.096  Sum_probs=33.2

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      .++|....+.++.+....-...-..+.|.|.+|+|||++|+.+++..
T Consensus       135 ~lig~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~s  181 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNAS  181 (444)
T ss_pred             cccccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHhc
Confidence            46777777766666554322222346799999999999999998853

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=94.78  E-value=0.065  Score=51.51  Aligned_cols=45  Identities=18%  Similarity=0.200  Sum_probs=33.9

Q ss_pred             CeeechhhHHHHHHHHhc-------C-----C--CCceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDLLIE-------G-----P--PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-------~-----~--~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.+..++.+...+..       .     +  ..-.-+.++|++|+|||+||+.+..
T Consensus        72 ~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~  130 (412)
T PRK05342         72 YVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLAR  130 (412)
T ss_pred             HeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHH
Confidence            489999988887655421       1     1  1235688999999999999999987

>PRK06761 hypothetical protein; Provisional

Probab=94.78  E-value=0.056  Score=49.11  Aligned_cols=24  Identities=17%  Similarity=0.156  Sum_probs=21.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHccC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ++|.|.|.+|+||||+++.+.+..
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L   27 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDIL   27 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            579999999999999999999843

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=94.76  E-value=0.21  Score=44.56  Aligned_cols=95  Identities=16%  Similarity=0.091  Sum_probs=57.2

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY  221 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  221 (334)
                      +.-+++-|-.++.++|-+...-.           =...+=+..+|++|.|||-+|+.|.|  +....|-.++     .  
T Consensus       174 vty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravan--rtdacfirvi-----g--  244 (435)
T KOG0729|consen  174 VTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVAN--RTDACFIRVI-----G--  244 (435)
T ss_pred             cccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhc--ccCceEEeeh-----h--
Confidence            33445666677777776665321           13456788899999999999999999  6655553332     1  


Q ss_pred             CHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCC-eEEEEEeCCC
Q 038944          222 DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTK-RYLNVIDDVW  272 (334)
Q Consensus       222 ~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~k-r~LlVlDdvw  272 (334)
                        .++.+.    --++        -.  .+...|.+.-++| -|+|.+|.+.
T Consensus       245 --selvqk----yvge--------ga--rmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  245 --SELVQK----YVGE--------GA--RMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             --HHHHHH----Hhhh--------hH--HHHHHHHHHhcccceEEEEeeccc
Confidence              111111    1111        11  4555666666554 5778888874

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=94.76  E-value=0.023  Score=49.28  Aligned_cols=23  Identities=17%  Similarity=0.267  Sum_probs=20.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|++|+|||||+..+..+
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~   28 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGD   28 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcC
Confidence            46889999999999999999876

>PLN02924 thymidylate kinase

Probab=94.74  E-value=0.11  Score=45.60  Aligned_cols=55  Identities=9%  Similarity=-0.022  Sum_probs=35.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      .-..|.|-|..|+||||+++.+.+.-... .+....+-..+......+.+++++..
T Consensus        15 ~g~~IviEGiDGsGKsTq~~~L~~~l~~~-g~~v~~~~ep~~~~~~g~~ir~~l~~   69 (220)
T PLN02924         15 RGALIVLEGLDRSGKSTQCAKLVSFLKGL-GVAAELWRFPDRTTSVGQMISAYLSN   69 (220)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCceeeeCCCCCChHHHHHHHHHhC
Confidence            34689999999999999999999843322 24433322222234455666666653

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=94.74  E-value=0.15  Score=42.77  Aligned_cols=120  Identities=13%  Similarity=0.085  Sum_probs=60.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeE--EEEEcCCCCCHHHHHHHHHH---HhCCCC--Cc-cccch-hhHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCH--AWVPGTYPYDADQMLDIVIK---FLMPSS--RL-SEIMD-KNYEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~--~wv~vs~~~~~~~il~~il~---~~~~~~--~~-~~~~~-~~~~~  250 (334)
                      ..|-|++-.|.||||.|--+.-. .....+.+.  =|+.-........++....-   +.+...  .. ....+ .....
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~r-a~~~g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~   84 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALR-ALGHGKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKA   84 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHH-HHHCCCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHH
Confidence            57788888999999998665431 122223332  13333323343444433200   001100  00 00000 01113


Q ss_pred             HHHHHHHHcCCCe-EEEEEeCCCCh-----hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          251 KKIILHEYLMTKR-YLNVIDDVWNI-----EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       251 l~~~l~~~L~~kr-~LlVlDdvw~~-----~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      .....++.+...+ =|+|||.+-..     -..+.+...+.....+.-||+|-|+.
T Consensus        85 ~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        85 AWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            4455556665444 59999998533     23445555554444566799999976

Alternate name: corrinoid adenosyltransferase.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=94.74  E-value=0.022  Score=47.25  Aligned_cols=21  Identities=14%  Similarity=0.117  Sum_probs=17.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+|.|..|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999974

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=94.73  E-value=0.068  Score=45.39  Aligned_cols=52  Identities=12%  Similarity=0.066  Sum_probs=30.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCce--------eeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYF--------DCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F--------~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      .+..|+|.+|+||||++..+..+......|        ..+.|++...+  ...+.+.+...
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~~~   92 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLRAL   92 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHHHH
Confidence            488899999999999998887643332222        23566655544  44555444433

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=94.72  E-value=0.13  Score=49.49  Aligned_cols=97  Identities=10%  Similarity=-0.005  Sum_probs=50.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCC-------c-c--ccchhh
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSR-------L-S--EIMDKN  247 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~-------~-~--~~~~~~  247 (334)
                      -..++|+|..|+|||||++.+......    ++.....+.. .-++.++..+.+..-.....       . +  ......
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~~~~----dv~vig~IGerg~ev~ef~~~~l~~~gl~rsvvv~~~~d~s~~~rl~a~  230 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRYTQA----DVVVVGLIGERGREVKEFIEHSLQAAGMAKSVVVAAPADESPLMRIKAT  230 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhcccCC----CeEEEEEEeeecHHHHHHHHHHhhhcccceEEEEEecCCCChhhhHHHH
Confidence            457999999999999999998874321    2222222222 22334444344433221110       0 0  011111


Q ss_pred             HHHHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHH
Q 038944          248 YEMKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       248 ~~~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                        .....+.+++  +++..|+++||+-.- ..+.++.
T Consensus       231 --e~a~~iAEyfr~~g~~Vll~~Dsltr~a~A~REis  265 (434)
T PRK07196        231 --ELCHAIATYYRDKGHDVLLLVDSLTRYAMAQREIA  265 (434)
T ss_pred             --HHHHHHHHHhhhccCCEEEeecchhHHHhhhhHHH
Confidence              2333444443  689999999999432 3444333

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=94.72  E-value=0.031  Score=45.67  Aligned_cols=22  Identities=18%  Similarity=0.276  Sum_probs=19.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||+..+.++
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~   23 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYD   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999999864

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

>PRK06820 type III secretion system ATPase; Validated

Probab=94.72  E-value=0.18  Score=48.74  Aligned_cols=23  Identities=17%  Similarity=0.310  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|+|..|+|||||++.+...
T Consensus       164 qri~I~G~sG~GKStLl~~I~~~  186 (440)
T PRK06820        164 QRIGIFAAAGVGKSTLLGMLCAD  186 (440)
T ss_pred             CEEEEECCCCCChHHHHHHHhcc
Confidence            37899999999999999998873

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=94.70  E-value=0.16  Score=49.18  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..++|+|..|+|||||++.+.+.
T Consensus       158 Gq~i~I~G~sG~GKStLl~~I~~~  181 (438)
T PRK07721        158 GQRVGIFAGSGVGKSTLMGMIARN  181 (438)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcc
Confidence            468999999999999999988874

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=94.68  E-value=0.62  Score=43.43  Aligned_cols=47  Identities=9%  Similarity=0.142  Sum_probs=30.0

Q ss_pred             CCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh-HHHhhcc
Q 038944          261 TKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI-KMFTFLL  307 (334)
Q Consensus       261 ~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~-~va~~~~  307 (334)
                      +++-++|+|++..  .+..+.+...+-.-..++.+|+||.+. .+..++-
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~  154 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIK  154 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHH
Confidence            4455567899974  467888888775544567777777664 4443433

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=94.68  E-value=0.057  Score=46.04  Aligned_cols=23  Identities=22%  Similarity=0.055  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..|+|.|..|+||||+++.+.+.
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~   26 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKL   26 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999999874

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.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=94.68  E-value=0.2  Score=48.07  Aligned_cols=89  Identities=12%  Similarity=0.084  Sum_probs=48.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh----h--HHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK----N--YEM  250 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~----~--~~~  250 (334)
                      ..++|+|..|+|||||.+.+.+....    ++...+.+.... .+.++....+..-..+....  ...+.    .  --.
T Consensus       138 q~~~I~G~sG~GKTtLl~~I~~~~~~----~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~~  213 (411)
T TIGR03496       138 QRMGIFAGSGVGKSTLLGMMARYTEA----DVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAAF  213 (411)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCCCC----CEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHH
Confidence            47899999999999999988874321    233344455443 34444454443311110000  00000    0  001


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 038944          251 KKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       251 l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      ..-.+-+++  +|+..|+++||+-
T Consensus       214 ~a~tiAEyfr~~G~~Vll~~Dslt  237 (411)
T TIGR03496       214 YATAIAEYFRDQGKDVLLLMDSLT  237 (411)
T ss_pred             HHHHHHHHHHHCCCCEEEEEeChH
Confidence            222333444  6899999999994

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK08356 hypothetical protein; Provisional

Probab=94.68  E-value=0.028  Score=48.21  Aligned_cols=22  Identities=18%  Similarity=0.080  Sum_probs=19.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ..+|.|+|++|+||||+|+.+-
T Consensus         5 ~~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          5 KMIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             cEEEEEECCCCCCHHHHHHHHH
Confidence            3679999999999999999993

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=94.67  E-value=0.059  Score=54.55  Aligned_cols=75  Identities=13%  Similarity=0.059  Sum_probs=54.1

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      ++++|.+..++.|...+...    +.+-++|.+|+||||+|+.+.+.. -..+|+...|..-+ ..+...+++.+..+++
T Consensus        31 ~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~l-~~~~~~~~~~~~np-~~~~~~~~~~v~~~~G  104 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAELL-PKEELQDILVYPNP-EDPNNPKIRTVPAGKG  104 (637)
T ss_pred             HHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHHc-ChHhHHHheEeeCC-CcchHHHHHHHHHhcC
Confidence            45789888888877766654    368889999999999999998732 12345777786653 3466777777776555


Q ss_pred             C
Q 038944          236 P  236 (334)
Q Consensus       236 ~  236 (334)
                      .
T Consensus       105 ~  105 (637)
T PRK13765        105 K  105 (637)
T ss_pred             H
Confidence            4

>PLN02348 phosphoribulokinase

Probab=94.67  E-value=0.047  Score=51.68  Aligned_cols=27  Identities=15%  Similarity=0.158  Sum_probs=23.7

Q ss_pred             CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          175 GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       175 ~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .....-+|+|.|.+|+||||+|+.+.+
T Consensus        45 ~~~~p~IIGIaG~SGSGKSTfA~~L~~   71 (395)
T PLN02348         45 ADDGTVVIGLAADSGCGKSTFMRRLTS   71 (395)
T ss_pred             cCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            334678999999999999999999987

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=94.66  E-value=0.028  Score=47.51  Aligned_cols=23  Identities=9%  Similarity=0.140  Sum_probs=20.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|+|..|.|||||++.+..-
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~   26 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAAL   26 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999999973

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=94.65  E-value=0.25  Score=47.90  Aligned_cols=45  Identities=16%  Similarity=0.240  Sum_probs=34.1

Q ss_pred             CeeechhhHHHHHHHHhcC-CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEG-PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|....++++...+..- ..... +.|.|..|+||+++|+.++..
T Consensus       140 ~lig~s~~~~~l~~~i~~~a~~~~~-vli~Ge~GtGK~~lA~~ih~~  185 (445)
T TIGR02915       140 GLITSSPGMQKICRTIEKIAPSDIT-VLLLGESGTGKEVLARALHQL  185 (445)
T ss_pred             ceeecCHHHHHHHHHHHHHhCCCCC-EEEECCCCcCHHHHHHHHHHh
Confidence            5788888888877776542 22344 459999999999999999874

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=94.61  E-value=0.027  Score=47.04  Aligned_cols=22  Identities=9%  Similarity=0.119  Sum_probs=19.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|.|+|+.|+||||+++.+.+
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~   24 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQ   24 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3588899999999999999987

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

Probab=94.60  E-value=0.018  Score=46.41  Aligned_cols=45  Identities=27%  Similarity=0.167  Sum_probs=31.5

Q ss_pred             eechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          159 VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ||....++++.+.+..-...-.-|.|.|..|+||+++|+.++...
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~   45 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYS   45 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhc
Confidence            466666777777665422223457899999999999999999853

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.58  E-value=0.14  Score=48.38  Aligned_cols=24  Identities=8%  Similarity=0.109  Sum_probs=21.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.+++.++|+.|+||||++..+..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~  228 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGW  228 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999888765

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=94.58  E-value=0.14  Score=49.46  Aligned_cols=96  Identities=14%  Similarity=0.078  Sum_probs=50.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCH-HHHHHHHHHHhCCCCCcc----ccchh----h-H
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDA-DQMLDIVIKFLMPSSRLS----EIMDK----N-Y  248 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~-~~il~~il~~~~~~~~~~----~~~~~----~-~  248 (334)
                      -..++|+|..|+|||||++.+.....    -+......+...... .+.....   ++......    ...++    . +
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~~~----~~v~vi~~iGergrev~e~~~~~---l~~~l~~tvvV~atsddsp~~R~~  229 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKGCL----APIKVVALIGERGREIPEFIEKN---LGGDLENTVIVVATSDDSPLMRKY  229 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhccC----CCEEEEEeeCccchhHHHHHHHH---hcCcccceEEEEECCCCCHHHhhH
Confidence            35789999999999999999987422    233444445444322 3333332   23211100    00000    0 0


Q ss_pred             -HHHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHH
Q 038944          249 -EMKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       249 -~~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                       -.....+-+++  +|+..|+++||+-.- ..+.++.
T Consensus       230 ~~~~a~~iAEyFrd~G~~Vll~~DslTr~A~A~REi~  266 (434)
T PRK08472        230 GAFCAMSVAEYFKNQGLDVLFIMDSVTRFAMAQREIG  266 (434)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEecccchHHHHHHHHHH
Confidence             01122333444  699999999999432 4444443

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=94.58  E-value=0.053  Score=54.35  Aligned_cols=49  Identities=14%  Similarity=0.014  Sum_probs=36.5

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++..+.|.+-.+.|.++.-....+-.+|.++|+.|+||||+|+.+..
T Consensus       366 ~~pP~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~  414 (568)
T PRK05537        366 LEIPEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMV  414 (568)
T ss_pred             CCCChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHH
Confidence            4445556676666666665554445566899999999999999999987

>TIGR01287 nifH nitrogenase iron protein

Probab=94.58  E-value=0.025  Score=51.28  Aligned_cols=22  Identities=14%  Similarity=0.163  Sum_probs=18.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|+|+|-||+||||++..+..
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~   22 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAA   22 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHH
Confidence            3689999999999998877753

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.

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=94.57  E-value=0.029  Score=50.13  Aligned_cols=24  Identities=17%  Similarity=0.086  Sum_probs=21.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|+|+.|+|||||.+.++.
T Consensus        27 ~G~i~~iiGpNG~GKSTLLk~l~g   50 (258)
T COG1120          27 KGEITGILGPNGSGKSTLLKCLAG   50 (258)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            357999999999999999999986

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=94.57  E-value=0.03  Score=45.38  Aligned_cols=23  Identities=13%  Similarity=0.255  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +-|.++|..|+|||||++.+...
T Consensus         2 krimliG~~g~GKTTL~q~L~~~   24 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGE   24 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCC
Confidence            46889999999999999999875

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

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=94.56  E-value=0.028  Score=51.11  Aligned_cols=22  Identities=9%  Similarity=0.045  Sum_probs=18.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|+|-||+||||++-.+..
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~   23 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAA   23 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHH
Confidence            6899999999999998877653

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=94.53  E-value=0.03  Score=48.73  Aligned_cols=24  Identities=17%  Similarity=0.072  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            358999999999999999999753

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.

>PF00488 MutS_V: MutS domain V C-terminus

Probab=94.52  E-value=0.27  Score=43.49  Aligned_cols=113  Identities=13%  Similarity=0.059  Sum_probs=57.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHccC---CC-----CCceee----EEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhh
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSS---YV-----KHYFDC----HAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKN  247 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~---~~-----~~~F~~----~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~  247 (334)
                      ++.-|.|+...||||+.+.|.--.   ++     .+.+..    .++..++..-++           ....   ..-..+
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~~d~~-----------~~~~---S~F~~E  109 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGDDDSI-----------ESGL---STFMAE  109 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES---SS-----------TTSS---SHHHHH
T ss_pred             eEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeeccccccc-----------cccc---ccHHHh
Confidence            689999999999999999885321   11     112211    233333322110           0000   000001


Q ss_pred             HHHHHHHHHHHcCCCeEEEEEeCCCChh--------HHHHHHhhCCCCCCCeEEEEecCChHHHhhccccC
Q 038944          248 YEMKKIILHEYLMTKRYLNVIDDVWNIE--------VCDIIREILPDNQNRSRVLITLTEIKMFTFLLETL  310 (334)
Q Consensus       248 ~~~l~~~l~~~L~~kr~LlVlDdvw~~~--------~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~~~  310 (334)
                      +.++...+..  .+++-|+++|.+-...        .|.. ...|.. ..++.+|+||...+++.......
T Consensus       110 ~~~~~~il~~--~~~~sLvliDE~g~gT~~~eg~ai~~ai-le~l~~-~~~~~~i~~TH~~~l~~~~~~~~  176 (235)
T PF00488_consen  110 MKRLSSILRN--ATEKSLVLIDELGRGTNPEEGIAIAIAI-LEYLLE-KSGCFVIIATHFHELAELLERNP  176 (235)
T ss_dssp             HHHHHHHHHH----TTEEEEEESTTTTSSHHHHHHHHHHH-HHHHHH-TTT-EEEEEES-GGGGGHHHHST
T ss_pred             HHHHHhhhhh--cccceeeecccccCCCChhHHHHHHHHH-HHHHHH-hccccEEEEeccchhHHHhhhCc
Confidence            1133333322  3578899999997531        2332 233322 14789999999999988765433

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.52  E-value=0.18  Score=42.25  Aligned_cols=83  Identities=13%  Similarity=0.137  Sum_probs=44.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccch-hhHHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMD-KNYEMKKIILHEY  258 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~-~~~~~l~~~l~~~  258 (334)
                      .++.|.|.+|+||||+|..+....  ..   ...++.-...++ .+....|-.............+ ..  .+...+..+
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~~--~~---~~~~iat~~~~~-~e~~~ri~~h~~~R~~~w~t~E~~~--~l~~~i~~~   73 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQS--GL---QVLYIATAQPFD-DEMAARIAHHRQRRPAHWQTVEEPL--DLAELLRAD   73 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHHc--CC---CcEeCcCCCCCh-HHHHHHHHHHHhcCCCCCeEecccc--cHHHHHHhh
Confidence            368999999999999999887631  11   123444344444 3455555444333221111111 11  344455554


Q ss_pred             cCCCeEEEEEeCC
Q 038944          259 LMTKRYLNVIDDV  271 (334)
Q Consensus       259 L~~kr~LlVlDdv  271 (334)
                      ..+.. ++++|.+
T Consensus        74 ~~~~~-~VlID~L   85 (170)
T PRK05800         74 AAPGR-CVLVDCL   85 (170)
T ss_pred             cCCCC-EEEehhH
Confidence            43322 6888886

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=94.51  E-value=0.035  Score=52.04  Aligned_cols=47  Identities=17%  Similarity=0.164  Sum_probs=37.3

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+-+.+||.++.+..|...+.++.  +.-+-|.|..|+||||+|+.+++
T Consensus        14 ~pf~~ivGq~~~k~al~~~~~~p~--~~~vli~G~~GtGKs~~ar~~~~   60 (350)
T CHL00081         14 FPFTAIVGQEEMKLALILNVIDPK--IGGVMIMGDRGTGKSTTIRALVD   60 (350)
T ss_pred             CCHHHHhChHHHHHHHHHhccCCC--CCeEEEEcCCCCCHHHHHHHHHH
Confidence            345678999988888877776643  45566999999999999999975

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=94.50  E-value=0.22  Score=41.27  Aligned_cols=46  Identities=11%  Similarity=0.122  Sum_probs=29.0

Q ss_pred             CCeEEEEEeCCCCh---hHHHHHHhhCCC-CCCCeEEEEecCChHHHhhc
Q 038944          261 TKRYLNVIDDVWNI---EVCDIIREILPD-NQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       261 ~kr~LlVlDdvw~~---~~w~~l~~~l~~-~~~gsrIivTTr~~~va~~~  306 (334)
                      ++.-|++||+.-..   ..-..+...+.. ...|+.+|+||...+.+..+
T Consensus        98 ~~~~llllDEp~~gld~~~~~~l~~~l~~~~~~~~~vii~TH~~~~~~~~  147 (162)
T cd03227          98 KPRPLYILDEIDRGLDPRDGQALAEAILEHLVKGAQVIVITHLPELAELA  147 (162)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHhh
Confidence            36789999998643   222233332221 11277899999999988754

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=94.49  E-value=0.031  Score=48.37  Aligned_cols=24  Identities=17%  Similarity=0.097  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||++.+..-
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G~   50 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNGL   50 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999863

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.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=94.47  E-value=0.033  Score=46.28  Aligned_cols=21  Identities=19%  Similarity=0.180  Sum_probs=19.9

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +|.|.|+.|+||||+|+.+.+
T Consensus         2 iI~i~G~~GSGKstia~~la~   22 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAE   22 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            799999999999999999987

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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=94.46  E-value=0.11  Score=48.51  Aligned_cols=63  Identities=21%  Similarity=0.200  Sum_probs=44.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHH
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQML  227 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il  227 (334)
                      ..++|.+.....+...+..+.    -+-+.|.+|+|||+||+.+..  .....|   .+|.........+++
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~~----~vll~G~PG~gKT~la~~lA~--~l~~~~---~~i~~t~~l~p~d~~   86 (329)
T COG0714          24 KVVVGDEEVIELALLALLAGG----HVLLEGPPGVGKTLLARALAR--ALGLPF---VRIQCTPDLLPSDLL   86 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcCC----CEEEECCCCccHHHHHHHHHH--HhCCCe---EEEecCCCCCHHHhc
Confidence            348898887777766666543    478999999999999999998  333333   455556666555543

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=94.46  E-value=0.047  Score=46.95  Aligned_cols=118  Identities=12%  Similarity=0.064  Sum_probs=56.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC----CCCHHHHHHHHHHHhCCCCCccccchhhHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY----PYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKK  252 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~  252 (334)
                      .+..++.+.|.+|.||||++..+.....    ....+.+....    -+....+..    .-.....  ......-..+.
T Consensus        13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~~----~~~~v~i~~D~~r~~~p~~~~~~~----~~~~~~~--~~~~~~a~~~~   82 (199)
T PF06414_consen   13 EKPTLIIIAGQPGSGKSTLARQLLEEFG----GGGIVVIDADEFRQFHPDYDELLK----ADPDEAS--ELTQKEASRLA   82 (199)
T ss_dssp             SS-EEEEEES-TTSTTHHHHHHHHHHT-----TT-SEEE-GGGGGGGSTTHHHHHH----HHCCCTH--HHHHHHHHHHH
T ss_pred             cCCEEEEEeCCCCCCHHHHHHHhhhhcc----CCCeEEEehHHHHHhccchhhhhh----hhhhhhH--HHHHHHHHHHH
Confidence            4678889999999999999999987321    12223332211    112223222    1111111  11111111566


Q ss_pred             HHHHHHcCCCeEEEEEeCCCCh-hHHHHHHhhCCCCCCCeEEEEecCChHHHh
Q 038944          253 IILHEYLMTKRYLNVIDDVWNI-EVCDIIREILPDNQNRSRVLITLTEIKMFT  304 (334)
Q Consensus       253 ~~l~~~L~~kr~LlVlDdvw~~-~~w~~l~~~l~~~~~gsrIivTTr~~~va~  304 (334)
                      ..+.+....+++=+|+|..-.. +....+...+...+-...|++..-+.+++.
T Consensus        83 ~~~~~~a~~~~~nii~E~tl~~~~~~~~~~~~~k~~GY~v~l~~v~~~~e~s~  135 (199)
T PF06414_consen   83 EKLIEYAIENRYNIIFEGTLSNPSKLRKLIREAKAAGYKVELYYVAVPPELSI  135 (199)
T ss_dssp             HHHHHHHHHCT--EEEE--TTSSHHHHHHHHHHHCTT-EEEEEEE---HHHHH
T ss_pred             HHHHHHHHHcCCCEEEecCCCChhHHHHHHHHHHcCCceEEEEEEECCHHHHH
Confidence            6667776677888888988654 444446666654333344555455555543

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>cd04124 RabL2 RabL2 subfamily

Probab=94.45  E-value=0.26  Score=40.49  Aligned_cols=21  Identities=10%  Similarity=0.252  Sum_probs=18.2

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||+..+.++
T Consensus         3 i~vvG~~~vGKTsli~~~~~~   23 (161)
T cd04124           3 IILLGDSAVGKSKLVERFLMD   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999877653

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

>PLN02796 D-glycerate 3-kinase

Probab=94.43  E-value=0.037  Score=51.52  Aligned_cols=25  Identities=16%  Similarity=-0.005  Sum_probs=22.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-+|+|.|..|+|||||++.+..-
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~l  123 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYL  123 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            5678999999999999999999873

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=94.43  E-value=0.028  Score=49.86  Aligned_cols=20  Identities=15%  Similarity=0.212  Sum_probs=17.3

Q ss_pred             EEccCCccHHHHHHHHHccC
Q 038944          184 ILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       184 IvG~gGvGKTtLa~~v~~~~  203 (334)
                      |+|++|+||||+++.+.+..
T Consensus         1 ViGpaGSGKTT~~~~~~~~~   20 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWL   20 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            68999999999999998853

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.42  E-value=0.033  Score=49.18  Aligned_cols=126  Identities=15%  Similarity=0.195  Sum_probs=67.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc--C----------CCCC-------cee---eEEEEEcCCCC------------CHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS--S----------YVKH-------YFD---CHAWVPGTYPY------------DAD  224 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~--~----------~~~~-------~F~---~~~wv~vs~~~------------~~~  224 (334)
                      --.++|+|++|+|||||.+.+..=  +          .+..       -|+   .--|-+|-++-            ...
T Consensus        29 GEfvsilGpSGcGKSTLLriiAGL~~p~~G~V~~~g~~v~~p~~~~~~vFQ~~~LlPW~Tv~~NV~l~l~~~~~~~~e~~  108 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIAGLEKPTSGEVLLDGRPVTGPGPDIGYVFQEDALLPWLTVLDNVALGLELRGKSKAEAR  108 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCCCceEEECCcccCCCCCCEEEEeccCcccchhhHHhhheehhhccccchHhHH
Confidence            358999999999999999999631  1          1111       122   23365554321            123


Q ss_pred             HHHHHHHHHhCCCCCcc---ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEE
Q 038944          225 QMLDIVIKFLMPSSRLS---EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVL  294 (334)
Q Consensus       225 ~il~~il~~~~~~~~~~---~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIi  294 (334)
                      .....+++.++......   ...+-.+.+.. .|-+.|....=++.||.-...       ...+.+.....  ..+.-|+
T Consensus       109 ~~a~~~L~~VgL~~~~~~~P~qLSGGMrQRV-aiARAL~~~P~lLLlDEPFgALDalTR~~lq~~l~~lw~--~~~~Tvl  185 (248)
T COG1116         109 ERAKELLELVGLAGFEDKYPHQLSGGMRQRV-AIARALATRPKLLLLDEPFGALDALTREELQDELLRLWE--ETRKTVL  185 (248)
T ss_pred             HHHHHHHHHcCCcchhhcCccccChHHHHHH-HHHHHHhcCCCEEEEcCCcchhhHHHHHHHHHHHHHHHH--hhCCEEE
Confidence            45667777766543321   11222211333 344455556667889987654       22333333332  2345577


Q ss_pred             EecCChHHHhhcc
Q 038944          295 ITLTEIKMFTFLL  307 (334)
Q Consensus       295 vTTr~~~va~~~~  307 (334)
                      +.|.+-+=|-.++
T Consensus       186 lVTHdi~EAv~Ls  198 (248)
T COG1116         186 LVTHDVDEAVYLA  198 (248)
T ss_pred             EEeCCHHHHHhhh
Confidence            7777766665544

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=94.42  E-value=0.22  Score=48.75  Aligned_cols=99  Identities=12%  Similarity=0.006  Sum_probs=57.3

Q ss_pred             eEEEEEccCCccHHHHH-HHHHccCCCCCceee-EEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc-----ccchhh-H--
Q 038944          180 SVVVILDSIGLDKAAFA-GEAYNSSYVKHYFDC-HAWVPGTYPY-DADQMLDIVIKFLMPSSRLS-----EIMDKN-Y--  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~il~~il~~~~~~~~~~-----~~~~~~-~--  248 (334)
                      .-++|.|-.|+|||||| ..+.+..    .-+. ++++-+.+.. .+.++...+.+.-.......     +..... +  
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~q~----~~dv~~V~~~IGeR~rev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r~~a  238 (497)
T TIGR03324       163 QRELILGDRQTGKTAIAIDTILNQK----GRNVLCIYCAIGQRASAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQYIA  238 (497)
T ss_pred             CEEEeecCCCCCHHHHHHHHHHHhc----CCCcEEEEEEeccCcHHHHHHHHHhhhcCCcceeEEEEeCCCCCHHHHHHH
Confidence            35789999999999996 5777742    2343 6788888764 45566666665422211100     000000 0  


Q ss_pred             HHHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHHh
Q 038944          249 EMKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIRE  282 (334)
Q Consensus       249 ~~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~~  282 (334)
                      --....+-+++  +|+..|||+||+-.. ..+.++..
T Consensus       239 p~~a~aiAEyfrd~G~~VLlv~DdlTr~A~A~REisL  275 (497)
T TIGR03324       239 PYAATSIGEHFMEQGRDVLIVYDDLTQHARAYRELSL  275 (497)
T ss_pred             HHHHHHHHHHHHhCCCCEEEEEcChhHHHHHHHHHHh
Confidence            01122344444  789999999999543 55555543

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=94.42  E-value=0.43  Score=49.22  Aligned_cols=23  Identities=22%  Similarity=0.203  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -..++|+|..|.|||||++.+..
T Consensus       491 G~~iaIvG~sGsGKSTLlklL~g  513 (694)
T TIGR03375       491 GEKVAIIGRIGSGKSTLLKLLLG  513 (694)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999965

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=94.41  E-value=0.03  Score=50.70  Aligned_cols=22  Identities=14%  Similarity=0.161  Sum_probs=19.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|+|-||+||||++..+..
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~   23 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTA   23 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHH
Confidence            6899999999999998877753

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=94.41  E-value=0.031  Score=50.33  Aligned_cols=22  Identities=14%  Similarity=0.161  Sum_probs=18.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|.|-||+||||++..+..
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~   23 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSA   23 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHH
Confidence            5788999999999998877654

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.

>cd01862 Rab7 Rab7 subfamily

Probab=94.41  E-value=0.034  Score=45.98  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=19.5

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||+..+.++
T Consensus         2 ki~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           2 KVIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3789999999999999988765

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-

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=94.41  E-value=0.18  Score=49.52  Aligned_cols=99  Identities=15%  Similarity=0.065  Sum_probs=54.6

Q ss_pred             eEEEEEccCCccHHHH-HHHHHccCCCCCceee-EEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh---h-H--
Q 038944          180 SVVVILDSIGLDKAAF-AGEAYNSSYVKHYFDC-HAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK---N-Y--  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtL-a~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~---~-~--  248 (334)
                      .-++|.|-.|+|||+| +..+.+.  ..  -+. ++++.+.+.. .+.++...+.+.-..+....  ...+.   . +  
T Consensus       163 Qr~~Ifg~~g~GKt~lal~~i~~~--~~--~dv~~V~~~IGer~~ev~e~~~~~~~~~~l~~tvvv~atsd~p~~~r~~a  238 (502)
T PRK09281        163 QRELIIGDRQTGKTAIAIDTIINQ--KG--KDVICIYVAIGQKASTVAQVVRKLEEHGAMEYTIVVAATASDPAPLQYLA  238 (502)
T ss_pred             cEEEeecCCCCCchHHHHHHHHHh--cC--CCeEEEEEEecCChHHHHHHHHHHhhcCCccceEEEEeCCCCCHHHHHHH
Confidence            3689999999999999 4666653  22  234 3777777765 44556665554322111100  00000   0 0  


Q ss_pred             HHHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHHh
Q 038944          249 EMKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIRE  282 (334)
Q Consensus       249 ~~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~~  282 (334)
                      -...-.+-+++  +|+..|+|+||+-.- ..+.++..
T Consensus       239 ~~~a~tiAEyfrd~G~~VLli~DdlTr~A~A~REisl  275 (502)
T PRK09281        239 PYAGCAMGEYFMDNGKDALIVYDDLSKQAVAYRQLSL  275 (502)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEecCchHHHHHHHHHHH
Confidence            01122233333  589999999999543 56665543

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=94.40  E-value=0.033  Score=48.42  Aligned_cols=24  Identities=17%  Similarity=0.192  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl   52 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGI   52 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999863

>cd04163 Era Era subfamily

Probab=94.40  E-value=0.038  Score=44.92  Aligned_cols=24  Identities=13%  Similarity=0.165  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+|+++|..|+|||||...+...
T Consensus         3 ~~~i~~~G~~g~GKttl~~~l~~~   26 (168)
T cd04163           3 SGFVAIVGRPNVGKSTLLNALVGQ   26 (168)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999998764

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.

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

Probab=94.39  E-value=0.052  Score=55.61  Aligned_cols=44  Identities=16%  Similarity=0.299  Sum_probs=34.8

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++||+++.+++++.|.....+-+|  .+|.+|+|||+++.-+..
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~KNNPv--LiGEpGVGKTAIvEGLA~  213 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTKNNPV--LVGEPGVGKTAIVEGLAQ  213 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCCCCCe--EecCCCCCHHHHHHHHHH
Confidence            44789999999999999986544443  579999999997755544

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

Probab=94.39  E-value=0.099  Score=43.84  Aligned_cols=45  Identities=11%  Similarity=0.203  Sum_probs=31.8

Q ss_pred             EEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          182 VVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      +.|.|.+|+|||++|......     .....+++.-++.++. ++...|..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~-em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFDD-EMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCH-HHHHHHHH
Confidence            678999999999999988652     2235677777777765 34444444

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=94.38  E-value=0.33  Score=50.54  Aligned_cols=136  Identities=13%  Similarity=0.174  Sum_probs=81.0

Q ss_pred             chhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHH-HHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCC
Q 038944          161 LDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFA-GEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR  239 (334)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~  239 (334)
                      ....+.+|.+.+...    .|+.|+|..|.||||-. +.+++...   .....+-++=++......+-..+.++++.+..
T Consensus        51 v~~~~~~i~~ai~~~----~vvii~getGsGKTTqlP~~lle~g~---~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G  123 (845)
T COG1643          51 VTAVRDEILKAIEQN----QVVIIVGETGSGKTTQLPQFLLEEGL---GIAGKIGCTQPRRLAARSVAERVAEELGEKLG  123 (845)
T ss_pred             cHHHHHHHHHHHHhC----CEEEEeCCCCCChHHHHHHHHHhhhc---ccCCeEEecCchHHHHHHHHHHHHHHhCCCcC
Confidence            456678888888764    49999999999999965 55555321   11223333333444667788888888887543


Q ss_pred             cc-----------------ccchhhHHHHHHHHH-HHcCCCeEEEEEeCCCChh-----HHHHHHhhCCCCCCCeEEEEe
Q 038944          240 LS-----------------EIMDKNYEMKKIILH-EYLMTKRYLNVIDDVWNIE-----VCDIIREILPDNQNRSRVLIT  296 (334)
Q Consensus       240 ~~-----------------~~~~~~~~~l~~~l~-~~L~~kr~LlVlDdvw~~~-----~w~~l~~~l~~~~~gsrIivT  296 (334)
                      ..                 .-+.+.  .+...++ ..+-.+=-.||+|.+-...     .+.-+...++.-...-||||+
T Consensus       124 ~~VGY~iRfe~~~s~~Trik~mTdG--iLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIim  201 (845)
T COG1643         124 ETVGYSIRFESKVSPRTRIKVMTDG--ILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIM  201 (845)
T ss_pred             ceeeEEEEeeccCCCCceeEEeccH--HHHHHHhhCcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence            21                 223444  5555555 3333444578899996542     122222222222224889998


Q ss_pred             cCChHHHhh
Q 038944          297 LTEIKMFTF  305 (334)
Q Consensus       297 Tr~~~va~~  305 (334)
                      |=.-+...+
T Consensus       202 SATld~~rf  210 (845)
T COG1643         202 SATLDAERF  210 (845)
T ss_pred             ecccCHHHH
Confidence            776555443

>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=94.38  E-value=0.037  Score=48.05  Aligned_cols=25  Identities=16%  Similarity=0.122  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .. .+++|+|..|.|||||++.+..-
T Consensus        22 ~~-e~~~i~G~nGsGKSTLl~~l~G~   46 (214)
T cd03297          22 NE-EVTGIFGASGAGKSTLLRCIAGL   46 (214)
T ss_pred             cc-eeEEEECCCCCCHHHHHHHHhCC
Confidence            45 89999999999999999999753

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.

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=94.38  E-value=0.29  Score=47.23  Aligned_cols=90  Identities=13%  Similarity=0.118  Sum_probs=49.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHHHhCCCCCcc--ccchhh-H-----H
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIKFLMPSSRLS--EIMDKN-Y-----E  249 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~~~~~~~~~~--~~~~~~-~-----~  249 (334)
                      -..++|+|..|+|||||.+.+.+...    -+....+.+.. ..++..+..+.+..........  ...+.. +     -
T Consensus       145 Gq~~~I~G~sG~GKStLl~~I~~~~~----~~~~vi~~iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~~~~  220 (422)
T TIGR02546       145 GQRIGIFAGAGVGKSTLLGMIARGAS----ADVNVIALIGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERLKAA  220 (422)
T ss_pred             CCEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHHHHH
Confidence            34789999999999999999998422    23333344443 3345555544443321111000  000100 0     0


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      .....+.+++  ++++.|+++|++-
T Consensus       221 ~~a~~~AE~f~~~g~~Vl~~~Dslt  245 (422)
T TIGR02546       221 YTATAIAEYFRDQGKRVLLMMDSLT  245 (422)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCch
Confidence            1223344444  6889999999994

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=94.37  E-value=0.035  Score=47.28  Aligned_cols=23  Identities=17%  Similarity=0.166  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G   40 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNG   40 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999975

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.

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=94.37  E-value=0.032  Score=47.47  Aligned_cols=21  Identities=19%  Similarity=0.246  Sum_probs=19.2

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|.|++|+||||+|+.+.+.
T Consensus         2 I~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            789999999999999999873

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd00879 Sar1 Sar1 subfamily

Probab=94.35  E-value=0.065  Score=45.33  Aligned_cols=24  Identities=8%  Similarity=0.019  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+.|+|.+|+|||||...+.++
T Consensus        19 ~~ki~ilG~~~~GKStLi~~l~~~   42 (190)
T cd00879          19 EAKILFLGLDNAGKTTLLHMLKDD   42 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            345599999999999999998864

Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.

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

Probab=94.35  E-value=0.067  Score=48.97  Aligned_cols=81  Identities=7%  Similarity=0.028  Sum_probs=46.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCC--CceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVK--HYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~--~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      -++|-++|++|.|||+|.+.+..+-.++  ..+....-+.++    ...++..=...        ...-..  .+-+++.
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEin----shsLFSKWFsE--------SgKlV~--kmF~kI~  242 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEIN----SHSLFSKWFSE--------SGKLVA--KMFQKIQ  242 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEe----hhHHHHHHHhh--------hhhHHH--HHHHHHH
Confidence            4789999999999999999999865443  233333333332    12222221111        111222  4556666


Q ss_pred             HHcCCCe--EEEEEeCCCC
Q 038944          257 EYLMTKR--YLNVIDDVWN  273 (334)
Q Consensus       257 ~~L~~kr--~LlVlDdvw~  273 (334)
                      +.+.++.  .++.+|.|.+
T Consensus       243 ELv~d~~~lVfvLIDEVES  261 (423)
T KOG0744|consen  243 ELVEDRGNLVFVLIDEVES  261 (423)
T ss_pred             HHHhCCCcEEEEEeHHHHH
Confidence            6665554  4556788853

>PF14516 AAA_35: AAA-like domain

Probab=94.35  E-value=0.36  Score=45.08  Aligned_cols=112  Identities=15%  Similarity=0.105  Sum_probs=68.0

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC----C-CCHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY----P-YDADQMLDI  229 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~-~~~~~il~~  229 (334)
                      .+-.|.|...-+++.+.|....   ..+.|.|+..+|||+|...+.+..+. ..+. .+++....    . .+....++.
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~~G---~~~~I~apRq~GKTSll~~l~~~l~~-~~~~-~v~id~~~~~~~~~~~~~~f~~~   84 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQPG---SYIRIKAPRQMGKTSLLLRLLERLQQ-QGYR-CVYIDLQQLGSAIFSDLEQFLRW   84 (331)
T ss_pred             CCcccCchHHHHHHHHHHhcCC---CEEEEECcccCCHHHHHHHHHHHHHH-CCCE-EEEEEeecCCCcccCCHHHHHHH
Confidence            3445678766777777776632   48999999999999999998874332 2343 34565543    1 256666666


Q ss_pred             HHHHhCCCCCcc----ccc-----hhhHHHHHHHHHHHc---CCCeEEEEEeCCCC
Q 038944          230 VIKFLMPSSRLS----EIM-----DKNYEMKKIILHEYL---MTKRYLNVIDDVWN  273 (334)
Q Consensus       230 il~~~~~~~~~~----~~~-----~~~~~~l~~~l~~~L---~~kr~LlVlDdvw~  273 (334)
                      ++..+.....-.    ..+     ...  .....+.+++   .+++.+|+||++..
T Consensus        85 ~~~~i~~~L~l~~~l~~~w~~~~~~~~--~~~~~~~~~ll~~~~~~lVL~iDEiD~  138 (331)
T PF14516_consen   85 FCEEISRQLKLDEKLDEYWDEEIGSKI--SCTEYFEEYLLKQIDKPLVLFIDEIDR  138 (331)
T ss_pred             HHHHHHHHcCCChhHHHHHHHhcCChh--hHHHHHHHHHHhcCCCCEEEEEechhh
Confidence            655554332210    111     111  3444455543   36899999999964

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=94.35  E-value=0.16  Score=52.40  Aligned_cols=97  Identities=19%  Similarity=0.017  Sum_probs=58.5

Q ss_pred             HHHHHHh-cCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---c
Q 038944          167 ELLDLLI-EGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---E  242 (334)
Q Consensus       167 ~l~~~L~-~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~  242 (334)
                      .|=.+|- .+=+.-+++-|+|.+|+|||||+..+.....  ..=..++|+.....++.     ..+++++......   .
T Consensus        47 ~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~--~~G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~  119 (790)
T PRK09519         47 ALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQ--AAGGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQ  119 (790)
T ss_pred             HHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHH--HcCCcEEEECCccchhH-----HHHHHcCCChhHeEEec
Confidence            3334444 2335567889999999999999966543211  11245689988777774     3667776643321   1


Q ss_pred             cchhhHHHHHHHHHHHcC-CCeEEEEEeCCC
Q 038944          243 IMDKNYEMKKIILHEYLM-TKRYLNVIDDVW  272 (334)
Q Consensus       243 ~~~~~~~~l~~~l~~~L~-~kr~LlVlDdvw  272 (334)
                      ....+  .....+...+. ++--|||+|-+-
T Consensus       120 ~~~~E--~~l~~i~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        120 PDTGE--QALEIADMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             CCCHH--HHHHHHHHHhhcCCCeEEEEcchh
Confidence            11222  45555555553 455689999974

>cd04176 Rap2 Rap2 subgroup

Probab=94.35  E-value=0.19  Score=41.05  Aligned_cols=22  Identities=32%  Similarity=0.366  Sum_probs=18.4

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||.....+.
T Consensus         3 ki~i~G~~~vGKTsl~~~~~~~   24 (163)
T cd04176           3 KVVVLGSGGVGKSALTVQFVSG   24 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999766654

The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=94.35  E-value=0.065  Score=49.54  Aligned_cols=24  Identities=8%  Similarity=0.109  Sum_probs=21.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +-..|.++|+.|+||||+++.+..
T Consensus       132 ~~~~I~l~G~~GsGKStvg~~La~  155 (309)
T PRK08154        132 RRRRIALIGLRGAGKSTLGRMLAA  155 (309)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999987

>cd04155 Arl3 Arl3 subfamily

Probab=94.34  E-value=0.033  Score=46.20  Aligned_cols=24  Identities=13%  Similarity=0.065  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|+|.+|+|||||.+.+.+.
T Consensus        14 ~~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          14 EPRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             ccEEEEEccCCCCHHHHHHHHhcC
Confidence            456999999999999999999874

Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.

>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=94.34  E-value=0.037  Score=46.68  Aligned_cols=24  Identities=17%  Similarity=0.134  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||++.+..-
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGL   49 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999863

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.

>PRK14532 adenylate kinase; Provisional

Probab=94.32  E-value=0.033  Score=47.30  Aligned_cols=20  Identities=10%  Similarity=0.152  Sum_probs=18.6

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |.++|++|+||||+|+.+..
T Consensus         3 i~~~G~pGsGKsT~a~~la~   22 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVE   22 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            77899999999999999987

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.32  E-value=0.055  Score=53.85  Aligned_cols=45  Identities=20%  Similarity=0.257  Sum_probs=36.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..++.+...+....  ..-+-|+|.+|+|||++|+.+++.
T Consensus        65 ~~iiGqs~~i~~l~~al~~~~--~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGPN--PQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999888775543  234578999999999999999863

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=94.31  E-value=0.038  Score=44.25  Aligned_cols=23  Identities=13%  Similarity=0.257  Sum_probs=20.4

Q ss_pred             EEEEEccCCccHHHHHHHHHccC
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      -|+++|.+|+|||||+..+....
T Consensus         3 ki~~~G~~~~GKstl~~~l~~~~   25 (161)
T TIGR00231         3 KIVIVGDPNVGKSTLLNRLLGNK   25 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999998754

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.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=94.30  E-value=0.038  Score=48.41  Aligned_cols=57  Identities=7%  Similarity=0.204  Sum_probs=34.8

Q ss_pred             HHHHHHHcCCCeEEEEEeCCCC---hhHHHHHHhhCC--CCCCCeEEEEecCChHHHhhccc
Q 038944          252 KIILHEYLMTKRYLNVIDDVWN---IEVCDIIREILP--DNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       252 ~~~l~~~L~~kr~LlVlDdvw~---~~~w~~l~~~l~--~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      .-.+-+.|-.+.-+|+-|+-=-   ...=+.+...|.  ....|.-||+.|.+..+|..|..
T Consensus       150 RVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~~~dr  211 (226)
T COG1136         150 RVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAKYADR  211 (226)
T ss_pred             HHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHhCCE
Confidence            3445566666777888888632   121222222222  12347789999999999997754

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=94.29  E-value=0.031  Score=47.25  Aligned_cols=21  Identities=19%  Similarity=0.234  Sum_probs=19.4

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +|+|.|+.|+||||+++.+.+
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.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=94.29  E-value=0.097  Score=47.67  Aligned_cols=25  Identities=20%  Similarity=0.206  Sum_probs=23.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..++.|+|.+|+|||||...+.+
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~  126 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLM  126 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHH
Confidence            5689999999999999999999988

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.28  E-value=0.087  Score=49.40  Aligned_cols=46  Identities=17%  Similarity=0.216  Sum_probs=31.4

Q ss_pred             CeeechhhHHHHHHHHhcC----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEG----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++.|..+.++-|.+.+.-.          -.+-+-+..+|++|.|||-||+.|+..
T Consensus       213 DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATE  268 (491)
T KOG0738|consen  213 DIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATE  268 (491)
T ss_pred             hhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHh
Confidence            3555555555555544321          123466788999999999999999983

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=94.28  E-value=0.21  Score=49.15  Aligned_cols=99  Identities=15%  Similarity=0.087  Sum_probs=56.9

Q ss_pred             eEEEEEccCCccHHHHH-HHHHccCCCCCceee-EEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh--hHH---
Q 038944          180 SVVVILDSIGLDKAAFA-GEAYNSSYVKHYFDC-HAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK--NYE---  249 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~--~~~---  249 (334)
                      .-++|.|-.|+|||||| ..+.+..    ..+. ++++.+.+.. .+.++...+...-..+....  ...+.  ...   
T Consensus       162 Qr~~I~g~~g~GKt~Lal~~i~~~~----~~dv~~V~~~IGer~rev~e~~~~~~~~~~l~~tvvV~atsd~p~~~r~~a  237 (501)
T TIGR00962       162 QRELIIGDRQTGKTAVAIDTIINQK----DSDVYCVYVAIGQKASTVAQVVRKLEEHGAMDYTIVVAATASDSASLQYLA  237 (501)
T ss_pred             CEEEeecCCCCCccHHHHHHHHhhc----CCCeEEEEEEccCChHHHHHHHHHHHhcCccceeEEEEecCCCCHHHHHHH
Confidence            36889999999999995 6777632    2345 4788887764 55666666665322111100  00000  000   


Q ss_pred             -HHHHHHHHHc--CCCeEEEEEeCCCC-hhHHHHHHh
Q 038944          250 -MKKIILHEYL--MTKRYLNVIDDVWN-IEVCDIIRE  282 (334)
Q Consensus       250 -~l~~~l~~~L--~~kr~LlVlDdvw~-~~~w~~l~~  282 (334)
                       -....+-+++  +|+..|||+||+-. ...+.++..
T Consensus       238 ~~~a~aiAEyfrd~G~~VLlv~Ddltr~A~A~REisl  274 (501)
T TIGR00962       238 PYTGCTMAEYFRDNGKHALIIYDDLSKHAVAYRQISL  274 (501)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEecchHHHHHHHHHHHH
Confidence             1122333343  68999999999954 356666553

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.

>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase

Probab=94.27  E-value=0.18  Score=49.95  Aligned_cols=93  Identities=9%  Similarity=-0.009  Sum_probs=55.7

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      ....+|.++|.+|+||||+|+.+....         -|+.++++.    + ..                  ++.......
T Consensus       367 ~~p~LVil~G~pGSGKST~A~~l~~~~---------g~~~vn~D~----l-g~------------------~~~~~~~a~  414 (526)
T TIGR01663       367 APCEMVIAVGFPGAGKSHFCKKFFQPA---------GYKHVNADT----L-GS------------------TQNCLTACE  414 (526)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHc---------CCeEECcHH----H-HH------------------HHHHHHHHH
Confidence            457899999999999999999888631         244554431    1 00                  113444556


Q ss_pred             HHcCCCeEEEEEeCCCCh----hHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          257 EYLMTKRYLNVIDDVWNI----EVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~----~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      +.|...+- +|+|+....    ..|-.+....   +-..+++.-+...++|..
T Consensus       415 ~~L~~G~s-VVIDaTn~~~~~R~~~i~lAk~~---gv~v~~i~~~~p~e~~~~  463 (526)
T TIGR01663       415 RALDQGKR-CAIDNTNPDAASRAKFLQCARAA---GIPCRCFLFNAPLAQAKH  463 (526)
T ss_pred             HHHhCCCc-EEEECCCCCHHHHHHHHHHHHHc---CCeEEEEEeCCCHHHHHH
Confidence            66644333 678998654    3555554442   224556665556666543

Note that the EC number for the kinase function is: 2.7.1.78

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=94.26  E-value=0.15  Score=49.25  Aligned_cols=24  Identities=13%  Similarity=0.127  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..++|+|..|+|||||.+.+.+.
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~  198 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARY  198 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCC
Confidence            357899999999999999999873

>cd04127 Rab27A Rab27a subfamily

Probab=94.26  E-value=0.37  Score=40.15  Aligned_cols=22  Identities=18%  Similarity=0.276  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.+.
T Consensus         6 ki~ivG~~~vGKTsli~~~~~~   27 (180)
T cd04127           6 KFLALGDSGVGKTSFLYQYTDN   27 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4679999999999999988764

The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=94.24  E-value=0.047  Score=44.82  Aligned_cols=22  Identities=27%  Similarity=0.321  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         2 ki~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999988764

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=94.23  E-value=0.19  Score=49.22  Aligned_cols=99  Identities=14%  Similarity=0.066  Sum_probs=56.1

Q ss_pred             eEEEEEccCCccHHHHH-HHHHccCCCCCceee-EEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc-----ccchhh-H--
Q 038944          180 SVVVILDSIGLDKAAFA-GEAYNSSYVKHYFDC-HAWVPGTYPY-DADQMLDIVIKFLMPSSRLS-----EIMDKN-Y--  248 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~il~~il~~~~~~~~~~-----~~~~~~-~--  248 (334)
                      .-++|.|-.|+|||||| ..+.+..    .-+. ++++-+.+.. .+.++...+...-..+....     +..... +  
T Consensus       163 QR~~I~g~~g~GKt~Lal~~i~~~~----~~dv~~V~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atsd~~~~~r~~a  238 (502)
T PRK13343        163 QRELIIGDRQTGKTAIAIDAIINQK----DSDVICVYVAIGQKASAVARVIETLREHGALEYTTVVVAEASDPPGLQYLA  238 (502)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHhhc----CCCEEEEEEEeccChHHHHHHHHHHHhcCccceeEEEEecccccHHHHHHH
Confidence            36889999999999995 6676631    2334 4777777765 45566666554322111100     010000 0  


Q ss_pred             HHHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHHh
Q 038944          249 EMKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIRE  282 (334)
Q Consensus       249 ~~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~~  282 (334)
                      --....+-+++  +||..|+|+||+-.. ..+.++..
T Consensus       239 p~~a~aiAEyfrd~G~~VLlv~DdlTr~A~A~REisL  275 (502)
T PRK13343        239 PFAGCAIAEYFRDQGQDALIVYDDLSKHAAAYRELSL  275 (502)
T ss_pred             HHHHHHHHHHHHhCCCCEEEEecchHHHHHHHHHHHH
Confidence            01112334444  689999999999543 56665553

>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=94.23  E-value=0.038  Score=48.77  Aligned_cols=24  Identities=13%  Similarity=0.130  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||++.+..-
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~   49 (235)
T cd03261          26 GEILAIIGPSGSGKSTLLRLIVGL   49 (235)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999863

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.

>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=94.23  E-value=0.035  Score=48.23  Aligned_cols=22  Identities=14%  Similarity=0.169  Sum_probs=18.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|.|-||+||||++..+..
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~   22 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSA   22 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHH
Confidence            4789999999999997776643

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=94.22  E-value=0.069  Score=49.88  Aligned_cols=44  Identities=20%  Similarity=0.218  Sum_probs=35.1

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+||.+..+..++-.+.++.  ..-+.|.|..|+|||||++.+..
T Consensus         4 ~~ivgq~~~~~al~~~~~~~~--~g~vli~G~~G~gKttl~r~~~~   47 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDPK--IGGVMVMGDRGTGKSTAVRALAA   47 (337)
T ss_pred             cccccHHHHHHHHHHHhcCCC--CCeEEEEcCCCCCHHHHHHHHHH
Confidence            468899988888776666543  44567999999999999999964

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=94.19  E-value=0.042  Score=45.04  Aligned_cols=21  Identities=14%  Similarity=0.289  Sum_probs=19.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||+..+.+.
T Consensus         3 i~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999988764

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>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=94.18  E-value=0.04  Score=48.11  Aligned_cols=24  Identities=13%  Similarity=0.075  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        30 G~~~~i~G~nGsGKSTLl~~l~Gl   53 (220)
T cd03293          30 GEFVALVGPSGCGKSTLLRIIAGL   53 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999864

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.

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=94.18  E-value=0.22  Score=48.19  Aligned_cols=23  Identities=17%  Similarity=0.281  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|+|..|+|||||.+.+...
T Consensus       164 q~~~I~G~sG~GKStLl~~I~~~  186 (440)
T TIGR01026       164 QRIGIFAGSGVGKSTLLGMIARN  186 (440)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999999874

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=94.17  E-value=0.041  Score=47.63  Aligned_cols=24  Identities=13%  Similarity=0.029  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|+|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          26 GEIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999864

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=94.17  E-value=0.037  Score=52.96  Aligned_cols=25  Identities=20%  Similarity=0.187  Sum_probs=22.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+.|+|+|..|+|||||++.+.+.
T Consensus       218 ~~~~IvI~G~~gsGKTTL~~~La~~  242 (399)
T PRK08099        218 FVRTVAILGGESSGKSTLVNKLANI  242 (399)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4788999999999999999999873

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=94.16  E-value=0.082  Score=45.59  Aligned_cols=42  Identities=19%  Similarity=0.239  Sum_probs=31.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..+..+.-.....    .-+.++|.+|+|||+||+.+-.
T Consensus         3 ~dI~GQe~aKrAL~iAAaG~----h~lLl~GppGtGKTmlA~~l~~   44 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAAGG----HHLLLIGPPGTGKTMLARRLPS   44 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHHCC------EEEES-CCCTHHHHHHHHHH
T ss_pred             hhhcCcHHHHHHHHHHHcCC----CCeEEECCCCCCHHHHHHHHHH
Confidence            46788888777776555542    4689999999999999999864

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>cd04113 Rab4 Rab4 subfamily

Probab=94.16  E-value=0.043  Score=44.96  Aligned_cols=21  Identities=19%  Similarity=0.301  Sum_probs=19.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 i~v~G~~~vGKTsli~~l~~~   23 (161)
T cd04113           3 FIIIGSSGTGKSCLLHRFVEN   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998764

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

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=94.16  E-value=0.04  Score=48.00  Aligned_cols=24  Identities=13%  Similarity=0.010  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (220)
T cd03263          28 GEIFGLLGHNGAGKTTTLKMLTGE   51 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999863

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.

>PRK14490 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional

Probab=94.16  E-value=0.069  Score=50.67  Aligned_cols=32  Identities=9%  Similarity=0.071  Sum_probs=25.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceee
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDC  211 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~  211 (334)
                      +.-+|+|+|..|+|||||+..+..  ..+..+.+
T Consensus         4 ~~~~i~i~G~~gsGKTTl~~~l~~--~l~~~~~V   35 (369)
T PRK14490          4 HPFEIAFCGYSGSGKTTLITALVR--RLSERFSV   35 (369)
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHH--HHhhCceE
Confidence            356999999999999999999998  44444433

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=94.16  E-value=0.037  Score=40.77  Aligned_cols=21  Identities=24%  Similarity=0.357  Sum_probs=18.6

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++.+.|.+|+||||++..+..
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~   21 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAA   21 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            478899999999999998876

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PF11868 DUF3388: Protein of unknown function (DUF3388); InterPro: IPR024514 This domain is found in a family of bacterial proteins that are functionally uncharacterised

Probab=94.14  E-value=0.24  Score=40.59  Aligned_cols=88  Identities=16%  Similarity=0.246  Sum_probs=53.3

Q ss_pred             hhHHHHHHHHhc--CCCCceEEEEEccCCccHHH--HHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCC
Q 038944          163 DRMEELLDLLIE--GPPQLSVVVILDSIGLDKAA--FAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSS  238 (334)
Q Consensus       163 ~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTt--La~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~  238 (334)
                      +++--|+++|.+  ...+-++|+|-||+-+|||.  +|..||.+.         -|.-+|...    +-+.+..++....
T Consensus        36 eeLGlLVDFmaEl~K~~Gh~lIGiRGmPRVGKTEsivAasVcAnK---------rW~f~SSTl----ikQTvRs~L~~dE  102 (192)
T PF11868_consen   36 EELGLLVDFMAELFKEEGHKLIGIRGMPRVGKTESIVAASVCANK---------RWLFLSSTL----IKQTVRSQLIEDE  102 (192)
T ss_pred             hHhccHHHHHHHHHHhcCceEEeecCCCccCchhHHHHHhhhcCc---------eEEEeeHHH----HHHHHHHHhhhcc
Confidence            445556666643  23456899999999999997  667777642         477777532    1222223333221


Q ss_pred             CccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC-----hhHHHHHHhhC
Q 038944          239 RLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN-----IEVCDIIREIL  284 (334)
Q Consensus       239 ~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~-----~~~w~~l~~~l  284 (334)
                      .                     +...+.++|.+-+     +..|.-+...+
T Consensus       103 ~---------------------~~~~ifIIDGivSt~r~~e~H~~Lvreim  132 (192)
T PF11868_consen  103 Y---------------------NENNIFIIDGIVSTRRSNERHWQLVREIM  132 (192)
T ss_pred             c---------------------CcCcEEEEeeeeeeccCCHHHHHHHHHHH
Confidence            1                     2346778888753     35787777654

Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=94.13  E-value=0.041  Score=47.70  Aligned_cols=23  Identities=13%  Similarity=0.108  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G   48 (213)
T cd03259          26 GEFLALLGPSGCGKTTLLRLIAG   48 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999976

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.

>cd04106 Rab23_lke Rab23-like subfamily

Probab=94.13  E-value=0.43  Score=38.83  Aligned_cols=21  Identities=10%  Similarity=0.218  Sum_probs=19.1

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.+.
T Consensus         3 v~~vG~~~~GKTsl~~~~~~~   23 (162)
T cd04106           3 VIVVGNGNVGKSSMIQRFVKG   23 (162)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999998864

Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G

>smart00175 RAB Rab subfamily of small GTPases

Probab=94.13  E-value=0.044  Score=44.83  Aligned_cols=21  Identities=10%  Similarity=0.390  Sum_probs=19.2

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||.+.+.+.
T Consensus         3 v~v~G~~~~GKTtli~~l~~~   23 (164)
T smart00175        3 IILIGDSGVGKSSLLSRFTDG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999865

Rab GTPases are implicated in vesicle trafficking.

>cd00876 Ras Ras family

Probab=94.12  E-value=0.052  Score=44.08  Aligned_cols=21  Identities=29%  Similarity=0.357  Sum_probs=18.9

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|+|++|+|||||...+.+.
T Consensus         2 i~i~G~~~~GKTsli~~l~~~   22 (160)
T cd00876           2 VVVLGAGGVGKSAITIQFVKG   22 (160)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            689999999999999988764

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

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=94.12  E-value=0.042  Score=47.69  Aligned_cols=24  Identities=13%  Similarity=0.181  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||++.+..-
T Consensus        28 G~~~~l~G~nGsGKSTLl~~i~Gl   51 (214)
T TIGR02673        28 GEFLFLTGPSGAGKTTLLKLLYGA   51 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999763

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.

>PRK00698 tmk thymidylate kinase; Validated

Probab=94.11  E-value=0.044  Score=47.00  Aligned_cols=23  Identities=13%  Similarity=-0.049  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|+|.|+.|+||||+++.+.+.
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~   26 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKEL   26 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999873

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=94.10  E-value=0.041  Score=48.73  Aligned_cols=23  Identities=17%  Similarity=0.150  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||++.+..
T Consensus        28 Ge~~~l~G~nGsGKSTLl~~l~G   50 (243)
T TIGR02315        28 GEFVAIIGPSGAGKSTLLRCINR   50 (243)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999975

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.

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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	334
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	4e-19
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 87.2 bits (216), Expect = 4e-19
 Identities = 40/265 (15%), Positives = 79/265 (29%), Gaps = 33/265 (12%)

Query: 56  LLQKMGHREIKNPDLTTVMDEI---NCFTYESEKVIDTFINSISE--------QKSQSSC 104
            L +      K+   + +MD +      T   E+ +                  K  +  
Sbjct: 8   CLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDS 67

Query: 105 SEDIFDALQGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSS-------KSRD 157
               ++AL        D+   +     + S    +       + + +         +   
Sbjct: 68  YVSFYNALLH--EGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVV 125

Query: 158 TVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSY-VKHYFDCH-AWV 215
            V     +  +   L +   +   V I    G  K+  A EA      ++  F     WV
Sbjct: 126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185

Query: 216 PGTYPYDAD--QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLNVIDDV 271
                  +     L  +   L      S+ +  N E  K  L   ++    R L ++DDV
Sbjct: 186 SVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDV 245

Query: 272 WNIEVCDIIREILPDNQNRSRVLIT 296
           W+  V       L    ++ ++L+T
Sbjct: 246 WDSWV-------LKAFDSQCQILLT 263

>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 = 73.1 bits (179), Expect = 2e-14
 Identities = 38/274 (13%), Positives = 83/274 (30%), Gaps = 34/274 (12%)

Query: 51  DISCLLLQKMGHREIKNPDLTTVMDEINCFTYESEKVIDTF----------INSISEQKS 100
           +I C  L     R I + +    +  +      +E   +             N +   + 
Sbjct: 4   EIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRR 63

Query: 101 QSSCSEDIFDAL---------QGLQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISS 151
           Q+S    + D             L+  I         L+ +        +  + +  + +
Sbjct: 64  QASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGN 123

Query: 152 SSKSRDTVGLDDRMEELLDLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYNSS--YVKHY 208
             K       +  ++ ++  L E        + +    G  K+  A +A + S   +   
Sbjct: 124 VPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGIN 183

Query: 209 FDCHAWVPGTYPYDAD------QMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTK 262
           +D   W+  +             +L ++       +  S     +  +K++I +  +   
Sbjct: 184 YDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRP 243

Query: 263 RYLNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
             L V DDV   E       I    + R R L+T
Sbjct: 244 NTLFVFDDVVQEET------IRWAQELRLRCLVT 271

>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 = 69.5 bits (169), Expect = 4e-13
 Identities = 56/311 (18%), Positives = 110/311 (35%), Gaps = 74/311 (23%)

Query: 35  HAETEIVTSWLSEFQ---DDISCLLLQKMGHREIKNPDLTTVMDEI-NCFTYESEKVIDT 90
           H + E       E Q    DI  +         + N D   V D   +  + E       
Sbjct: 6   HMDFET-----GEHQYQYKDILSVFEDAF----VDNFDCKDVQDMPKSILSKEE------ 50

Query: 91  FINSISEQKSQSSCSEDIFDALQGLQSRITDIKQRMQQLKHMDSE-IIDRIKT--FEAEA 147
            I+ I   K   S +  +F  L   Q  +  +++ ++++  ++ + ++  IKT   +   
Sbjct: 51  -IDHIIMSKDAVSGTLRLFWTLLSKQEEM--VQKFVEEVLRINYKFLMSPIKTEQRQPSM 107

Query: 148 GISSSSKSRDTVGLDD---------RMEELLDL---LIEGPPQLSVVV--ILDSIGLDKA 193
                 + RD +  D+         R++  L L   L+E  P  +V++  +L   G  K 
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL---GSGKT 164

Query: 194 AFAGEAYNSSYVKHYFDCHA-WVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYE--- 249
             A +   S  V+   D    W+        + +L+++        +L   +D N+    
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML-------QKLLYQIDPNWTSRS 217

Query: 250 --MKKIILH---------EYLMTKRYLN---VIDDVWNIEVCDIIREILPDNQNRSRVLI 295
                I L            L +K Y N   V+ +V N +  +       +     ++L+
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF-----NLS--CKILL 270

Query: 296 TLTEIKMFTFL 306
           T    ++  FL
Sbjct: 271 TTRFKQVTDFL 281

>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 = 50.6 bits (120), Expect = 4e-07
 Identities = 40/305 (13%), Positives = 86/305 (28%), Gaps = 76/305 (24%)

Query: 10  ERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLL-LQKMGHREIKNP 68
           ++L   +     +  D +      +H+    +   L   +   +CLL L       ++N 
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS-KPYENCLLVL-----LNVQNA 256

Query: 69  DLTTVMDEINC---FTYESEKVIDTFINSISEQKSQSSC--------SEDIF-------- 109
                 + ++C    T   ++V D    + +   S             + +         
Sbjct: 257 KAWNAFN-LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP 315

Query: 110 -----DALQG-------LQSRITDIKQRMQQLKHMDSEIIDRIKTFEAEAGISSSSKSRD 157
                + L         +   I D        KH++ + +  I        I SS    +
Sbjct: 316 QDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI--------IESSLNVLE 367

Query: 158 TVGLDDRMEELL----DLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHA 213
                   + L        I  P  L  ++  D I  D      + +  S V+       
Sbjct: 368 PAEYRKMFDRLSVFPPSAHI--PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ----- 420

Query: 214 WVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRY------LNV 267
               T        L++ +K           ++  Y + + I+  Y + K +         
Sbjct: 421 PKESTI-SIPSIYLELKVK-----------LENEYALHRSIVDHYNIPKTFDSDDLIPPY 468

Query: 268 IDDVW 272
           +D  +
Sbjct: 469 LDQYF 473

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	334
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.95
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.88
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.88
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.79
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.78
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.25
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.14
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.08
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.06
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.06
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.01
2fna_A	357	Conserved hypothetical protein; structural genomic	98.88
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.75
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.74
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.51
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.48
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.33
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.29
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.21
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.06
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.0
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.98
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.97
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.95
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.94
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.92
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.86
3co5_A	143	Putative two-component system transcriptional RES	97.82
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.82
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.81
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.81
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.81
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.78
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.74
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.74
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.73
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.69
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.67
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.63
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.62
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.58
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.57
3pvs_A	447	Replication-associated recombination protein A; ma	97.55
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.54
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.48
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.48
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.46
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.43
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.34
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.33
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.33
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.33
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.31
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.3
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.27
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.27
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.2
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.19
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.03
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.95
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.93
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.92
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.88
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.87
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.84
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.83
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.81
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.77
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	96.77
2qgz_A	308	Helicase loader, putative primosome component; str	96.75
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	96.72
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.71
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.71
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.67
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.66
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.65
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.63
3bos_A	242	Putative DNA replication factor; P-loop containing	96.59
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.54
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.45
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.43
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.42
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.42
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.42
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.39
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.37
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.33
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.33
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.3
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.28
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.24
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.24
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	96.22
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.2
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.15
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.13
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.13
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.11
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.09
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.08
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.04
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.0
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.99
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.98
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.98
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.96
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.93
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.91
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.9
3io5_A	333	Recombination and repair protein; storage dimer, i	95.89
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.88
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.86
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.86
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.84
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.84
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.84
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.84
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.84
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.82
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.81
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.8
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	95.8
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.79
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.79
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.77
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.77
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.76
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.75
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.74
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.74
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.69
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.69
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.68
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.67
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.67
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.66
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.66
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.66
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.62
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.62
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.6
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.59
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.59
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.57
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.56
1via_A	175	Shikimate kinase; structural genomics, transferase	95.56
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.55
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	95.55
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.55
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.54
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.53
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.52
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.52
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.51
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.5
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.49
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.48
3ice_A	422	Transcription termination factor RHO; transcriptio	95.48
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.48
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.47
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.46
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	95.45
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.44
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.43
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.43
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.42
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.42
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.42
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.4
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.39
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.39
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.36
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.35
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.35
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.34
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.34
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.34
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.33
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.32
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.29
2xxa_A	433	Signal recognition particle protein; protein trans	95.26
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.25
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.23
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.23
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.23
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.22
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.22
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.21
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.19
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.14
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.14
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.14
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.14
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	95.13
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.12
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.1
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.08
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.08
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.07
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.04
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.03
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.03
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.01
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.97
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.95
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.95
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	94.95
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.94
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	94.92
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.92
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.92
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.91
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.91
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	94.91
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.91
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.9
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	94.9
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.89
2og2_A	359	Putative signal recognition particle receptor; nuc	94.89
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.79
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.79
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.78
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	94.78
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.76
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.7
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.68
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.67
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.64
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	94.64
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.61
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.61
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.59
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.59
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.58
1g6h_A	257	High-affinity branched-chain amino acid transport	94.58
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.54
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.53
3l0o_A	427	Transcription termination factor RHO; helicase, RH	94.53
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.51
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.51
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.49
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.48
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.46
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.45
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.41
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.39
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.37
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.37
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.35
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.33
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.3
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.29
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.29
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.29
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.28
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.26
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	94.25
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.24
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.24
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	94.24
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.23
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.22
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.21
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.2
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.19
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.19
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	94.19
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	94.14
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.13
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	94.11
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.11
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.1
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.08
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.06
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.06
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	94.05
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	94.04
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.04
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.04
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.99
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	93.97
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.95
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.93
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	93.93
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	93.88
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.88
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.88
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.86
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.84
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.82
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	93.82
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	93.8
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.79
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.73
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.72
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	93.71
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	93.7
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.67
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	93.66
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.65
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	93.62
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.61
3end_A	307	Light-independent protochlorophyllide reductase ir	93.61
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	93.59
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.56
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.56
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.55
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.53
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.53
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.52
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	93.5
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	93.49
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.47
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.47
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.45
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.45
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.41
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.39
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.39
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.38
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.35
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.32
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.31
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.31
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.29
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.29
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.28
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.25
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.23
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	93.17
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.17
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.16
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.16
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.12
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.12
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.09
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	93.09
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.08
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.06
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.05
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.05
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.01
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	93.0
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.0
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	92.98
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	92.96
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	92.95
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	92.94
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.94
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	92.93
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	92.93
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	92.92
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	92.92
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	92.92
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.92
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	92.91
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	92.89
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.89
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	92.89
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	92.89
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	92.85
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	92.85
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.85
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	92.82
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	92.79
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	92.78
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	92.78
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.77
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.73
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.72
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	92.71
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	92.71
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.7
3llu_A	196	RAS-related GTP-binding protein C; structural geno	92.69
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	92.68
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	92.64
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.61
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	92.6
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.6
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	92.59
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	92.58
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	92.58
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	92.54
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.53
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.52
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.49
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	92.49
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	92.45
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.44
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	92.44
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	92.42
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	92.42
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.41
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.34
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	92.33
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.33
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	92.31
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	92.31
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	92.3
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	92.29
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.23
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	92.21
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	92.19
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	92.18
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	92.18
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	92.17
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	92.16
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	92.16
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	92.15
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	92.14
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.13
2fh5_B	214	SR-beta, signal recognition particle receptor beta	92.11
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	92.1
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.09
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.09
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	92.09
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	92.08
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.08
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.07
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	92.07
1p9r_A	418	General secretion pathway protein E; bacterial typ	92.05
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.03
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	92.0
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	91.99
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	91.99
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	91.98
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	91.97
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	91.95
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	91.93
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	91.92
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	91.91
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	91.89
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	91.89
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	91.88
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	91.87
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	91.85
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.8
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	91.8
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	91.78
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	91.76
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.76
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	91.72
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	91.72
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	91.69
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	91.68
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	91.67
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	91.66
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.63
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	91.6
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	91.58
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	91.56
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.51
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	91.46
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	91.44
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	91.42
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	91.39
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	91.34
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	91.34
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	91.32
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	91.29
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	91.28
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	91.25
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	91.24
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	91.21
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	91.18
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	91.14
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	91.1
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	91.09
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	91.08
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	91.06
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	91.06
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	91.05
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	91.02
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	91.02
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	91.01
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	91.0
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	90.99
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	90.98
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	90.94
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	90.94
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	90.92
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	90.92
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	90.9
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	90.87
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	90.85
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	90.79
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	90.76
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	90.74
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	90.66
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	90.64
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	90.63
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	90.54
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	90.48
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	90.44
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	90.43
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	90.42
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	90.39
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.39
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	90.37
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	90.34

>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=5.1e-28  Score=238.87  Aligned_cols=167  Identities=14%  Similarity=0.159  Sum_probs=137.8

Q ss_pred             eechhhHHHHHHHHhcC-CCCceEEEEEccCCccHHHHHHHHHc--cCCCCCceeeEEEEEcCCCC--CHHHHHHHHHHH
Q 038944          159 VGLDDRMEELLDLLIEG-PPQLSVVVILDSIGLDKAAFAGEAYN--SSYVKHYFDCHAWVPGTYPY--DADQMLDIVIKF  233 (334)
Q Consensus       159 vGr~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~--~~~~~~~F~~~~wv~vs~~~--~~~~il~~il~~  233 (334)
                      |||+.++++|.++|..+ +...++|+|+||||+||||||+.+|+  +.+++.+|++++||++++.+  ++..++..|+.+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            69999999999999865 45689999999999999999999998  67899999999999999985  899999999999


Q ss_pred             hCCCCC--cc---ccchhhHHHHHHHHHHHcCCC-eEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          234 LMPSSR--LS---EIMDKNYEMKKIILHEYLMTK-RYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       234 ~~~~~~--~~---~~~~~~~~~l~~~l~~~L~~k-r~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      ++....  ..   +..+..  .+...+++.|++| ||||||||||+.+.+ .+..     .+||+||||||+..||..++
T Consensus       211 l~~~~~~~~~~~~~~~~~~--~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~~  282 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSV--VLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVEISNAAS  282 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHH--HHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGGGGGGCC
T ss_pred             HhcCcccccccccccccHH--HHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHHHHHHcC
Confidence            987532  10   122334  7889999999996 999999999998755 2211     16999999999999999887


Q ss_pred             c-cCcccccccCC---------------CChhHHHHHHHhcc
Q 038944          308 E-TLFSLLICVSR---------------TPRDIQQAVISVVD  333 (334)
Q Consensus       308 ~-~~~~~l~~l~~---------------~~~~l~~i~~~Iv~  333 (334)
                      . ...+.|.+|+.               .++++.+++++|++
T Consensus       283 ~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~  324 (549)
T 2a5y_B          283 QTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIE  324 (549)
T ss_dssp             SCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHH
T ss_pred             CCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHH
Confidence            3 35688888872               33789999999885

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.88  E-value=1.2e-22  Score=207.57  Aligned_cols=151  Identities=17%  Similarity=0.123  Sum_probs=119.3

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceee-EEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDC-HAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      ..|||+.++++|.++|...+ ..++++|+||||+||||||+.+|++.+++.+|++ ++||++++.++...++..|++.+.
T Consensus       129 ~~VGRe~eLeeL~elL~~~d-~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~  207 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLELR-PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY  207 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHCC-SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhccC-CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHh
Confidence            35999999999999998643 3789999999999999999999998788899997 899999999999898888877532


Q ss_pred             C---CCCcc-c---cchhhHHHHHHHHHHHc---CCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          236 P---SSRLS-E---IMDKNYEMKKIILHEYL---MTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       236 ~---~~~~~-~---~~~~~~~~l~~~l~~~L---~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      .   ..... +   ......+.+...+++.|   .+|||||||||||+.+.|+.+.       .||+||||||+..++..
T Consensus       208 ~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va~~  280 (1221)
T 1vt4_I          208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDF  280 (1221)
T ss_dssp             HHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHHHH
T ss_pred             hcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHHHh
Confidence            2   11000 0   01111226677777766   7899999999999998888752       68999999999999986


Q ss_pred             ccccCccccc
Q 038944          306 LLETLFSLLI  315 (334)
Q Consensus       306 ~~~~~~~~l~  315 (334)
                      +.....+.+.
T Consensus       281 l~g~~vy~Le  290 (1221)
T 1vt4_I          281 LSAATTTHIS  290 (1221)
T ss_dssp             HHHHSSCEEE
T ss_pred             cCCCeEEEec
Confidence            6655556666

>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=99.88  E-value=7.5e-23  Score=218.53  Aligned_cols=159  Identities=19%  Similarity=0.164  Sum_probs=122.4

Q ss_pred             CCCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCC-CCCcee-eEEEEEcCCCCC--HHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSY-VKHYFD-CHAWVPGTYPYD--ADQMLD  228 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~-~~~~F~-~~~wv~vs~~~~--~~~il~  228 (334)
                      ..+..+|||++++++|.++|...+...++++|+||||+||||||+.+|++.+ ...+|. ...||++++.++  ....+.
T Consensus       121 ~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  200 (1249)
T 3sfz_A          121 QRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQ  200 (1249)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHH
T ss_pred             CCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHH
Confidence            3456799999999999999987767789999999999999999999999643 245564 567999998654  445577


Q ss_pred             HHHHHhCCCCCccccchhhHHHHHHHHHHHcCCC--eEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh-
Q 038944          229 IVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTK--RYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF-  305 (334)
Q Consensus       229 ~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~k--r~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~-  305 (334)
                      .++..+..............+.+...++..|.++  ||||||||||+...|..+       .+||+||||||+..|+.. 
T Consensus       201 ~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~~~~  273 (1249)
T 3sfz_A          201 NLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVTDSV  273 (1249)
T ss_dssp             HHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTTTTC
T ss_pred             HHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHHHhh
Confidence            7888887654321111122338899999999877  999999999998776653       468999999999999955 


Q ss_pred             ccccCcccccc-cC
Q 038944          306 LLETLFSLLIC-VS  318 (334)
Q Consensus       306 ~~~~~~~~l~~-l~  318 (334)
                      ++....+.+.. |+
T Consensus       274 ~~~~~~~~~~~~l~  287 (1249)
T 3sfz_A          274 MGPKHVVPVESGLG  287 (1249)
T ss_dssp             CSCBCCEECCSSCC
T ss_pred             cCCceEEEecCCCC
Confidence            45556666664 65

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.79  E-value=2.4e-19  Score=139.78  Aligned_cols=83  Identities=25%  Similarity=0.309  Sum_probs=77.2

Q ss_pred             chHHHHHHHHHHHHhhhhhccccccchhHhhhHHhHHHhhhccccchHHHHHHHHHHhccc--ccCCchHHHHHHHHHHH
Q 038944            3 ISFRLFSERLRRVLAGEEVTLPDAAKLPIQNLHAETEIVTSWLSEFQDDISCLLLQKMGHR--EIKNPDLTTVMDEINCF   80 (334)
Q Consensus         3 ~~~~~~~~kl~~~l~~~e~~l~~~~~~~i~~L~~~l~~l~~~~~~~~~~~~~~~l~~a~~~--~~~~~~v~~Wl~~lr~~   80 (334)
                      ++++++++||++++ .+|+.++.|+++++++|+++|+            +|++||.+++.+  +..++.++.|+++||++
T Consensus         1 a~v~~ll~KL~~ll-~~E~~l~~gv~~~i~~Lk~eL~------------~m~a~L~da~~~~~~~~d~~vk~W~~~vrdl   67 (115)
T 3qfl_A            1 AAISNLIPKLGELL-TEEFKLHKGVKKNIEDLGKELE------------SMNAALIKIGEVPREQLDSQDKLWADEVREL   67 (115)
T ss_dssp             CTTCSHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHTTSCGGGCCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHH-HHHHHHHhchHHHHHHHHHHHH------------HHHHHHHHHHHhccccCCHHHHHHHHHHHHH
Confidence            57889999999999 6899999999999999999999            999999999987  56899999999999999


Q ss_pred             HHhHHHHHHHHHhhhhcc
Q 038944           81 TYESEKVIDTFINSISEQ   98 (334)
Q Consensus        81 ayd~ED~lD~~~~~~~~~   98 (334)
                      |||+||+||+|.++....
T Consensus        68 aYD~ED~iD~f~~~~~~~   85 (115)
T 3qfl_A           68 SYVIEDVVDKFLVQVDGI   85 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhccc
Confidence            999999999999988653

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.78  E-value=2.8e-19  Score=177.72  Aligned_cols=144  Identities=18%  Similarity=0.195  Sum_probs=108.1

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCC-CCcee-eEEEEEcCCCCCHHHHHHHH-
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYV-KHYFD-CHAWVPGTYPYDADQMLDIV-  230 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F~-~~~wv~vs~~~~~~~il~~i-  230 (334)
                      .+..+|||+.+++.|.++|.......++++|+||||+||||||..+|++..+ ..+|+ .++|++++.. +...++..+ 
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~  200 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQ  200 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHH
T ss_pred             CCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHH
Confidence            3556999999999999999865556899999999999999999999986544 67894 7999999876 344444444 


Q ss_pred             --HHHhCCCCC--ccccchhhHHHHHHHHHHHcCC--CeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHh
Q 038944          231 --IKFLMPSSR--LSEIMDKNYEMKKIILHEYLMT--KRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFT  304 (334)
Q Consensus       231 --l~~~~~~~~--~~~~~~~~~~~l~~~l~~~L~~--kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~  304 (334)
                        +..++....  .....+..  .+...+...+.+  +++||||||+|+...+..    +   ..||+||||||+..++.
T Consensus       201 ~l~~~l~~~~~~~~~~~~~~~--~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~----l---~~~~~ilvTsR~~~~~~  271 (591)
T 1z6t_A          201 NLCTRLDQDESFSQRLPLNIE--EAKDRLRILMLRKHPRSLLILDDVWDSWVLKA----F---DSQCQILLTTRDKSVTD  271 (591)
T ss_dssp             HHHHHHCSSCCSCSSCCCSHH--HHHHHHHHHHHHTCTTCEEEEEEECCHHHHHT----T---CSSCEEEEEESCGGGGT
T ss_pred             HHHHHhccccccccCCCCCHH--HHHHHHHHHHccCCCCeEEEEeCCCCHHHHHH----h---cCCCeEEEECCCcHHHH
Confidence              445542111  00122333  777788888865  789999999999765542    3   45899999999999887


Q ss_pred             hcc
Q 038944          305 FLL  307 (334)
Q Consensus       305 ~~~  307 (334)
                      .+.
T Consensus       272 ~~~  274 (591)
T 1z6t_A          272 SVM  274 (591)
T ss_dssp             TCC
T ss_pred             hcC
Confidence            654

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.25  E-value=1.3e-11  Score=116.58  Aligned_cols=145  Identities=13%  Similarity=0.147  Sum_probs=96.7

Q ss_pred             CCCCeeechhhHHHHHHHH-hc---C-CCCceEEEE--EccCCccHHHHHHHHHccCCCCCc-----ee-eEEEEEcCCC
Q 038944          154 KSRDTVGLDDRMEELLDLL-IE---G-PPQLSVVVI--LDSIGLDKAAFAGEAYNSSYVKHY-----FD-CHAWVPGTYP  220 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L-~~---~-~~~~~vi~I--vG~gGvGKTtLa~~v~~~~~~~~~-----F~-~~~wv~vs~~  220 (334)
                      .+..++||+.+++.|.++| ..   + ......+.|  +|++|+|||||++.+++.  ....     |. ..+|+.....
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~   97 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVNAFNA   97 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEEGGGC
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHH--HHHHHhccCCceeEEEEECCCC
Confidence            3467999999999999998 42   2 023345555  999999999999999984  2221     22 3578887777


Q ss_pred             CCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcC--CCeEEEEEeCCCCh--------hHHHHHHhhC---CCC
Q 038944          221 YDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLNVIDDVWNI--------EVCDIIREIL---PDN  287 (334)
Q Consensus       221 ~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~--~kr~LlVlDdvw~~--------~~w~~l~~~l---~~~  287 (334)
                      .+...++..++.+++...+. ...+..  .+...+.+.+.  +++++|||||+|..        +.+..+...+   +..
T Consensus        98 ~~~~~~~~~l~~~l~~~~~~-~~~~~~--~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~  174 (412)
T 1w5s_A           98 PNLYTILSLIVRQTGYPIQV-RGAPAL--DILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSR  174 (412)
T ss_dssp             CSHHHHHHHHHHHHTCCCCC-TTCCHH--HHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCT
T ss_pred             CCHHHHHHHHHHHhCCCCCC-CCCCHH--HHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccC
Confidence            88999999999999765321 112223  55566666664  78999999999763        3344333332   211


Q ss_pred             C--CCeEEEEecCChHHH
Q 038944          288 Q--NRSRVLITLTEIKMF  303 (334)
Q Consensus       288 ~--~gsrIivTTr~~~va  303 (334)
                      .  ....||+||+..++.
T Consensus       175 ~~~~~v~lI~~~~~~~~~  192 (412)
T 1w5s_A          175 DGVNRIGFLLVASDVRAL  192 (412)
T ss_dssp             TSCCBEEEEEEEEETHHH
T ss_pred             CCCceEEEEEEeccccHH
Confidence            2  344588888766644

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.14  E-value=7.4e-11  Score=110.35  Aligned_cols=143  Identities=12%  Similarity=-0.023  Sum_probs=97.4

Q ss_pred             CCCeeechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHccCCCCCc--------eeeEEEEEcCCCC-CH
Q 038944          155 SRDTVGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY--------FDCHAWVPGTYPY-DA  223 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~--------F~~~~wv~vs~~~-~~  223 (334)
                      +..++||+.+++.+.++|..  .....+.+.|+|++|+||||||+.+++.  ....        ....+|++.+... +.
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~   96 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNE--IEEVKKEDEEYKDVKQAYVNCREVGGTP   96 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHH--HHHHHHHSSSSTTCEEEEEEHHHHCSCH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHhhhhcCCCCceEEEEECccCCCCH
Confidence            47799999999999988865  2334568999999999999999999983  2111        2345777777666 88


Q ss_pred             HHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCChhH--HHHH-HhhCCCCCCCeEEEEecCCh
Q 038944          224 DQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEV--CDII-REILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       224 ~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~--w~~l-~~~l~~~~~gsrIivTTr~~  300 (334)
                      ..++..++.++.+...........  .+...+.+.+..++.+|||||++....  +..+ ...+.....+..||+||+..
T Consensus        97 ~~~~~~l~~~l~~~~~~~~~~~~~--~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~  174 (384)
T 2qby_B           97 QAVLSSLAGKLTGFSVPKHGINLG--EYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDI  174 (384)
T ss_dssp             HHHHHHHHHHHHCSCCCSSSSCTH--HHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSST
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCHH--HHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCC
Confidence            899999999884322110112223  667778888877777999999975421  1122 22222111678899998875


Q ss_pred             H
Q 038944          301 K  301 (334)
Q Consensus       301 ~  301 (334)
                      .
T Consensus       175 ~  175 (384)
T 2qby_B          175 N  175 (384)
T ss_dssp             T
T ss_pred             c
Confidence            3

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.08  E-value=1.1e-09  Score=102.47  Aligned_cols=149  Identities=13%  Similarity=0.085  Sum_probs=102.8

Q ss_pred             CCCCeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDI  229 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~  229 (334)
                      .+..++||+.+++.+..++..    ..+..+.+.|+|++|+|||||++.+.+...-... ...+|+..+...+...++..
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~   93 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGE   93 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHH
Confidence            346799999999999999875    2223458999999999999999999984221111 24567777788888999999


Q ss_pred             HHHHhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCC--hhHHHHHHhhCCCCC----CCeEEEEecCChH
Q 038944          230 VIKFLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWN--IEVCDIIREILPDNQ----NRSRVLITLTEIK  301 (334)
Q Consensus       230 il~~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~----~gsrIivTTr~~~  301 (334)
                      ++..++..... ......  .+...+...+  .+++.+|+||+++.  ......+...+....    .+..||+||+...
T Consensus        94 l~~~l~~~~~~-~~~~~~--~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~  170 (389)
T 1fnn_A           94 IARSLNIPFPR-RGLSRD--EFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDA  170 (389)
T ss_dssp             HHHHTTCCCCS-SCCCHH--HHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTH
T ss_pred             HHHHhCccCCC-CCCCHH--HHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCch
Confidence            99998754321 112222  5555555555  36789999999965  456666666654311    4677888888775


Q ss_pred             HHhhc
Q 038944          302 MFTFL  306 (334)
Q Consensus       302 va~~~  306 (334)
                      ....+
T Consensus       171 ~~~~l  175 (389)
T 1fnn_A          171 VLNNL  175 (389)
T ss_dssp             HHHTS
T ss_pred             HHHHh
Confidence            54433

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.06  E-value=1.1e-10  Score=108.88  Aligned_cols=146  Identities=11%  Similarity=0.104  Sum_probs=96.2

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC--CCCceEEEEEccCCccHHHHHHHHHccCCCCCce---eeEEEEEcCCCCCHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG--PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF---DCHAWVPGTYPYDADQML  227 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~~~~~~il  227 (334)
                      ..+..++||+.+++.+.+++...  ......+.|+|++|+|||||++.+++.  ....|   ...+|+..+...+...++
T Consensus        17 ~~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~   94 (386)
T 2qby_A           17 YIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTPYRVL   94 (386)
T ss_dssp             CCCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSHHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCHHHHH
Confidence            34567999999999999998752  344568899999999999999999983  32222   245677776666788888


Q ss_pred             HHHHHHhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCCh------hHHHHHHhhCCC-CCCCeEEEEecC
Q 038944          228 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNI------EVCDIIREILPD-NQNRSRVLITLT  298 (334)
Q Consensus       228 ~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~------~~w~~l~~~l~~-~~~gsrIivTTr  298 (334)
                      ..++.+++..... ...+..  .+...+.+.+  .+++.+||||+++..      +.+..+...+.. ...+..+|+||+
T Consensus        95 ~~i~~~l~~~~~~-~~~~~~--~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~  171 (386)
T 2qby_A           95 ADLLESLDVKVPF-TGLSIA--ELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITN  171 (386)
T ss_dssp             HHHTTTTSCCCCS-SSCCHH--HHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEES
T ss_pred             HHHHHHhCCCCCC-CCCCHH--HHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEEC
Confidence            8888887654321 111222  4555555555  356899999999652      344444433311 233566788888


Q ss_pred             ChHHH
Q 038944          299 EIKMF  303 (334)
Q Consensus       299 ~~~va  303 (334)
                      .....
T Consensus       172 ~~~~~  176 (386)
T 2qby_A          172 DVKFV  176 (386)
T ss_dssp             CGGGG
T ss_pred             CCChH
Confidence            76543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.06  E-value=5.8e-10  Score=104.01  Aligned_cols=142  Identities=11%  Similarity=0.046  Sum_probs=96.1

Q ss_pred             CCCCeeechhhHHHHHHHHhcC--CCCceEEEEEccCCccHHHHHHHHHccCCCCCc------eeeEEEEEcCCCCCHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIEG--PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY------FDCHAWVPGTYPYDADQ  225 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~------F~~~~wv~vs~~~~~~~  225 (334)
                      .+..++||+.+++.+..+|..-  ......+.|+|++|+||||||+.+++.  ....      -...+|++.+...+...
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~   94 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARHRETPYR   94 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTTSCSHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCcCCCHHH
Confidence            3467999999999999998542  344568899999999999999999983  2111      12457788888889999


Q ss_pred             HHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCChh----HHHHHH---hhCCCC--CCCeEEE
Q 038944          226 MLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNIE----VCDIIR---EILPDN--QNRSRVL  294 (334)
Q Consensus       226 il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~~----~w~~l~---~~l~~~--~~gsrIi  294 (334)
                      ++..++.+++..... ......  .+...+.+.+  .+++.+|+|||+....    ..+.+.   ......  ..+..+|
T Consensus        95 ~~~~l~~~l~~~~~~-~~~~~~--~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I  171 (387)
T 2v1u_A           95 VASAIAEAVGVRVPF-TGLSVG--EVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLV  171 (387)
T ss_dssp             HHHHHHHHHSCCCCS-SCCCHH--HHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEE
T ss_pred             HHHHHHHHhCCCCCC-CCCCHH--HHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEE
Confidence            999999999764332 122223  5566666666  4568999999997642    222222   222111  3456777


Q ss_pred             EecCCh
Q 038944          295 ITLTEI  300 (334)
Q Consensus       295 vTTr~~  300 (334)
                      .||+..
T Consensus       172 ~~t~~~  177 (387)
T 2v1u_A          172 GITNSL  177 (387)
T ss_dssp             EECSCS
T ss_pred             EEECCC
Confidence            787765

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.01  E-value=6.3e-10  Score=102.32  Aligned_cols=137  Identities=9%  Similarity=0.087  Sum_probs=89.6

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC------CCHHHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP------YDADQML  227 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~------~~~~~il  227 (334)
                      .+..++||+.+.+.|.+++..+    +++.|+|++|+|||||++.+.+..  .     .+|+.+...      .+...++
T Consensus        10 ~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~~--~-----~~~~~~~~~~~~~~~~~~~~~~   78 (350)
T 2qen_A           10 RREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNER--P-----GILIDCRELYAERGHITREELI   78 (350)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHS--S-----EEEEEHHHHHHTTTCBCHHHHH
T ss_pred             ChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHHc--C-----cEEEEeecccccccCCCHHHHH
Confidence            4567899999999999998763    689999999999999999999843  1     567766433      2566777


Q ss_pred             HHHHHHhCCC--------------CCccccchhhHHHHHHHHHHHcCC-CeEEEEEeCCCChh---------HHHHHHhh
Q 038944          228 DIVIKFLMPS--------------SRLSEIMDKNYEMKKIILHEYLMT-KRYLNVIDDVWNIE---------VCDIIREI  283 (334)
Q Consensus       228 ~~il~~~~~~--------------~~~~~~~~~~~~~l~~~l~~~L~~-kr~LlVlDdvw~~~---------~w~~l~~~  283 (334)
                      ..+...+...              ..........++.+...+.+.... ++++|||||++...         .+..+...
T Consensus        79 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~  158 (350)
T 2qen_A           79 KELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYA  158 (350)
T ss_dssp             HHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHH
Confidence            7777665430              000000011122566666665542 38999999997632         23434333


Q ss_pred             CCCCCCCeEEEEecCChHH
Q 038944          284 LPDNQNRSRVLITLTEIKM  302 (334)
Q Consensus       284 l~~~~~gsrIivTTr~~~v  302 (334)
                      +.. ..+.++|+|++...+
T Consensus       159 ~~~-~~~~~~il~g~~~~~  176 (350)
T 2qen_A          159 YDS-LPNLKIILTGSEVGL  176 (350)
T ss_dssp             HHH-CTTEEEEEEESSHHH
T ss_pred             HHh-cCCeEEEEECCcHHH
Confidence            222 247889999988654

>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=98.88  E-value=3e-09  Score=97.87  Aligned_cols=136  Identities=11%  Similarity=0.069  Sum_probs=83.6

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCC-----CCHHHHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYP-----YDADQMLD  228 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~il~  228 (334)
                      .+..++||+.+.+.|.+ +..     +++.|+|++|+|||||++.+.+..  ..   ..+|+.....     .+...++.
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~~--~~---~~~~~~~~~~~~~~~~~~~~~~~   79 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINEL--NL---PYIYLDLRKFEERNYISYKDFLL   79 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHHH--TC---CEEEEEGGGGTTCSCCCHHHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHhc--CC---CEEEEEchhhccccCCCHHHHHH
Confidence            45578999999999999 644     599999999999999999999842  22   2478876642     34455555


Q ss_pred             HHHHHhC-------------CCC-----Ccc-cc------chhhHHHHHHHHHHHcCCCeEEEEEeCCCCh------hHH
Q 038944          229 IVIKFLM-------------PSS-----RLS-EI------MDKNYEMKKIILHEYLMTKRYLNVIDDVWNI------EVC  277 (334)
Q Consensus       229 ~il~~~~-------------~~~-----~~~-~~------~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~------~~w  277 (334)
                      .+.+.+.             ...     +.. ..      ....++.+...+.+.-. ++++|||||++..      +.+
T Consensus        80 ~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~~~~~  158 (357)
T 2fna_A           80 ELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRGVNLL  158 (357)
T ss_dssp             HHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTTCCCH
T ss_pred             HHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCchhHH
Confidence            5544331             000     000 00      01112255556655433 4899999999642      223


Q ss_pred             HHHHhhCCCCCCCeEEEEecCChHH
Q 038944          278 DIIREILPDNQNRSRVLITLTEIKM  302 (334)
Q Consensus       278 ~~l~~~l~~~~~gsrIivTTr~~~v  302 (334)
                      ..+.... +...+.++|+|++....
T Consensus       159 ~~l~~~~-~~~~~~~~i~~g~~~~~  182 (357)
T 2fna_A          159 PALAYAY-DNLKRIKFIMSGSEMGL  182 (357)
T ss_dssp             HHHHHHH-HHCTTEEEEEEESSHHH
T ss_pred             HHHHHHH-HcCCCeEEEEEcCchHH
Confidence            3333222 22246889999998764

>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=98.75  E-value=1.3e-08  Score=86.93  Aligned_cols=118  Identities=11%  Similarity=0.145  Sum_probs=75.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      .+++|++..++.+.+++....  ...+.|+|++|+|||+||+.+++... ...+. ....+..+...+...+        
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~--------   85 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDVV--------   85 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSTTSSHHHHHHHHHHHHH-GGGGGGGEEEEETTCTTCHHHH--------
T ss_pred             HHHcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHHHh-ccccccceEEeccccccChHHH--------
Confidence            468999999999999998754  22389999999999999999987311 11111 1233333333322221        


Q ss_pred             CCCCCccccchhhHHHHHHHHHHHc------CCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          235 MPSSRLSEIMDKNYEMKKIILHEYL------MTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~L------~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                                       ...+....      .+++.+|+|||++..  ..++.+...+.....+.++|+||+...
T Consensus        86 -----------------~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~  143 (226)
T 2chg_A           86 -----------------RHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (226)
T ss_dssp             -----------------HHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             -----------------HHHHHHHhcccCCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence                             11222221      357899999999753  455666655544455788898887653

>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=98.74  E-value=3.7e-08  Score=85.03  Aligned_cols=136  Identities=14%  Similarity=0.059  Sum_probs=76.6

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|++..++.+..++..+. ....+.|+|++|+||||||+.+++.......+.      ......... ...+.....
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~------~~~~~~~~~-~~~~~~~~~   94 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGIT------ATPCGVCDN-CREIEQGRF   94 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSC------SSCCSCSHH-HHHHHTTCC
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCcccHH-HHHHhccCC
Confidence            458999999999999997653 234789999999999999999987422111110      000000000 011110000


Q ss_pred             CCCCcc--ccchhhHHHHHHHHHHHc-----CCCeEEEEEeCCC--ChhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          236 PSSRLS--EIMDKNYEMKKIILHEYL-----MTKRYLNVIDDVW--NIEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       236 ~~~~~~--~~~~~~~~~l~~~l~~~L-----~~kr~LlVlDdvw--~~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      ......  ......  .....+.+.+     .+++.+|||||++  +...++.+...+.....+..+|+||+...
T Consensus        95 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~  167 (250)
T 1njg_A           95 VDLIEIDAASRTKV--EDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ  167 (250)
T ss_dssp             SSEEEEETTCGGGH--HHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGG
T ss_pred             cceEEecCcccccH--HHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChH
Confidence            000000  000111  1122233332     3567999999995  45677778777655556788888887653

>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=98.51  E-value=8.6e-08  Score=87.02  Aligned_cols=120  Identities=13%  Similarity=0.125  Sum_probs=73.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      .+++|++..++.+.+++..+..  +.+.++|++|+||||+|+.+.+... ...+. ..+++..+...+... +++++   
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~~~-i~~~~---   93 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDGNM--PHMIISGMPGIGKTTSVHCLAHELL-GRSYADGVLELNASDDRGIDV-VRNQI---   93 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCCC--CCEEEECSTTSSHHHHHHHHHHHHH-GGGHHHHEEEECTTSCCSHHH-HHTHH---
T ss_pred             HHHHCCHHHHHHHHHHHHcCCC--CeEEEECcCCCCHHHHHHHHHHHhc-CCcccCCEEEecCccccChHH-HHHHH---
Confidence            5689999999999999987542  2388999999999999999987311 11111 233443333222111 11111   


Q ss_pred             CCCCCccccchhhHHHHHHHHHH---Hc-CCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          235 MPSSRLSEIMDKNYEMKKIILHE---YL-MTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~---~L-~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                                        ..+..   .+ .+++.++|+||++.  ...++.+...+.....++++|+||...
T Consensus        94 ------------------~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~  147 (323)
T 1sxj_B           94 ------------------KHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  147 (323)
T ss_dssp             ------------------HHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             ------------------HHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCCh
Confidence                              11110   12 45689999999975  345555555554344568888888654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.48  E-value=3.5e-07  Score=83.28  Aligned_cols=112  Identities=7%  Similarity=0.029  Sum_probs=75.7

Q ss_pred             eeechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHccCCC---CC---ceeeEEEEEcCCCCCHHHHHHH
Q 038944          158 TVGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYNSSYV---KH---YFDCHAWVPGTYPYDADQMLDI  229 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~---~~---~F~~~~wv~vs~~~~~~~il~~  229 (334)
                      +.||+++.+.|...|..  .....+.+.|+|++|+|||++++.|.+....   ..   .| ..++++...-.+...++..
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~-~~v~INc~~~~t~~~~~~~  100 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIF-DYIHIDALELAGMDALYEK  100 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCE-EEEEEETTCCC--HHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCce-EEEEEeccccCCHHHHHHH
Confidence            68999999999988875  2345678899999999999999999974211   11   23 3566776777788999999


Q ss_pred             HHHHhCCCCCccccchhhHHHHHHHHHHH--cCCCeEEEEEeCCCC
Q 038944          230 VIKFLMPSSRLSEIMDKNYEMKKIILHEY--LMTKRYLNVIDDVWN  273 (334)
Q Consensus       230 il~~~~~~~~~~~~~~~~~~~l~~~l~~~--L~~kr~LlVlDdvw~  273 (334)
                      |++++.+.... ......  .+...+...  -.++.++++||++..
T Consensus       101 I~~~L~g~~~~-~~~~~~--~L~~~f~~~~~~~~~~~ii~lDE~d~  143 (318)
T 3te6_A          101 IWFAISKENLC-GDISLE--ALNFYITNVPKAKKRKTLILIQNPEN  143 (318)
T ss_dssp             HHHHHSCCC---CCCCHH--HHHHHHHHSCGGGSCEEEEEEECCSS
T ss_pred             HHHHhcCCCCC-chHHHH--HHHHHHHHhhhccCCceEEEEecHHH
Confidence            99999765321 111111  333333332  246789999999865

>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=98.33  E-value=3.5e-07  Score=83.15  Aligned_cols=121  Identities=10%  Similarity=0.092  Sum_probs=73.6

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCCCHHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      -.+++|++..++.+.+++..+.  .+.+.++|++|+||||+|+.+++... ...+. ....+..+...+. ..++     
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~-~~~~-----   94 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALARELF-GENWRHNFLELNASDERGI-NVIR-----   94 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHHHHH-GGGHHHHEEEEETTCHHHH-HTTH-----
T ss_pred             HHHhhCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHHHhc-CCcccCceEEeeccccCch-HHHH-----
Confidence            4568999999999999998754  33489999999999999999987311 11111 1223332211000 0000     


Q ss_pred             hCCCCCccccchhhHHHHHHHHHHH--c-CCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          234 LMPSSRLSEIMDKNYEMKKIILHEY--L-MTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       234 ~~~~~~~~~~~~~~~~~l~~~l~~~--L-~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                                      .....+...  + .+++.++++||++.  ...++.+...+.....++++|+||...
T Consensus        95 ----------------~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~  150 (327)
T 1iqp_A           95 ----------------EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYS  150 (327)
T ss_dssp             ----------------HHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             ----------------HHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCc
Confidence                            111111111  1 26788999999975  356666766654444578888888664

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.29  E-value=3.6e-07  Score=75.84  Aligned_cols=46  Identities=15%  Similarity=0.249  Sum_probs=38.9

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..++|+++.++.+.+++....  ...+.|+|++|+||||||+.+.+.
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999997743  445789999999999999999873

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.21  E-value=2.1e-06  Score=76.69  Aligned_cols=49  Identities=16%  Similarity=0.229  Sum_probs=39.2

Q ss_pred             CCCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.+++|.+..++.|.+.+...           -....-+.|+|++|+|||+||+.+.+.
T Consensus        15 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           15 RYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            4456899999999998887431           123456899999999999999999983

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.06  E-value=2.9e-06  Score=70.47  Aligned_cols=117  Identities=13%  Similarity=0.089  Sum_probs=60.9

Q ss_pred             hhHHHHHHHHhcCC-CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc
Q 038944          163 DRMEELLDLLIEGP-PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS  241 (334)
Q Consensus       163 ~~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~  241 (334)
                      ...+.+.+++..-. ..-..+.|+|++|+|||||++.+++.......+ ...++      +..+++..+.........  
T Consensus        21 ~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~-~~~~~------~~~~~~~~~~~~~~~~~~--   91 (180)
T 3ec2_A           21 RALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGI-RGYFF------DTKDLIFRLKHLMDEGKD--   91 (180)
T ss_dssp             HHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCC-CCCEE------EHHHHHHHHHHHHHHTCC--
T ss_pred             HHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCC-eEEEE------EHHHHHHHHHHHhcCchH--
Confidence            34444444444322 234689999999999999999998732101111 11223      345555555444332211  


Q ss_pred             ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHH--HHHhhCCC-CCCCeEEEEecCCh
Q 038944          242 EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCD--IIREILPD-NQNRSRVLITLTEI  300 (334)
Q Consensus       242 ~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~--~l~~~l~~-~~~gsrIivTTr~~  300 (334)
                           .  .+...+.     +.-+|||||++.  .+.|.  .+...+.. ...|..+|+||...
T Consensus        92 -----~--~~~~~~~-----~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~  143 (180)
T 3ec2_A           92 -----T--KFLKTVL-----NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYS  143 (180)
T ss_dssp             -----S--HHHHHHH-----TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCC
T ss_pred             -----H--HHHHHhc-----CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence                 1  2222221     446899999983  23333  22222211 12466788887643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.00  E-value=5.7e-06  Score=74.66  Aligned_cols=125  Identities=14%  Similarity=0.079  Sum_probs=68.3

Q ss_pred             CeeechhhHHHHHHHHhc-------------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCH
Q 038944          157 DTVGLDDRMEELLDLLIE-------------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDA  223 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-------------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  223 (334)
                      +++|.+..++.|.+++..             .......+.++|.+|+|||+||+.+.+............++.++.    
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~----  107 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTR----  107 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECG----
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcH----
Confidence            378998888888776542             123455789999999999999987765311111111111233321    


Q ss_pred             HHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCC-----------ChhHHHHHHhhCCCCCCCeE
Q 038944          224 DQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW-----------NIEVCDIIREILPDNQNRSR  292 (334)
Q Consensus       224 ~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw-----------~~~~w~~l~~~l~~~~~gsr  292 (334)
                              ..+.....  .. ...  .+...+...   +..+|+||++.           +......+...+.....+..
T Consensus       108 --------~~l~~~~~--g~-~~~--~~~~~~~~~---~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~  171 (309)
T 3syl_A          108 --------DDLVGQYI--GH-TAP--KTKEVLKRA---MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLV  171 (309)
T ss_dssp             --------GGTCCSST--TC-HHH--HHHHHHHHH---TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCE
T ss_pred             --------HHhhhhcc--cc-cHH--HHHHHHHhc---CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEE
Confidence                    01111111  00 111  222222222   23499999997           34455666666554455677


Q ss_pred             EEEecCChH
Q 038944          293 VLITLTEIK  301 (334)
Q Consensus       293 IivTTr~~~  301 (334)
                      ||.||....
T Consensus       172 ~i~~~~~~~  180 (309)
T 3syl_A          172 VILAGYADR  180 (309)
T ss_dssp             EEEEECHHH
T ss_pred             EEEeCChHH
Confidence            888886543

>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=97.98  E-value=1.5e-05  Score=71.92  Aligned_cols=121  Identities=11%  Similarity=0.079  Sum_probs=73.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      .+++|++..++.+.+++..+.  .+.+.++|++|+||||+|+.+.+... ...+. ....++.+....            
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~------------   81 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERG------------   81 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTC--CCCEEEESSSSSSHHHHHHHHHHHHH-TTCHHHHCEEEETTSTTC------------
T ss_pred             HHHhCCHHHHHHHHHHHhCCC--CCeEEEECcCCcCHHHHHHHHHHHhc-CCcccCCeEEEeCccccC------------
Confidence            458999999999988887643  23388999999999999999987310 11111 112233332111            


Q ss_pred             CCCCCccccchhhHHHHHHHHHHH--c-CCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          235 MPSSRLSEIMDKNYEMKKIILHEY--L-MTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~--L-~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                              .....  .....+...  + .+++.++++|++..  ....+.+...+.....+.++|+||....
T Consensus        82 --------~~~~~--~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~  143 (319)
T 2chq_A           82 --------IDVVR--HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (319)
T ss_dssp             --------TTTSS--HHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGG
T ss_pred             --------hHHHH--HHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence                    00011  222222211  2 36688999999864  3556667767655556788888876543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.97  E-value=1.4e-05  Score=63.96  Aligned_cols=46  Identities=11%  Similarity=0.022  Sum_probs=35.0

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++|....+.++.+.+..-...-.-+-|+|.+|+|||++|+.+++.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHh
Confidence            5789999999998887642212233679999999999999999985

>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=97.95  E-value=1.7e-05  Score=69.63  Aligned_cols=48  Identities=15%  Similarity=0.176  Sum_probs=35.8

Q ss_pred             CCCeeechhhHHHHHHHHh---cCC-------CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLI---EGP-------PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.+.+++.   ...       ...+-+.++|++|+|||++|+.+.+.
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~   62 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE   62 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3568999888877766543   211       23456789999999999999999983

>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=97.94  E-value=4.5e-05  Score=70.46  Aligned_cols=46  Identities=20%  Similarity=0.198  Sum_probs=38.5

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|++..++.+.+.+..+.. ...+.|+|++|+||||+|+.+.+.
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~~-~~~~ll~G~~G~GKT~la~~la~~   61 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGRI-HHAYLFSGTRGVGKTSIARLLAKG   61 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTCC-CSEEEEESCTTSSHHHHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHHhCCC-CeEEEEECCCCCCHHHHHHHHHHH
Confidence            4589999999999999876532 246789999999999999999874

>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=97.92  E-value=2.3e-05  Score=71.49  Aligned_cols=49  Identities=22%  Similarity=0.272  Sum_probs=38.7

Q ss_pred             CCCCeeechhhHHHHHHHHh----------cCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLI----------EGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~----------~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.+++|.+..++.|.+.+.          ......+-+.++|++|+|||+||+.+.+.
T Consensus        16 ~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           16 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            34568999999999988873          11223457899999999999999999983

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.86  E-value=5e-05  Score=69.00  Aligned_cols=118  Identities=14%  Similarity=0.139  Sum_probs=72.5

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      -.+++|.+..++.+.+++..+. ...++.+.|++|+||||+|+.+.+.  ...   ....++.+. ... ..++.++.  
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~--l~~---~~~~i~~~~-~~~-~~i~~~~~--   94 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHD--VNA---DMMFVNGSD-CKI-DFVRGPLT--   94 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHH--TTE---EEEEEETTT-CCH-HHHHTHHH--
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHH--hCC---CEEEEcccc-cCH-HHHHHHHH--
Confidence            4678999999999999998654 3357788899999999999999883  321   223344332 221 11111111  


Q ss_pred             CCCCCccccchhhHHHHHHHHHHH--cCCCeEEEEEeCCCCh---hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          235 MPSSRLSEIMDKNYEMKKIILHEY--LMTKRYLNVIDDVWNI---EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~--L~~kr~LlVlDdvw~~---~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                                         .....  +.+++.+++|||+..-   +..+.+...+.....+.++|+||....
T Consensus        95 -------------------~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~  147 (324)
T 3u61_B           95 -------------------NFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNID  147 (324)
T ss_dssp             -------------------HHHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGG
T ss_pred             -------------------HHHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCcc
Confidence                               11111  1347789999999753   345555544433234567888876543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.82  E-value=1.4e-05  Score=63.94  Aligned_cols=47  Identities=15%  Similarity=0.092  Sum_probs=33.3

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -+++|.+..++++.+.+..-.....-+-|+|.+|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            35789999998888887641111223679999999999999999984

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.82  E-value=0.00013  Score=64.58  Aligned_cols=48  Identities=17%  Similarity=0.146  Sum_probs=36.2

Q ss_pred             CCCeeechhhHHHHHHH-------Hhc-CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDL-------LIE-GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~-------L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|.....+.++..       +.. ......-+.++|++|+|||+||+.+.+.
T Consensus        32 ~~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           32 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             hcCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            34578888777777663       322 2345678899999999999999999984

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.81  E-value=2.4e-05  Score=65.96  Aligned_cols=88  Identities=14%  Similarity=0.068  Sum_probs=49.9

Q ss_pred             hHHHHHHHHhcCCC--CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc
Q 038944          164 RMEELLDLLIEGPP--QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS  241 (334)
Q Consensus       164 ~~~~l~~~L~~~~~--~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~  241 (334)
                      ..+.+..++.....  ....+.|+|.+|+||||||+.+++..  ........|++.      ..++..+........   
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~--~~~~~~~~~~~~------~~~~~~~~~~~~~~~---  105 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANEL--AKRNVSSLIVYV------PELFRELKHSLQDQT---  105 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHH--HTTTCCEEEEEH------HHHHHHHHHC---CC---
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHH--HHcCCeEEEEEh------HHHHHHHHHHhccch---
Confidence            34455556554322  12678999999999999999999842  222234455543      345555544332111   


Q ss_pred             ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 038944          242 EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       242 ~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~  273 (334)
                          ..  .+...+..     .-+|||||++.
T Consensus       106 ----~~--~~~~~~~~-----~~~lilDei~~  126 (202)
T 2w58_A          106 ----MN--EKLDYIKK-----VPVLMLDDLGA  126 (202)
T ss_dssp             ----CH--HHHHHHHH-----SSEEEEEEECC
T ss_pred             ----HH--HHHHHhcC-----CCEEEEcCCCC
Confidence                11  33333332     13999999965

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.81  E-value=0.00014  Score=66.38  Aligned_cols=48  Identities=19%  Similarity=0.234  Sum_probs=37.5

Q ss_pred             CCCeeechhhHHHHHHHHhc----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.|.+.+..          .....+-+.++|++|+|||+||+.+.+.
T Consensus        11 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~   68 (322)
T 1xwi_A           11 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE   68 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH
Confidence            35688999998888877631          1123467889999999999999999984

>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=97.81  E-value=1.8e-05  Score=75.51  Aligned_cols=121  Identities=16%  Similarity=0.204  Sum_probs=65.0

Q ss_pred             Cee-echhhH--HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee--eEEEEEcCCCCCHHHHHHHHH
Q 038944          157 DTV-GLDDRM--EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD--CHAWVPGTYPYDADQMLDIVI  231 (334)
Q Consensus       157 ~~v-Gr~~~~--~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~il~~il  231 (334)
                      +++ |.....  ..+..+...... ...+.|+|.+|+||||||+.+.+  .....|.  ...+++      ...+..++.
T Consensus       106 ~fv~g~~n~~a~~~~~~~a~~~~~-~~~lll~Gp~G~GKTtLa~aia~--~l~~~~~~~~v~~v~------~~~~~~~~~  176 (440)
T 2z4s_A          106 NFVVGPGNSFAYHAALEVAKHPGR-YNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYIT------SEKFLNDLV  176 (440)
T ss_dssp             GCCCCTTTHHHHHHHHHHHHSTTS-SCCEEEECSSSSSHHHHHHHHHH--HHHHHCCSSCEEEEE------HHHHHHHHH
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCC-CCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEee------HHHHHHHHH
Confidence            344 644332  333333333322 66799999999999999999998  3322221  123443      333444454


Q ss_pred             HHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh----hHHHHHHhhCCC-CCCCeEEEEecCC
Q 038944          232 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI----EVCDIIREILPD-NQNRSRVLITLTE  299 (334)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~----~~w~~l~~~l~~-~~~gsrIivTTr~  299 (334)
                      ..+....             ...+...+..+.-+|+|||+...    ..-+.+...+.. ...|..||+||.+
T Consensus       177 ~~~~~~~-------------~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          177 DSMKEGK-------------LNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             HHHHTTC-------------HHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             HHHHccc-------------HHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            4443211             11223333435679999999643    222333333211 1346788888875

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.78  E-value=0.00018  Score=66.36  Aligned_cols=48  Identities=25%  Similarity=0.243  Sum_probs=37.8

Q ss_pred             CCCeeechhhHHH---HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEE---LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.   +...+..+....+.+.++|++|+|||+||+.+.+.
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999988776   45555555444568899999999999999999984

>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=97.74  E-value=0.00024  Score=64.04  Aligned_cols=48  Identities=25%  Similarity=0.207  Sum_probs=38.2

Q ss_pred             CCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.|.+++...           -...+.+.++|++|+||||||+.+.+.
T Consensus        14 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           14 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH
Confidence            346899999888888876531           134567899999999999999999984

>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=97.74  E-value=4.9e-05  Score=70.36  Aligned_cols=47  Identities=9%  Similarity=0.104  Sum_probs=37.9

Q ss_pred             CCeeechhhHHHHHHHHhc----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIE----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..++.|.+.+..          .....+-+.++|++|+|||+||+.+.+.
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~  140 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ  140 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999888742          1123567889999999999999999983

>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=2.5e-05  Score=71.66  Aligned_cols=135  Identities=9%  Similarity=0.030  Sum_probs=71.8

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCCCHHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      -.+++|.+..++.+..++..+..  +.+.++|++|+||||+|+.+.+.......+. ....+..+....... +++.+..
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  112 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSANL--PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISI-VREKVKN  112 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTTC--CCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHH-HTTHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHhcCCC--CEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHH-HHHHHHH
Confidence            45689999999999999877542  2388999999999999999987311000111 122233333222222 2222221


Q ss_pred             hCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          234 LMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       234 ~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      +...... ....    .   .....-.++.-+|++|++..  ....+.+...+.......++|++|...
T Consensus       113 ~~~~~~~-~~~~----~---~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~  173 (353)
T 1sxj_D          113 FARLTVS-KPSK----H---DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYV  173 (353)
T ss_dssp             HHHSCCC-CCCT----T---HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             Hhhhccc-ccch----h---hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCch
Confidence            1110000 0000    0   00111124557999999853  344555555544334457777776543

>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=8.9e-05  Score=68.07  Aligned_cols=44  Identities=9%  Similarity=-0.032  Sum_probs=35.2

Q ss_pred             CCeeechhhHHHHHHHH-hcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLL-IEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L-~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+...+.+.+++ ..+. ... +.|+|+.|+||||+++.+.+
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~-~~~-~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRD-LPH-LLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTC-CCC-EEEECSTTSSHHHHHHTHHH
T ss_pred             HHhcCCHHHHHHHHHHHhhCCC-CCe-EEEECCCCCCHHHHHHHHHH
Confidence            45889998888888887 4433 223 89999999999999998876

>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=97.67  E-value=0.00022  Score=67.96  Aligned_cols=49  Identities=20%  Similarity=0.251  Sum_probs=38.4

Q ss_pred             CCCCeeechhhHHHHHHHHhc----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIE----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.+++|.+..++.|.+.+..          .....+-+.++|++|+|||+||+.+.+.
T Consensus       132 ~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          132 KWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             CGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            345689999999999887731          1123467889999999999999999984

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.63  E-value=0.00011  Score=68.61  Aligned_cols=49  Identities=18%  Similarity=0.190  Sum_probs=38.7

Q ss_pred             CCCCeeechhhHHHHHHHHhcC----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEG----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.+++|.+..++.|.+++...          ....+-+.|+|.+|+|||+||+.+.+.
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~  171 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE  171 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            3457899999999998887321          123467899999999999999999883

>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=97.62  E-value=9.7e-05  Score=68.29  Aligned_cols=48  Identities=21%  Similarity=0.242  Sum_probs=37.2

Q ss_pred             CCCeeechhhHHHHHHHHhc----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.|.+.+..          .....+-+.++|++|+|||+||+.+.+.
T Consensus        50 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~  107 (355)
T 2qp9_X           50 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE  107 (355)
T ss_dssp             GGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            34689999999999887731          1122345788999999999999999984

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.58  E-value=5.2e-05  Score=66.88  Aligned_cols=47  Identities=19%  Similarity=0.203  Sum_probs=33.8

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.+..+..+.+.+..-.....-+.|+|.+|+|||+||+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            35789999999888777542112245679999999999999999984

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.57  E-value=6e-05  Score=61.97  Aligned_cols=46  Identities=15%  Similarity=0.224  Sum_probs=38.7

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..++|++.+++.+.+.+....  ...+.|+|.+|+||||||+.+.+.
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~--~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRT--KNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             cchhhcchHHHHHHHHHHhCCC--CCceEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999997643  445689999999999999999874

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.55  E-value=0.00026  Score=67.46  Aligned_cols=46  Identities=15%  Similarity=0.199  Sum_probs=37.5

Q ss_pred             CCCeeechhhH---HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRM---EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~---~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..+   ..|...+..+.  ...+.++|.+|+||||||+.+.+.
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~~--~~~vLL~GppGtGKTtlAr~ia~~   73 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAGH--LHSMILWGPPGTGKTTLAEVIARY   73 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHTC--CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcCC--CcEEEEECCCCCcHHHHHHHHHHH
Confidence            45688988777   67777776654  467899999999999999999983

>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=97.54  E-value=4.3e-05  Score=69.26  Aligned_cols=48  Identities=17%  Similarity=0.205  Sum_probs=38.1

Q ss_pred             CCCeeechhhHHHHHHHHhc---CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE---GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|++..++.+..++..   .......+.|+|++|+|||+||+.+++.
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~   61 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHE   61 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHH
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            45689999999988888763   1223456889999999999999999883

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=97.48  E-value=0.00016  Score=69.80  Aligned_cols=47  Identities=13%  Similarity=0.160  Sum_probs=37.7

Q ss_pred             CCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..++.|.+++...           .....-+.|+|.+|+|||+||+.+.+.
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~  261 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE  261 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHH
Confidence            46899999999998877532           233456889999999999999999883

>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=97.48  E-value=8.3e-05  Score=67.62  Aligned_cols=37  Identities=22%  Similarity=0.184  Sum_probs=27.2

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+..++..+......+.|+|++|+||||||+.+.+.
T Consensus        24 ~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~   60 (324)
T 1l8q_A           24 EVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE   60 (324)
T ss_dssp             HHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            3444444443334567899999999999999999873

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.46  E-value=0.00037  Score=62.96  Aligned_cols=47  Identities=21%  Similarity=0.239  Sum_probs=37.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|....+.++.+.+..-.....-+.|+|.+|+|||++|+.+++.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHh
Confidence            45889999999998888652222335679999999999999999984

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.43  E-value=0.00015  Score=64.85  Aligned_cols=48  Identities=17%  Similarity=0.182  Sum_probs=38.2

Q ss_pred             CCCeeechhhHHHHHHHHhcC----------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG----------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.+.+++...          ....+.+.++|++|+||||||+.+.+.
T Consensus        20 ~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~   77 (297)
T 3b9p_A           20 WTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE   77 (297)
T ss_dssp             GGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            346899999999998887431          123467889999999999999999983

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.34  E-value=0.00028  Score=67.73  Aligned_cols=45  Identities=16%  Similarity=0.289  Sum_probs=37.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|++.+++.++..|....  ..-+.++|.+|+|||++|+.+...
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~--~~~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999997743  234578999999999999999873

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=97.33  E-value=0.0011  Score=53.79  Aligned_cols=105  Identities=15%  Similarity=0.137  Sum_probs=56.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc--------ccchhhHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS--------EIMDKNYEMK  251 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~--------~~~~~~~~~l  251 (334)
                      .+|.|.|++|+||||+|+.+ ..  ..  |.   ++      +..++++..+..-+......        ......  ..
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~--~g--~~---~i------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~   65 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KE--RG--AK---VI------VMSDVVRKRYSIEAKPGERLMDFAKRLREIYGDG--VV   65 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HH--TT--CE---EE------EHHHHHHHHHHHHC---CCHHHHHHHHHHHHCTT--HH
T ss_pred             cEEEEECCCCCCHHHHHHHH-HH--CC--Cc---EE------EHhHHHHHHHHhcCCChhHHHHHHHHHHhhCCHH--HH
Confidence            47999999999999999999 52  21  21   22      23455555554433111000        000111  23


Q ss_pred             HHHHHHHc-CCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHH
Q 038944          252 KIILHEYL-MTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMF  303 (334)
Q Consensus       252 ~~~l~~~L-~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va  303 (334)
                      ...+...+ ......+|+|.+.+...++.+...++   ....+|....+.+++
T Consensus        66 ~~~~~~~l~~~~~~~vi~dg~~~~~~~~~l~~~~~---~~~~~i~l~~~~~~~  115 (179)
T 3lw7_A           66 ARLCVEELGTSNHDLVVFDGVRSLAEVEEFKRLLG---DSVYIVAVHSPPKIR  115 (179)
T ss_dssp             HHHHHHHHCSCCCSCEEEECCCCHHHHHHHHHHHC---SCEEEEEEECCHHHH
T ss_pred             HHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHhC---CCcEEEEEECCHHHH
Confidence            34444555 23345688899977777777766553   234455444444443

>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=97.33  E-value=0.00069  Score=61.96  Aligned_cols=45  Identities=13%  Similarity=0.203  Sum_probs=36.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..++.|..++..+.  ++.+.++|++|+||||+|+.+.+.
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~--~~~~ll~Gp~G~GKTtla~~la~~   69 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALARE   69 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            457888888888888887654  223889999999999999999873

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.33  E-value=0.00061  Score=61.17  Aligned_cols=46  Identities=17%  Similarity=0.317  Sum_probs=37.1

Q ss_pred             CeeechhhHHHHHHHHhcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|.+..++.+...+...       ......+.++|.+|+||||+|+.+.+.
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~   70 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT   70 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHH
Confidence            4789999988888877642       123468999999999999999999873

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.31  E-value=0.0017  Score=54.90  Aligned_cols=86  Identities=9%  Similarity=0.000  Sum_probs=53.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCC-----------CCccccchh
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPS-----------SRLSEIMDK  246 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~-----------~~~~~~~~~  246 (334)
                      .-.++.|+|.+|+|||||+..+..     ..-...+|++....++...+.. +++.++..           ... ...+.
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-----~~~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~   91 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-----LSGKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPS-DFKEQ   91 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-----HHCSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCT-TTSHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-----HcCCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecC-CHHHH
Confidence            446999999999999999999876     1223567887776666665543 44333221           000 11111


Q ss_pred             hHHHHHHHHHHHcCCCeEEEEEeCCC
Q 038944          247 NYEMKKIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       247 ~~~~l~~~l~~~L~~kr~LlVlDdvw  272 (334)
                      .  .....++..+..+.-+||||.+-
T Consensus        92 ~--~~~~~~~~l~~~~~~lliiD~~~  115 (220)
T 2cvh_A           92 R--RVIGSLKKTVDSNFALVVVDSIT  115 (220)
T ss_dssp             H--HHHHHHHHHCCTTEEEEEEECCC
T ss_pred             H--HHHHHHHHHhhcCCCEEEEcCcH
Confidence            2  45556666665457799999974

>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=97.30  E-value=0.00036  Score=66.89  Aligned_cols=48  Identities=17%  Similarity=0.266  Sum_probs=34.7

Q ss_pred             CCCeeechhhHHHHHHHHh---cC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLI---EG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.++.++++.+.+.   ..       -...+-+.++|++|+||||||+.+.+.
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~   72 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGE   72 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3468999888777766543   21       111234779999999999999999983

>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=97.27  E-value=0.0012  Score=59.72  Aligned_cols=134  Identities=10%  Similarity=0.053  Sum_probs=75.9

Q ss_pred             echhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC-CCC-CceeeEEEEEcCC-CCCHHHHHHHHHHHhCC
Q 038944          160 GLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS-YVK-HYFDCHAWVPGTY-PYDADQMLDIVIKFLMP  236 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~-~~~-~~F~~~~wv~vs~-~~~~~~il~~il~~~~~  236 (334)
                      |-++.++.|.+.+..+.  .+..-++|++|+||||+|..+.+.. ... .|.+. .++..+. ...+.. .+++++.+..
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~-~~l~~~~~~~~id~-ir~li~~~~~   76 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDD-IRTIKDFLNY   76 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHH-HHHHHHHHTS
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCE-EEEcCCcCCCCHHH-HHHHHHHHhh
Confidence            34555667777776654  6788899999999999999997631 111 12222 3343332 222222 2233333321


Q ss_pred             CCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh-HHHhhccccCccc
Q 038944          237 SSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI-KMFTFLLETLFSL  313 (334)
Q Consensus       237 ~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~-~va~~~~~~~~~~  313 (334)
                      ..                    ..+++-++|+|++..  ....+.+...+-.-...+.+|++|.+. .+-..+.+. .++
T Consensus        77 ~p--------------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~  135 (305)
T 2gno_A           77 SP--------------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFR  135 (305)
T ss_dssp             CC--------------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEE
T ss_pred             cc--------------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEe
Confidence            11                    124567889999864  466777776665444567777766443 444444455 555


Q ss_pred             ccccC
Q 038944          314 LICVS  318 (334)
Q Consensus       314 l~~l~  318 (334)
                      +.+++
T Consensus       136 f~~l~  140 (305)
T 2gno_A          136 VVVNV  140 (305)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            55555

>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=97.27  E-value=0.00017  Score=70.06  Aligned_cols=48  Identities=13%  Similarity=0.133  Sum_probs=40.0

Q ss_pred             CCCeeechhhHHHHHHHHhcC---------------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG---------------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~---------------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|++..++.+.+||...               ....+.+.|+|++|+||||+|+.+.+.
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~  100 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE  100 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            356899999999999999751               013468999999999999999999984

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.20  E-value=0.0024  Score=64.92  Aligned_cols=45  Identities=16%  Similarity=0.215  Sum_probs=38.1

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -..++|++.+++.+++.|....  ..-+.++|.+|+||||+|+.+.+
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~--~~~vlL~G~~GtGKT~la~~la~  229 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccC--CCCeEEEcCCCCCHHHHHHHHHH
Confidence            3568999999999999997653  33467999999999999999986

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.19  E-value=0.00035  Score=61.13  Aligned_cols=48  Identities=23%  Similarity=0.241  Sum_probs=34.4

Q ss_pred             CCCeeechhhHHHHHHHH---hcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLL---IEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L---~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..++.+.+.+   ...       ....+-+.|+|++|+||||||+.+.+.
T Consensus        11 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            346889888877766543   221       012334789999999999999999884

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.03  E-value=0.00063  Score=61.04  Aligned_cols=25  Identities=12%  Similarity=0.061  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....+.++|++|+|||+||+.+.+.
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~   59 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRK   59 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4567889999999999999999984

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.95  E-value=0.00043  Score=63.07  Aligned_cols=48  Identities=15%  Similarity=0.160  Sum_probs=39.4

Q ss_pred             CCCeeechhhHHHHHHHHhcC---CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG---PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|++..++.+..++...   ......+.|+|++|+|||+||+.+.+.
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~   78 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYE   78 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            456899999999998888752   334556899999999999999999873

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.93  E-value=0.0064  Score=55.41  Aligned_cols=40  Identities=15%  Similarity=0.126  Sum_probs=29.1

Q ss_pred             hhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          162 DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       162 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++..+.+.+.+..+. -...+-++|+.|+||||+|+.+.+.
T Consensus         8 ~~~~~~l~~~i~~~~-~~~a~L~~G~~G~GKt~~a~~la~~   47 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRY   47 (334)
T ss_dssp             HHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCC-cceeEEEECCCCchHHHHHHHHHHH
Confidence            444566666665543 3357889999999999999988763

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.92  E-value=0.0022  Score=65.13  Aligned_cols=46  Identities=15%  Similarity=0.268  Sum_probs=38.2

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..++|++.+++.++..|....  ..-+-++|.+|+|||++|+.+.+.
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~--~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCC--CCCeEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999998743  223679999999999999999863

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.88  E-value=0.0014  Score=61.94  Aligned_cols=48  Identities=19%  Similarity=0.224  Sum_probs=37.3

Q ss_pred             CCCeeechhhHHHHHHHHhc-----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE-----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.++.|.++.+++|.+.+.-           +-...+=+-++|++|+|||+||+.+.+.
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          180 FDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             SGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             hhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            34678899888888776642           1234567889999999999999999983

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.87  E-value=0.0013  Score=62.04  Aligned_cols=54  Identities=22%  Similarity=0.217  Sum_probs=40.2

Q ss_pred             CCCCeeechhhHHHHHHHHhc-----------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          154 KSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .-.++.|.++.++.|.+.+.-           +-...+=+-++|++|+|||+||+.+.+  ....+|
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~--~~~~~~  234 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVAN--STKAAF  234 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHH--HHTCEE
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHH--HhCCCe
Confidence            345688999999988776642           113456688999999999999999998  444444

>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=96.84  E-value=0.00074  Score=61.17  Aligned_cols=69  Identities=13%  Similarity=0.104  Sum_probs=43.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEc--CCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPG--TYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      -+++.|+|++|+||||||..+...     .-..++|++.  +...+.               .   ..+  ++.....+.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs~~~eE~v~~---------------~---~~~--le~~l~~i~  177 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-----LGGKDKYATVRFGEPLSG---------------Y---NTD--FNVFVDDIA  177 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-----HHTTSCCEEEEBSCSSTT---------------C---BCC--HHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-----CCCCEEEEEecchhhhhh---------------h---hcC--HHHHHHHHH
Confidence            456789999999999999998873     1123456665  332110               0   011  225555566


Q ss_pred             HHcCCCeEEEEEeCCCC
Q 038944          257 EYLMTKRYLNVIDDVWN  273 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~  273 (334)
                      +.+...+ +||+|++-.
T Consensus       178 ~~l~~~~-LLVIDsI~a  193 (331)
T 2vhj_A          178 RAMLQHR-VIVIDSLKN  193 (331)
T ss_dssp             HHHHHCS-EEEEECCTT
T ss_pred             HHHhhCC-EEEEecccc
Confidence            6665445 999999854

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.83  E-value=0.0013  Score=61.45  Aligned_cols=53  Identities=19%  Similarity=0.222  Sum_probs=39.0

Q ss_pred             CCCeeechhhHHHHHHHHhc-----------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          155 SRDTVGLDDRMEELLDLLIE-----------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      -.++.|.++.+++|.+.+.-           +-...+=+-++|++|.|||.||+.+.+  ....+|
T Consensus       147 ~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~--e~~~~f  210 (405)
T 4b4t_J          147 YDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH--HTDCKF  210 (405)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHH--HHTCEE
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHH--hhCCCc
Confidence            35678899888888776532           113445678999999999999999998  444444

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.81  E-value=0.0014  Score=62.20  Aligned_cols=52  Identities=21%  Similarity=0.254  Sum_probs=38.9

Q ss_pred             CCeeechhhHHHHHHHHhc-----------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          156 RDTVGLDDRMEELLDLLIE-----------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .++.|.++.+++|.+.+.-           +-...+=|-++|++|+|||+||+.+.+  ....+|
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~--e~~~~f  271 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVAN--RTDATF  271 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHH--HHTCEE
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCCCe
Confidence            4678899888888776431           113456778999999999999999998  444444

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.77  E-value=0.0013  Score=62.25  Aligned_cols=47  Identities=21%  Similarity=0.306  Sum_probs=37.1

Q ss_pred             CCCeeechhhHHHHHHHHh----cC-------CCCceEEEEEccCCccHHHHHHHHHc
Q 038944          155 SRDTVGLDDRMEELLDLLI----EG-------PPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~----~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.++.|.++.+++|.+.+.    ..       -...+=+-++|++|+|||+||+.+.+
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~  237 (434)
T 4b4t_M          180 YSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAA  237 (434)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             hHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHH
Confidence            3567899999998877643    21       13456788899999999999999998

>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=96.77  E-value=0.002  Score=61.41  Aligned_cols=49  Identities=18%  Similarity=0.107  Sum_probs=36.9

Q ss_pred             CCCCeeechhhHHHHHH---HHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLD---LLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~---~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+++|.++.++.+..   ++..+....+-+-++|++|+|||+||+.+.+.
T Consensus        35 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           35 AASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             EETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             chhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            34679999988876544   44444334456788999999999999999984

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.75  E-value=0.00089  Score=60.53  Aligned_cols=39  Identities=13%  Similarity=0.296  Sum_probs=28.4

Q ss_pred             hHHHHHHHHhcCCC-CceEEEEEccCCccHHHHHHHHHcc
Q 038944          164 RMEELLDLLIEGPP-QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       164 ~~~~l~~~L~~~~~-~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....+.+++..... ....+.++|.+|+|||+||+.+.+.
T Consensus       136 ~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          136 AFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             HHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHH
Confidence            34455566655322 2467889999999999999999883

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=96.72  E-value=0.0031  Score=61.56  Aligned_cols=45  Identities=18%  Similarity=0.292  Sum_probs=34.1

Q ss_pred             CeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +++|.++-+..+.+.+.-    ......++.++|++|+||||||+.+..
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~  130 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAK  130 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            467877777776555431    223456899999999999999999988

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.71  E-value=0.0025  Score=64.82  Aligned_cols=94  Identities=12%  Similarity=0.137  Sum_probs=58.4

Q ss_pred             CCCeeechhhHHHHHHHHh----cC-------CCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCH
Q 038944          155 SRDTVGLDDRMEELLDLLI----EG-------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDA  223 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~----~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  223 (334)
                      -.++.|.++.+++|.+++.    ..       -...+-|-++|++|+|||+||+.+.+  ....+|   ..|+.+     
T Consensus       203 ~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~--elg~~~---~~v~~~-----  272 (806)
T 3cf2_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAFF---FLINGP-----  272 (806)
T ss_dssp             GGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHT--TTTCEE---EEEEHH-----
T ss_pred             hhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH--HhCCeE---EEEEhH-----
Confidence            3467888888888877653    22       13456788999999999999999999  555554   223211     


Q ss_pred             HHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCC
Q 038944          224 DQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       224 ~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw  272 (334)
                       +    ++    ....   .....  .+...+.........+|+||++.
T Consensus       273 -~----l~----sk~~---gese~--~lr~lF~~A~~~~PsIIfIDEiD  307 (806)
T 3cf2_A          273 -E----IM----SKLA---GESES--NLRKAFEEAEKNAPAIIFIDELD  307 (806)
T ss_dssp             -H----HH----SSCT---THHHH--HHHHHHHHHTTSCSEEEEEESGG
T ss_pred             -H----hh----cccc---hHHHH--HHHHHHHHHHHcCCeEEEEehhc
Confidence             1    11    1111   11112  33444444456678999999985

>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=96.71  E-value=0.0063  Score=52.17  Aligned_cols=95  Identities=7%  Similarity=0.020  Sum_probs=54.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCC----cc---ccchh
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR----LS---EIMDK  246 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~----~~---~~~~~  246 (334)
                      .-.++.|+|.+|+|||||+..+........    .-...+|+.....++...+. .+++.++....    ..   ...+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCH
Confidence            346999999999999999999887322211    12457888877766665543 34455543210    00   01111


Q ss_pred             h-HHHHHHHHHHHcC-CCeEEEEEeCCCC
Q 038944          247 N-YEMKKIILHEYLM-TKRYLNVIDDVWN  273 (334)
Q Consensus       247 ~-~~~l~~~l~~~L~-~kr~LlVlDdvw~  273 (334)
                      . ...+...+.+.+. .+.-+||||.+-.
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEeCchH
Confidence            1 1123334555553 4677999999853

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.66  E-value=0.0014  Score=55.37  Aligned_cols=37  Identities=16%  Similarity=0.207  Sum_probs=28.0

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.+.+......-.+++|+|..|+|||||++.+..
T Consensus         8 ~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~   44 (208)
T 3c8u_A            8 CQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAA   44 (208)
T ss_dssp             HHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3445555544334567999999999999999999876

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.65  E-value=0.0021  Score=54.09  Aligned_cols=41  Identities=20%  Similarity=0.131  Sum_probs=32.5

Q ss_pred             chhhHHHHHHHHhcC-CCCceEEEEEccCCccHHHHHHHHHc
Q 038944          161 LDDRMEELLDLLIEG-PPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       161 r~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +++.++.|.+.+... .....+++|+|..|+|||||++.+..
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            445667787777753 34567999999999999999999876

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.63  E-value=0.0017  Score=66.06  Aligned_cols=47  Identities=15%  Similarity=0.273  Sum_probs=37.8

Q ss_pred             CCeeechhhHHHHHHHHhcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.+..++.+...+...       ..+...+.++|++|+|||++|+.+.+.
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~  544 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAES  544 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            46899999998888887632       123447999999999999999999873

>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=96.59  E-value=0.0015  Score=55.88  Aligned_cols=59  Identities=7%  Similarity=0.059  Sum_probs=36.5

Q ss_pred             CCeeec---hhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcC
Q 038944          156 RDTVGL---DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGT  218 (334)
Q Consensus       156 ~~~vGr---~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs  218 (334)
                      .+++|.   ....+.+..++...  ....+.|+|++|+||||||+.+.+.  .........|++.+
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~   89 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLG   89 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGG
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHH
Confidence            456653   24445555555443  3567889999999999999999873  22122234556543

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=96.54  E-value=0.0012  Score=58.93  Aligned_cols=47  Identities=13%  Similarity=0.166  Sum_probs=37.0

Q ss_pred             CCeeechhhHHHHHHHHhcC------------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG------------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.+..++.+...+...            .....-+.++|.+|+|||++|+.+.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   73 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            35899999999998877541            122346779999999999999999883

>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=96.45  E-value=0.0016  Score=59.46  Aligned_cols=47  Identities=19%  Similarity=0.199  Sum_probs=35.1

Q ss_pred             CCeeechhhHHHHHHHHhcC---CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.+..++.+-..+...   ......+.++|++|+||||||+.+.+.
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~   74 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASE   74 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            35678777777766555432   234567899999999999999999983

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.43  E-value=0.004  Score=59.98  Aligned_cols=50  Identities=18%  Similarity=0.260  Sum_probs=35.7

Q ss_pred             CCCCCeeechhhHHHHHHHHh---cCC-------CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          153 SKSRDTVGLDDRMEELLDLLI---EGP-------PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-.+++|.++.+.++.+...   ...       .-.+=+.|+|.+|+||||||+.+.+.
T Consensus        28 ~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~   87 (499)
T 2dhr_A           28 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   87 (499)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            345678999888777665543   210       11223899999999999999999984

>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=96.42  E-value=0.016  Score=52.97  Aligned_cols=95  Identities=6%  Similarity=0.001  Sum_probs=57.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCC----cc---ccch
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR----LS---EIMD  245 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~----~~---~~~~  245 (334)
                      +.-.++.|+|.+|+|||||+..+........    .-..++|++....|+...+.. ++..++....    ..   ...+
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~~~~~~l~~l~~~~~~~  198 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNVDHDAVLDNVLYARAYT  198 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCCCHHHHHhceeEeecCC
Confidence            4457999999999999999998876422211    123678999888888777654 3455543211    00   0001


Q ss_pred             h-hHHHHHHHHHHHcC---CCeEEEEEeCCC
Q 038944          246 K-NYEMKKIILHEYLM---TKRYLNVIDDVW  272 (334)
Q Consensus       246 ~-~~~~l~~~l~~~L~---~kr~LlVlDdvw  272 (334)
                      . .+..+...+.+.+.   .+--+||+|.+-
T Consensus       199 ~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~  229 (343)
T 1v5w_A          199 SEHQMELLDYVAAKFHEEAGIFKLLIIDSIM  229 (343)
T ss_dssp             TTHHHHHHHHHHHHHHHSCSSEEEEEEETSG
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccEEEEechH
Confidence            1 11133334444443   566799999984

>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=96.42  E-value=0.0046  Score=56.94  Aligned_cols=87  Identities=18%  Similarity=0.076  Sum_probs=53.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-.++.|+|.+|+|||||+..+.....  ..=..++|++....++..     .+++++......   ...+.+  ++..
T Consensus        59 ~~G~i~~I~GppGsGKSTLal~la~~~~--~~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e--~~l~  129 (356)
T 3hr8_A           59 PRGRIVEIFGQESSGKTTLALHAIAEAQ--KMGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGE--QALE  129 (356)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHH--HHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHH--HHHH
Confidence            3457999999999999999998876321  111246788877777654     455555432211   111222  4555


Q ss_pred             HHHHHcC-CCeEEEEEeCCC
Q 038944          254 ILHEYLM-TKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L~-~kr~LlVlDdvw  272 (334)
                      .+...++ ++.-++|+|.+-
T Consensus       130 ~~~~l~~~~~~dlvVIDSi~  149 (356)
T 3hr8_A          130 IVDELVRSGVVDLIVVDSVA  149 (356)
T ss_dssp             HHHHHHHTSCCSEEEEECTT
T ss_pred             HHHHHhhhcCCCeEEehHhh
Confidence            5554442 445589999873

>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=96.42  E-value=0.0033  Score=64.77  Aligned_cols=46  Identities=17%  Similarity=0.317  Sum_probs=36.5

Q ss_pred             CeeechhhHHHHHHHHhcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|.+..++.+...+...       +.+...+.|+|.+|+|||++|+.+.+.
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~  611 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT  611 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            4789999888887777531       223468899999999999999999873

>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=96.39  E-value=0.0035  Score=56.11  Aligned_cols=27  Identities=19%  Similarity=0.158  Sum_probs=23.3

Q ss_pred             CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          175 GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       175 ~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ......+|+|+|..|+|||||++.+..
T Consensus        27 ~~~~~~ii~I~G~sGsGKSTla~~L~~   53 (290)
T 1odf_A           27 GNKCPLFIFFSGPQGSGKSFTSIQIYN   53 (290)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            345678999999999999999998876

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.37  E-value=0.0037  Score=58.75  Aligned_cols=52  Identities=19%  Similarity=0.222  Sum_probs=38.6

Q ss_pred             CCeeechhhHHHHHHHHhc----C-------CCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          156 RDTVGLDDRMEELLDLLIE----G-------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      .++.|.++.+++|.+.+.-    .       -...+=+-++|++|.|||.||+.+.+  ....+|
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~--e~~~~f  244 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVAN--QTSATF  244 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHH--HHTCEE
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHH--HhCCCE
Confidence            4577899888888776532    1       13456788999999999999999998  344444

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=96.33  E-value=0.003  Score=58.21  Aligned_cols=45  Identities=13%  Similarity=0.111  Sum_probs=35.7

Q ss_pred             eeechhhHHHHHHHHh-------------cCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          158 TVGLDDRMEELLDLLI-------------EGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~-------------~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|.+..++.+...+.             ........+.++|++|+|||++|+.+.+.
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~   74 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARL   74 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            6899998988888773             11123456889999999999999999984

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.33  E-value=0.014  Score=52.81  Aligned_cols=94  Identities=11%  Similarity=0.030  Sum_probs=57.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCc----eeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc----c---ccch-
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHY----FDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL----S---EIMD-  245 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~----~---~~~~-  245 (334)
                      .-.++.|+|.+|+|||||+..+.........    -..++|++....++..++.+ +++.++.....    .   ...+ 
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN-MAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHhCCCHHHHhccEEEEeCCCH
Confidence            3468999999999999999888764222211    23678999888888777654 44555443210    0   0011 


Q ss_pred             hhHHHHHHHHHHHcC--CCeEEEEEeCCC
Q 038944          246 KNYEMKKIILHEYLM--TKRYLNVIDDVW  272 (334)
Q Consensus       246 ~~~~~l~~~l~~~L~--~kr~LlVlDdvw  272 (334)
                      ..+..+...+...+.  .+--+||+|.+-
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  213 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVT  213 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTT
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcH
Confidence            111134455555553  466799999984

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.30  E-value=0.016  Score=52.41  Aligned_cols=95  Identities=8%  Similarity=0.074  Sum_probs=58.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCC---------ce-----eeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc--
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKH---------YF-----DCHAWVPGTYPYDADQMLDIVIKFLMPSSRL--  240 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---------~F-----~~~~wv~vs~~~~~~~il~~il~~~~~~~~~--  240 (334)
                      +.-.++-|+|.+|+||||||..+..+.....         ..     ..++|++....|+..++.+. ++.++.....  
T Consensus        96 ~~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~-~~~~g~~~~~~~  174 (322)
T 2i1q_A           96 ESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQM-AEHAGIDGQTVL  174 (322)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHH-HHHHTCCHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHH-HHHcCCCHHHHh
Confidence            3457999999999999999988875422211         11     46789998888888777643 4555443210  


Q ss_pred             -----cccchhh-HHHHHHHHHHHcC--CCeEEEEEeCCC
Q 038944          241 -----SEIMDKN-YEMKKIILHEYLM--TKRYLNVIDDVW  272 (334)
Q Consensus       241 -----~~~~~~~-~~~l~~~l~~~L~--~kr~LlVlDdvw  272 (334)
                           ....+.+ +..+...+.+.+.  .+--+||+|.+-
T Consensus       175 ~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          175 DNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             HTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             cCEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence                 0001111 1134455656554  455699999984

>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=96.28  E-value=0.0021  Score=52.01  Aligned_cols=22  Identities=9%  Similarity=0.078  Sum_probs=20.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|+.|+||||+++.+..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>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=96.24  E-value=0.0024  Score=52.23  Aligned_cols=22  Identities=5%  Similarity=0.083  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|++|+||||+++.+.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5789999999999999999988

>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=96.24  E-value=0.0026  Score=52.64  Aligned_cols=24  Identities=17%  Similarity=0.163  Sum_probs=21.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|++|+|||||++.+...
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            468999999999999999999874

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=96.22  E-value=0.0019  Score=56.72  Aligned_cols=49  Identities=18%  Similarity=0.278  Sum_probs=35.8

Q ss_pred             CCCCeeechhhHHHHHHHHhc----------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIE----------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-.+++|.+..++.+.+.+..          +....+-+.++|++|+|||+||+.+.+.
T Consensus         9 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A            9 RFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             CSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHH
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            345689999888888776541          1111223679999999999999999984

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.20  E-value=0.012  Score=56.76  Aligned_cols=43  Identities=16%  Similarity=0.114  Sum_probs=36.4

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      .++|.+..++.+...+..+.    -+.++|.+|+|||+||+.+.+..
T Consensus        23 ~ivGq~~~i~~l~~al~~~~----~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHTC----EEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhHHHHHHHHHHHHHHhcCC----eeEeecCchHHHHHHHHHHHHHH
Confidence            37899999988888777653    57899999999999999999843

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.15  E-value=0.0028  Score=53.10  Aligned_cols=23  Identities=9%  Similarity=0.180  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|+|++|+||||+++.+..
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            56899999999999999999987

>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=96.13  E-value=0.0032  Score=64.89  Aligned_cols=46  Identities=15%  Similarity=0.312  Sum_probs=38.3

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..++|++.++..+++.|....  ..-+.++|.+|+||||||+.+.+.
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHH
Confidence            3568999999999999997754  234678999999999999999873

>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=96.13  E-value=0.004  Score=50.77  Aligned_cols=24  Identities=25%  Similarity=0.335  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.++.|+|+.|+||||+++.+..
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            457899999999999999999876

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.11  E-value=0.01  Score=54.88  Aligned_cols=85  Identities=12%  Similarity=-0.009  Sum_probs=52.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKII  254 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~  254 (334)
                      .-.++-|.|.+|+||||||..+.....  ..=..++|++....++..     .++.++......   ...+.+  ++...
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~--~~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e--~~l~~  143 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQ--KAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGE--QALEI  143 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHH--HHHHH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHH--HCCCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHH--HHHHH
Confidence            345888999999999999988765321  111367899988877654     244454432110   111223  56666


Q ss_pred             HHHHcC-CCeEEEEEeCC
Q 038944          255 LHEYLM-TKRYLNVIDDV  271 (334)
Q Consensus       255 l~~~L~-~kr~LlVlDdv  271 (334)
                      +...++ ++--+||+|.+
T Consensus       144 l~~l~~~~~~~lVVIDsl  161 (366)
T 1xp8_A          144 MELLVRSGAIDVVVVDSV  161 (366)
T ss_dssp             HHHHHTTTCCSEEEEECT
T ss_pred             HHHHHhcCCCCEEEEeCh
Confidence            665554 34458999997

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.09  E-value=0.003  Score=52.11  Aligned_cols=23  Identities=13%  Similarity=0.299  Sum_probs=21.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++++|+|+.|+|||||++.+...
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            58999999999999999999873

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.08  E-value=0.0034  Score=51.23  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|++|+||||+|+.+..
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

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.04  E-value=0.0026  Score=51.68  Aligned_cols=22  Identities=9%  Similarity=0.279  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+|+|+.|+|||||++.+..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999987

>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=96.00  E-value=0.014  Score=53.83  Aligned_cols=111  Identities=11%  Similarity=0.034  Sum_probs=65.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCC---cc-ccchhhHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSR---LS-EIMDKNYEMKKII  254 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~---~~-~~~~~~~~~l~~~  254 (334)
                      -.+++|+|+.|+|||||.+.+...  +......++ +++..+...         .......   .. ...+..  .....
T Consensus       123 ~g~i~I~GptGSGKTTlL~~l~g~--~~~~~~~~i-~t~ed~~e~---------~~~~~~~~v~q~~~~~~~~--~~~~~  188 (356)
T 3jvv_A          123 RGLVLVTGPTGSGKSTTLAAMLDY--LNNTKYHHI-LTIEDPIEF---------VHESKKCLVNQREVHRDTL--GFSEA  188 (356)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHH--HHHHCCCEE-EEEESSCCS---------CCCCSSSEEEEEEBTTTBS--CHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc--ccCCCCcEE-EEccCcHHh---------hhhccccceeeeeeccccC--CHHHH
Confidence            359999999999999999988652  111111111 122111100         0000000   00 001112  45557


Q ss_pred             HHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhc
Q 038944          255 LHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       255 l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~  306 (334)
                      |...|....=+|++|.+-+.+.++.+....   ..|.-||+||...+.+..+
T Consensus       189 La~aL~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~~~~  237 (356)
T 3jvv_A          189 LRSALREDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAAKTI  237 (356)
T ss_dssp             HHHHTTSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHHHHH
T ss_pred             HHHHhhhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHHHHH
Confidence            888888888899999999888877765552   2366699999988877543

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=95.99  E-value=0.0021  Score=55.23  Aligned_cols=111  Identities=12%  Similarity=-0.027  Sum_probs=58.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      -.++.|.|..|+||||++..+...... ....+ ..+....  +.. ....+++.++............  ++...+.+.
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~-~g~kV-li~~~~~--d~r-~~~~i~srlG~~~~~~~~~~~~--~i~~~i~~~   84 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEY-ADVKY-LVFKPKI--DTR-SIRNIQSRTGTSLPSVEVESAP--EILNYIMSN   84 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHH-TTCCE-EEEEECC--CGG-GCSSCCCCCCCSSCCEEESSTH--HHHHHHHST
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHh-cCCEE-EEEEecc--Cch-HHHHHHHhcCCCccccccCCHH--HHHHHHHHH
Confidence            468899999999999988666542111 11222 2232222  111 1123344444322211122223  566666665


Q ss_pred             cCCCeE-EEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCC
Q 038944          259 LMTKRY-LNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTE  299 (334)
Q Consensus       259 L~~kr~-LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~  299 (334)
                      +.+.++ +|++|.+-.  .+..+.+.... +  .|-.||+|-+.
T Consensus        85 ~~~~~~dvViIDEaQ~l~~~~ve~l~~L~-~--~gi~Vil~Gl~  125 (223)
T 2b8t_A           85 SFNDETKVIGIDEVQFFDDRICEVANILA-E--NGFVVIISGLD  125 (223)
T ss_dssp             TSCTTCCEEEECSGGGSCTHHHHHHHHHH-H--TTCEEEEECCS
T ss_pred             hhCCCCCEEEEecCccCcHHHHHHHHHHH-h--CCCeEEEEecc
Confidence            655555 999999853  34444443322 2  26779999884

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.98  E-value=0.0046  Score=54.80  Aligned_cols=46  Identities=24%  Similarity=0.253  Sum_probs=33.0

Q ss_pred             CCeeechhhHHHHHHHHhc---C---------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIE---G---------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++.|.++.++.|.+.+..   .         ..... +.++|++|+|||||++.+...
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G-vlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG-VLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE-EEEESSTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe-EEEECCCCCcHHHHHHHHHHH
Confidence            4577888888887765421   1         11223 899999999999999999984

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.98  E-value=0.004  Score=51.31  Aligned_cols=22  Identities=9%  Similarity=0.205  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|.|++|+||||+++.+.+
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

>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=95.96  E-value=0.0046  Score=51.83  Aligned_cols=24  Identities=17%  Similarity=0.129  Sum_probs=21.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+|.|+|+.|+|||||++.+..
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~   47 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQ   47 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999976

>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=95.93  E-value=0.0077  Score=55.49  Aligned_cols=85  Identities=12%  Similarity=-0.039  Sum_probs=50.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKII  254 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~  254 (334)
                      .-.++.|.|.+|+||||||..+.....  ..=..++|++....++...     +..++......   ...+..  ++...
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~--~~g~~vlyid~E~s~~~~~-----a~~~g~~~~~l~i~~~~~~e--~~~~~  132 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGE--QALEI  132 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHH--HHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH--HCCCeEEEEeCCCCccHHH-----HHHcCCChhheeeeCCCCHH--HHHHH
Confidence            456899999999999999988775311  1112578898887777442     34454332110   011112  44444


Q ss_pred             HHHHc-CCCeEEEEEeCC
Q 038944          255 LHEYL-MTKRYLNVIDDV  271 (334)
Q Consensus       255 l~~~L-~~kr~LlVlDdv  271 (334)
                      +.... .++--+||+|.+
T Consensus       133 ~~~l~~~~~~~lVVIDsl  150 (356)
T 1u94_A          133 CDALARSGAVDVIVVDSV  150 (356)
T ss_dssp             HHHHHHHTCCSEEEEECG
T ss_pred             HHHHHhccCCCEEEEcCH
Confidence            44333 234458999997

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.91  E-value=0.0039  Score=52.09  Aligned_cols=23  Identities=13%  Similarity=0.251  Sum_probs=21.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|+|+.|+|||||++.+...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHhh
Confidence            58999999999999999999863

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.90  E-value=0.016  Score=52.36  Aligned_cols=42  Identities=19%  Similarity=0.174  Sum_probs=36.0

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++|.+..++.+...+..+.    -+.++|.+|+|||+||+.+.+
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~----~vll~G~pGtGKT~la~~la~   68 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG----HILLEGVPGLAKTLSVNTLAK   68 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC----CEEEESCCCHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHcCC----eEEEECCCCCcHHHHHHHHHH
Confidence            458999999998888887642    478899999999999999988

>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=95.89  E-value=0.033  Score=50.27  Aligned_cols=84  Identities=6%  Similarity=0.030  Sum_probs=52.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCc--eeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHH-HH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHY--FDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMK-KI  253 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l-~~  253 (334)
                      .++-|.|.+|+|||||+-++....  ...  =..++|++....++..     .+++++......   ...+.+  +. ..
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~~~--~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E--~~~l~   99 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVSSY--MRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLE--QLRID   99 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHHH--HHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHH--HHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH--HhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHH--HHHHH
Confidence            378999999999999987776521  111  1357899888888764     367777653321   111222  43 33


Q ss_pred             HHHHH--c-CCCeEEEEEeCCC
Q 038944          254 ILHEY--L-MTKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~--L-~~kr~LlVlDdvw  272 (334)
                      .+...  + .++.-|||+|-|-
T Consensus       100 i~~~l~~i~~~~~~lvVIDSI~  121 (333)
T 3io5_A          100 MVNQLDAIERGEKVVVFIDSLG  121 (333)
T ss_dssp             HHHHHHTCCTTCCEEEEEECST
T ss_pred             HHHHHHHhhccCceEEEEeccc
Confidence            22222  3 4567899999984

>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=95.88  E-value=0.068  Score=47.76  Aligned_cols=24  Identities=17%  Similarity=0.218  Sum_probs=21.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..+++++|.+|+||||++..+..
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~  127 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAA  127 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            356999999999999999988864

>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=95.86  E-value=0.013  Score=53.84  Aligned_cols=87  Identities=17%  Similarity=0.038  Sum_probs=52.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-.++.|+|.+|+|||||+..+.....  ..=..++|++....++..     ..+.++......   ...+..  ++..
T Consensus        59 ~~G~iv~I~G~pGsGKTtLal~la~~~~--~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e--~~l~  129 (349)
T 2zr9_A           59 PRGRVIEIYGPESSGKTTVALHAVANAQ--AAGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGE--QALE  129 (349)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHH--HHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHH--hCCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHH--HHHH
Confidence            3456899999999999999988875311  111357888888777653     244454332210   111222  5555


Q ss_pred             HHHHHcC-CCeEEEEEeCCC
Q 038944          254 ILHEYLM-TKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L~-~kr~LlVlDdvw  272 (334)
                      .+..... .+--+||+|.+-
T Consensus       130 ~~~~l~~~~~~~lIVIDsl~  149 (349)
T 2zr9_A          130 IADMLVRSGALDIIVIDSVA  149 (349)
T ss_dssp             HHHHHHTTTCCSEEEEECGG
T ss_pred             HHHHHHhcCCCCEEEEcChH
Confidence            5554443 345589999973

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.86  E-value=0.0051  Score=51.80  Aligned_cols=24  Identities=17%  Similarity=0.079  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..+++|+|..|+|||||++.+..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~   28 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALAR   28 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            456999999999999999999976

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.84  E-value=0.0044  Score=50.95  Aligned_cols=23  Identities=13%  Similarity=0.319  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.|.++|+.|+||||+++.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999976

>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=95.84  E-value=0.0055  Score=50.59  Aligned_cols=23  Identities=4%  Similarity=0.130  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|++|+||||+++.+..
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.84  E-value=0.0045  Score=50.62  Aligned_cols=54  Identities=6%  Similarity=-0.046  Sum_probs=36.4

Q ss_pred             HHHHHcCCCeEEEEEeCCCCh---h----------------HHHHHHhhCCCC-CCCeEEEEecCChHHHhhcc
Q 038944          254 ILHEYLMTKRYLNVIDDVWNI---E----------------VCDIIREILPDN-QNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       254 ~l~~~L~~kr~LlVlDdvw~~---~----------------~w~~l~~~l~~~-~~gsrIivTTr~~~va~~~~  307 (334)
                      .+-..+..+.-+++||.-...   .                .+..+...+..- ..|.-||++|.+.+.+..+.
T Consensus        93 ~iAral~~~p~~lllDEPt~~Ld~~~~~R~~~~~~~~vi~~~~~~l~~~l~~l~~~g~tvi~vtH~~~~~~~~~  166 (171)
T 4gp7_A           93 EMAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQMKKSIKGLQREGFRYVYILNSPEEVEEVV  166 (171)
T ss_dssp             HHHHHTTCEEEEEEECCCHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHSTTHHHHTCSEEEEECSHHHHHHEE
T ss_pred             HHHHHcCCcEEEEEEeCCHHHHHHHHhcccCCCCCHHHHHHHHHHhhhhhhhHHhcCCcEEEEeCCHHHhhhhh
Confidence            455667778889999987643   2                345666666532 23767888899888776543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.84  E-value=0.0048  Score=51.71  Aligned_cols=24  Identities=21%  Similarity=0.232  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|+|+.|+|||||++.+..
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999999986

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.84  E-value=0.0045  Score=51.84  Aligned_cols=22  Identities=18%  Similarity=0.166  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+|+|+.|+||||+++.+..
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

>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=95.82  E-value=0.029  Score=51.44  Aligned_cols=97  Identities=6%  Similarity=0.044  Sum_probs=54.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCce----eeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc-------ccc-
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF----DCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS-------EIM-  244 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~-------~~~-  244 (334)
                      +.-.++.|+|.+|+|||||+..+..........    ..++|++....+....+ ..+.+..+......       ... 
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~  207 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFN  207 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCC
Confidence            345799999999999999999988642111111    23488877666654443 33444433221000       000 


Q ss_pred             hhhHHHHHHHHHHHcC------CCeEEEEEeCCCCh
Q 038944          245 DKNYEMKKIILHEYLM------TKRYLNVIDDVWNI  274 (334)
Q Consensus       245 ~~~~~~l~~~l~~~L~------~kr~LlVlDdvw~~  274 (334)
                      .....++...+...+.      .+.-+||||.+-..
T Consensus       208 ~~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          208 SNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             hHHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence            0111144445555553      46779999998643

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.81  E-value=0.0036  Score=52.42  Aligned_cols=24  Identities=13%  Similarity=0.219  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~   41 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEA   41 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999773

>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=95.80  E-value=0.0079  Score=55.60  Aligned_cols=46  Identities=11%  Similarity=0.101  Sum_probs=35.0

Q ss_pred             CeeechhhHHHHHHHHhc----------------------------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIE----------------------------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~----------------------------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|.+..++.|...+..                            .......+.++|++|+|||++|+.+.+.
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHH
Confidence            478998888888777620                            0112346889999999999999999983

>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=95.80  E-value=0.0054  Score=53.34  Aligned_cols=47  Identities=19%  Similarity=0.281  Sum_probs=33.0

Q ss_pred             CCCeeechhhHHHHHHHHhc--C---------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIE--G---------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~--~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..+.++.+....  .         ..... +.|+|.+|+|||||++.+.+.
T Consensus        15 ~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g-~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           15 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCCCCHHHHHHHHHHH
Confidence            34678887776666554321  1         11223 899999999999999999984

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.79  E-value=0.006  Score=50.80  Aligned_cols=25  Identities=20%  Similarity=0.198  Sum_probs=22.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..+|+|+|+.|+||||+++.+..
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999999987

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.79  E-value=0.0048  Score=51.40  Aligned_cols=21  Identities=19%  Similarity=0.428  Sum_probs=19.8

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|.|+.|+||||+++.+.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            689999999999999999987

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.77  E-value=0.0063  Score=51.12  Aligned_cols=25  Identities=12%  Similarity=0.082  Sum_probs=22.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+|+|+|+.|+||||+++.+..
T Consensus        19 ~~~~~i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           19 SKTFIIGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3457999999999999999999987

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.77  E-value=0.0054  Score=50.72  Aligned_cols=22  Identities=14%  Similarity=0.208  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|+.|+|||||++.+..
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

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.76  E-value=0.0057  Score=51.13  Aligned_cols=24  Identities=13%  Similarity=0.259  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|+.|+||||+++.+...
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999999873

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.75  E-value=0.0051  Score=50.80  Aligned_cols=22  Identities=14%  Similarity=0.286  Sum_probs=19.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|+|..|+|||||++.+...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999764

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=95.74  E-value=0.0051  Score=50.61  Aligned_cols=22  Identities=23%  Similarity=0.264  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|++|+||||+++.+.+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999976

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.74  E-value=0.0053  Score=49.72  Aligned_cols=25  Identities=20%  Similarity=0.275  Sum_probs=20.9

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..+|.|.|+.|+||||+++.+.+
T Consensus         5 ~~~~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            5 HHMQHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             ---CEEEEESCTTSSHHHHHHHHHH
T ss_pred             cccceEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999999987

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.69  E-value=0.0055  Score=52.11  Aligned_cols=22  Identities=18%  Similarity=0.226  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+|+|+.|+||||+++.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999976

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.69  E-value=0.0063  Score=53.00  Aligned_cols=25  Identities=4%  Similarity=0.036  Sum_probs=22.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+|+|.|+.|+||||+|+.+..
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999999977

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.68  E-value=0.0063  Score=51.40  Aligned_cols=24  Identities=13%  Similarity=0.268  Sum_probs=21.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|+.|+|||||++.+...
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhh
Confidence            468999999999999999999873

>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=95.67  E-value=0.015  Score=55.28  Aligned_cols=63  Identities=10%  Similarity=0.046  Sum_probs=38.3

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHH
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIK  232 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~  232 (334)
                      .++.|..-.. -..++|+|.+|+|||||++.+..+... .+-+.++++.+.+.. ...+++.++.+
T Consensus       141 ~ID~L~pi~k-Gq~~~i~G~sGvGKTtL~~~l~~~~~~-~~~~i~V~~~iGerttev~el~~~l~~  204 (473)
T 1sky_E          141 VVDLLAPYIK-GGKIGLFGGAGVGKTVLIQELIHNIAQ-EHGGISVFAGVGERTREGNDLYHEMKD  204 (473)
T ss_dssp             HHHHHSCEET-TCEEEEECCSSSCHHHHHHHHHHHHHH-HTCCCEEEEEESSCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhcc-CCEEEEECCCCCCccHHHHHHHhhhhh-ccCcEEEEeeeccCchHHHHHHHHhhh
Confidence            4555543111 125899999999999999988764221 122445677777654 34455555543

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.66  E-value=0.011  Score=54.16  Aligned_cols=43  Identities=23%  Similarity=0.278  Sum_probs=31.0

Q ss_pred             eechhhHHHHHHHHhc--CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          159 VGLDDRMEELLDLLIE--GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       159 vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      |+.+.-.+.+++.+..  .......|.++|++|+||||+++.+..
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHH
Confidence            3445556666666643  234466799999999999999998765

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.66  E-value=0.036  Score=52.71  Aligned_cols=65  Identities=14%  Similarity=0.134  Sum_probs=44.0

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHH
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKF  233 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~  233 (334)
                      +.++.|..=. .-.-++|+|..|+|||+|++.+.+.. .+.+-+.++++-+.+.. .+.+++.++.+.
T Consensus       142 r~ID~l~pig-kGQr~~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          142 KVVDLLAPYA-KGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCEE-TTCEEEEEECTTSSHHHHHHHHHHHT-TTTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEecccccc-cCCeeeeecCCCCChHHHHHHHHHhh-HhhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            4566665311 12368999999999999999888742 12334567788888765 456777777765

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=95.66  E-value=0.0066  Score=50.92  Aligned_cols=22  Identities=23%  Similarity=0.234  Sum_probs=20.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+|+|+.|+||||+++.+..
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            4799999999999999999975

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=95.62  E-value=0.0054  Score=50.28  Aligned_cols=23  Identities=17%  Similarity=0.335  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|+|++|+||||+++.+.+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~   33 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELAS   33 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHH
Confidence            45788999999999999999986

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.62  E-value=0.0076  Score=50.38  Aligned_cols=26  Identities=23%  Similarity=0.318  Sum_probs=22.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....+|.|.|+.|+||||+++.+.+.
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34679999999999999999999873

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.60  E-value=0.007  Score=50.07  Aligned_cols=23  Identities=9%  Similarity=0.215  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|+.|+||||+++.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=95.59  E-value=0.0072  Score=49.89  Aligned_cols=24  Identities=17%  Similarity=0.112  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|.|+|+.|+||||+++.+.+
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999999987

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.59  E-value=0.0073  Score=49.80  Aligned_cols=23  Identities=22%  Similarity=0.221  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|++|+||||+|+.+.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999876

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.57  E-value=0.0059  Score=51.28  Aligned_cols=25  Identities=12%  Similarity=0.317  Sum_probs=21.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.|+|++|+|||||++.+...
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3568999999999999999999873

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.56  E-value=0.0054  Score=51.44  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=20.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++++|+|+.|+|||||++.+..
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            5789999999999999999975

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.56  E-value=0.0054  Score=50.08  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=20.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|.|++|+||||+|+.+..
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3689999999999999999987

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.55  E-value=0.0072  Score=52.82  Aligned_cols=23  Identities=13%  Similarity=0.032  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++.|+|+.|+||||||+.+...
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhc
Confidence            57899999999999999999763

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=95.55  E-value=0.0072  Score=53.40  Aligned_cols=49  Identities=18%  Similarity=0.264  Sum_probs=34.4

Q ss_pred             CCCCCeeechhhHHHHHHHHhc--C---------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE--G---------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~--~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-.+++|.+..+.++.+....  .         ..... +.|+|.+|+|||||++.+.+.
T Consensus        37 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~~   96 (278)
T 1iy2_A           37 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   96 (278)
T ss_dssp             CCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHHH
Confidence            3445688988777666554421  1         11223 889999999999999999984

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.55  E-value=0.011  Score=51.47  Aligned_cols=39  Identities=15%  Similarity=0.149  Sum_probs=28.1

Q ss_pred             hHHHHHHHHhcC---CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          164 RMEELLDLLIEG---PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       164 ~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+.++..+..+   .....+|.++|++|+||||+|+.+...
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~i~l~G~~GsGKSTla~~L~~~   55 (253)
T 2p5t_B           14 ALARNLRSLTRGKKSSKQPIAILLGGQSGAGKTTIHRIKQKE   55 (253)
T ss_dssp             HHHHHHHHHHTTCCCCSSCEEEEEESCGGGTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCCcccCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            334444444432   234578999999999999999999873

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.54  E-value=0.0072  Score=52.35  Aligned_cols=23  Identities=26%  Similarity=0.232  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+++|+|+.|+|||||++.+.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999984

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=95.53  E-value=0.0073  Score=49.48  Aligned_cols=24  Identities=8%  Similarity=0.023  Sum_probs=21.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+++.|+|..|+|||||+..+..
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~   26 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVA   26 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999887

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.52  E-value=0.0054  Score=49.08  Aligned_cols=25  Identities=8%  Similarity=0.044  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-..+.|+|..|+|||||++.+++.
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~   59 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQ   59 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999874

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=95.52  E-value=0.0079  Score=52.70  Aligned_cols=23  Identities=13%  Similarity=0.364  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|++|+||||+|+.+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            56899999999999999999986

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.51  E-value=0.0076  Score=54.51  Aligned_cols=24  Identities=13%  Similarity=0.167  Sum_probs=20.6

Q ss_pred             CCceEEEEEccCCccHHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .+.+||+|.|-|||||||.+-.+.
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA   69 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLS   69 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHH
Confidence            357999999999999999887775

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=95.50  E-value=0.039  Score=52.67  Aligned_cols=103  Identities=14%  Similarity=0.167  Sum_probs=61.3

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCC------CCc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPS------SRL  240 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~------~~~  240 (334)
                      .++.|..=. +-.-++|+|..|+|||+|++.+.++. .+.|-++++++-+.+.. .+.+++.++.+.-...      ...
T Consensus       155 vID~l~pig-kGqr~gIfgg~GvGKT~L~~~l~~~~-a~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rt  232 (498)
T 1fx0_B          155 VVNLLAPYR-RGGKIGLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKV  232 (498)
T ss_dssp             THHHHSCCC-TTCCEEEEECSSSSHHHHHHHHHHHT-TTTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCE
T ss_pred             Eeeeecccc-cCCeEEeecCCCCCchHHHHHHHHHH-HhhCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccce
Confidence            455554321 12358999999999999999888742 22345678888888766 4667777776542221      000


Q ss_pred             c---ccchh------hHHHHHHHHHHHc---CCCeEEEEEeCCC
Q 038944          241 S---EIMDK------NYEMKKIILHEYL---MTKRYLNVIDDVW  272 (334)
Q Consensus       241 ~---~~~~~------~~~~l~~~l~~~L---~~kr~LlVlDdvw  272 (334)
                      .   ..++.      .--...-.+-+++   +|+..|+++||+-
T Consensus       233 vvV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          233 ALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             EEEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence            0   00110      0002233344555   4689999999984

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=95.49  E-value=0.012  Score=51.11  Aligned_cols=36  Identities=14%  Similarity=-0.028  Sum_probs=26.2

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++..-.........+|.|.|++|+||||+|+.+.+
T Consensus        16 ~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           16 NELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             HHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            334333333233567899999999999999999976

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.48  E-value=0.0082  Score=49.29  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.+.|++|+||||+++.+.+
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999976

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.48  E-value=0.004  Score=57.78  Aligned_cols=53  Identities=11%  Similarity=-0.152  Sum_probs=32.8

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCC-CCceeeEEEEEcCCCC
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYV-KHYFDCHAWVPGTYPY  221 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~  221 (334)
                      ++++.+..=. .-..++|+|.+|+|||||++.+.+.... ...+.| +++-+.+..
T Consensus       163 raID~~~pi~-rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~-I~~lIGER~  216 (422)
T 3ice_A          163 RVLDLASPIG-RGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVL-MVLLIDERP  216 (422)
T ss_dssp             HHHHHHSCCB-TTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEE-EEEEESSCH
T ss_pred             eeeeeeeeec-CCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeE-EEEEecCCh
Confidence            4555555422 1247899999999999999988762110 112344 356677654

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.48  E-value=0.0092  Score=49.16  Aligned_cols=24  Identities=21%  Similarity=0.098  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|.+.|++|+||||+++.+..
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~   35 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLAD   35 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            457899999999999999999987

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=95.47  E-value=0.012  Score=53.47  Aligned_cols=25  Identities=16%  Similarity=0.139  Sum_probs=22.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..+++|+|..|+||||+++.+..
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag  151 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLAN  151 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3468999999999999999998865

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.46  E-value=0.014  Score=51.93  Aligned_cols=25  Identities=8%  Similarity=0.182  Sum_probs=22.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+|.|.|++|+||||+|+.+..
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3457899999999999999999987

>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=95.45  E-value=0.043  Score=51.28  Aligned_cols=94  Identities=6%  Similarity=-0.022  Sum_probs=52.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc----c---ccchh
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL----S---EIMDK  246 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~----~---~~~~~  246 (334)
                      .-.++.|+|.+|+|||||+..+.-......    .-...+|+.....++...+. .+.+.++.....    .   ...+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~-~~a~~~gl~~~~vleni~~~~~~~~  255 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLV-SIAQRFGLDPDDALNNVAYARAYNA  255 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHH-HHHHHcCCChHhHhhcEEEeccCCh
Confidence            346999999999999999997652211111    22357888877777766543 355665542110    0   00111


Q ss_pred             h-HHHHHHHHHHHc-CCCeEEEEEeCCC
Q 038944          247 N-YEMKKIILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       247 ~-~~~l~~~l~~~L-~~kr~LlVlDdvw  272 (334)
                      . ...+...+.+.+ ..+--+||+|.+-
T Consensus       256 ~~~~~~l~~~~~~l~~~~~~llVIDs~t  283 (400)
T 3lda_A          256 DHQLRLLDAAAQMMSESRFSLIVVDSVM  283 (400)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETGG
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEecchh
Confidence            0 002333333333 2456789999974

>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=95.44  E-value=0.084  Score=49.86  Aligned_cols=24  Identities=8%  Similarity=0.191  Sum_probs=21.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..||.++|.+|+||||++..+..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            468999999999999999887764

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=95.43  E-value=0.011  Score=49.50  Aligned_cols=51  Identities=14%  Similarity=0.033  Sum_probs=30.5

Q ss_pred             HHHHHHHHHcCCCeE-EEEEeCCCCh-----hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          250 MKKIILHEYLMTKRY-LNVIDDVWNI-----EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       250 ~l~~~l~~~L~~kr~-LlVlDdvw~~-----~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      ......++.+.+.+| |||||++-..     -..+.+...+.......-||+|+|..
T Consensus       107 ~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          107 AVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            455566667765555 9999998332     22333444333333345599999975

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.43  E-value=0.0081  Score=50.59  Aligned_cols=23  Identities=17%  Similarity=0.095  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|+|||||++.+..
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35899999999999999999875

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.42  E-value=0.0086  Score=50.13  Aligned_cols=23  Identities=13%  Similarity=-0.023  Sum_probs=21.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+|.|.|++|+||||+++.+.+.
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            68999999999999999999874

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.42  E-value=0.0094  Score=53.87  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=22.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+++|+|..|+|||||++.+..
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHh
Confidence            3457999999999999999999876

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=95.42  E-value=0.0059  Score=50.20  Aligned_cols=22  Identities=14%  Similarity=0.154  Sum_probs=20.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3689999999999999999977

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=95.40  E-value=0.009  Score=49.14  Aligned_cols=23  Identities=22%  Similarity=0.250  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|+.|+||||+++.+.+
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.39  E-value=0.0081  Score=49.82  Aligned_cols=23  Identities=13%  Similarity=0.225  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|++|+||||+++.+..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999987

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.39  E-value=0.017  Score=48.98  Aligned_cols=25  Identities=12%  Similarity=0.216  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+|.|+|.+|+|||||+..+...
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4688999999999999999888764

>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=95.36  E-value=0.032  Score=51.67  Aligned_cols=110  Identities=10%  Similarity=0.106  Sum_probs=59.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEE-EEEcCCCCCHHHHHHHHHHHhCCCCC-ccc---cchhhHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHA-WVPGTYPYDADQMLDIVIKFLMPSSR-LSE---IMDKNYEMKK  252 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~-wv~vs~~~~~~~il~~il~~~~~~~~-~~~---~~~~~~~~l~  252 (334)
                      .-.+++|+|..|+|||||.+.+..-  ........+ ++.-+-.+.           +..... -..   ..+..  .+.
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~--~~~~~~g~I~~~e~~~e~~-----------~~~~~~~v~Q~~~g~~~~--~~~  199 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDY--INQTKSYHIITIEDPIEYV-----------FKHKKSIVNQREVGEDTK--SFA  199 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHH--HHHHSCCEEEEEESSCCSC-----------CCCSSSEEEEEEBTTTBS--CSH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh--cCcCCCcEEEEecccHhhh-----------hccCceEEEeeecCCCHH--HHH
Confidence            3568999999999999999988752  111101222 222111110           000000 000   00112  344


Q ss_pred             HHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          253 IILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       253 ~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      ..+...|....=+|++|.+-+.+.+..+....   ..|.-|+.|+...+++..
T Consensus       200 ~~l~~~L~~~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~~~~~  249 (372)
T 2ewv_A          200 DALRAALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTAIDT  249 (372)
T ss_dssp             HHHHHHTTSCCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCSHHHH
T ss_pred             HHHHHHhhhCcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcchHHHH
Confidence            56667776666689999998776554433332   236668888887765543

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=95.35  E-value=0.007  Score=49.03  Aligned_cols=22  Identities=9%  Similarity=0.151  Sum_probs=20.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|.|+.|+||||+|+.+.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999987

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=95.35  E-value=0.0054  Score=51.61  Aligned_cols=22  Identities=14%  Similarity=0.132  Sum_probs=20.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|.|..|+||||+++.+..
T Consensus         1 ~~I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            1 MLIAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             CEEEEEEEEEEEHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3789999999999999999876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.34  E-value=0.0087  Score=49.34  Aligned_cols=21  Identities=19%  Similarity=0.226  Sum_probs=19.8

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +|+|.|+.|+||||+++.+.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.34  E-value=0.0064  Score=49.78  Aligned_cols=24  Identities=17%  Similarity=0.167  Sum_probs=17.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~   28 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHER   28 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999873

>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=95.34  E-value=0.017  Score=53.03  Aligned_cols=37  Identities=19%  Similarity=0.078  Sum_probs=28.2

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+.+.+........+|+|+|.+|+|||||+..+..
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            3445555554445678999999999999999988854

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.33  E-value=0.011  Score=51.30  Aligned_cols=24  Identities=4%  Similarity=0.047  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++|.|..|+|||||++.+..
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999876

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.32  E-value=0.011  Score=50.53  Aligned_cols=26  Identities=15%  Similarity=0.233  Sum_probs=23.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+||.|.|++|+||||.|+.+.+.
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            46789999999999999999999873

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.29  E-value=0.0094  Score=48.04  Aligned_cols=21  Identities=5%  Similarity=0.029  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|.|+.|+||||+++.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.26  E-value=0.053  Score=51.19  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=21.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++|.++|.+|+||||++..+..
T Consensus        98 ~~~~vI~ivG~~GvGKTT~a~~LA~  122 (433)
T 2xxa_A           98 QPPAVVLMAGLQGAGKTTSVGKLGK  122 (433)
T ss_dssp             SSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3468999999999999999888763

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.25  E-value=0.0078  Score=51.29  Aligned_cols=24  Identities=21%  Similarity=0.313  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999999863

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=95.23  E-value=0.012  Score=49.07  Aligned_cols=23  Identities=22%  Similarity=0.141  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|++|+||||+|+.+..
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999976

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.23  E-value=0.012  Score=47.63  Aligned_cols=24  Identities=13%  Similarity=0.228  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++++|..|.|||||.+.+..
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g   55 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            346999999999999999999986

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.23  E-value=0.012  Score=49.60  Aligned_cols=39  Identities=21%  Similarity=0.195  Sum_probs=27.8

Q ss_pred             hhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          162 DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       162 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+..+.+...+..  ....++.|+|.+|+|||||+..+...
T Consensus        15 ~~~~~~~~~~~~~--~~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           15 KRLAEKNREALRE--SGTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             HHHHHHHHHHHHH--HTCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcc--cCceEEEEEcCCCCCHHHHHHHHHHH
Confidence            3334444444432  24789999999999999999888764

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=95.22  E-value=0.0087  Score=54.37  Aligned_cols=46  Identities=17%  Similarity=0.146  Sum_probs=32.8

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|.+..+..+...+....  ..-+-++|.+|+|||+||+.+.+.
T Consensus        23 f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           23 FSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             chhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHHh
Confidence            3458898876665544443322  123889999999999999999874

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.22  E-value=0.019  Score=52.03  Aligned_cols=25  Identities=12%  Similarity=0.062  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+++|.|..|+|||||++.+..
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999999865

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.21  E-value=0.011  Score=51.66  Aligned_cols=23  Identities=13%  Similarity=0.179  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+|+|+|+.|+||||+++.+..
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999985

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.19  E-value=0.0066  Score=49.82  Aligned_cols=22  Identities=9%  Similarity=0.132  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++++|+|..|+|||||++.+..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~   24 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMP   24 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999876

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=95.14  E-value=0.011  Score=50.04  Aligned_cols=23  Identities=17%  Similarity=0.140  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...|.+.|++|+||||+++.+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999999987

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.14  E-value=0.012  Score=49.37  Aligned_cols=23  Identities=9%  Similarity=0.008  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|+.|+||||+++.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>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=95.14  E-value=0.013  Score=52.03  Aligned_cols=24  Identities=25%  Similarity=0.188  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999874

>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=95.14  E-value=0.013  Score=48.90  Aligned_cols=25  Identities=20%  Similarity=0.187  Sum_probs=22.6

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+-.+|+|.|+.|+||||+++.+.+
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999999887

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=95.13  E-value=0.02  Score=54.25  Aligned_cols=47  Identities=13%  Similarity=0.166  Sum_probs=36.0

Q ss_pred             CCeeechhhHHHHHHHHhcC------------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG------------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|.+..++.+...+...            ....+-+.++|++|+||||+|+.+...
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~   73 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            34899998888887766321            123456889999999999999999883

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.12  E-value=0.011  Score=49.62  Aligned_cols=25  Identities=8%  Similarity=0.262  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-+++.|+|+.|+|||||++.+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhh
Confidence            3568999999999999999999863

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.10  E-value=0.0094  Score=49.63  Aligned_cols=21  Identities=19%  Similarity=0.321  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|+|++|+|||||++.+..
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            477999999999999999987

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=95.08  E-value=0.013  Score=52.68  Aligned_cols=24  Identities=17%  Similarity=0.188  Sum_probs=21.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..+++|+|.+|+|||||++.+..
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            456999999999999999998863

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.08  E-value=0.011  Score=49.47  Aligned_cols=23  Identities=9%  Similarity=-0.145  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|+.|+||||+++.+.+
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.07  E-value=0.025  Score=51.21  Aligned_cols=24  Identities=17%  Similarity=0.286  Sum_probs=21.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++|+|.+|+||||++..+..
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~  127 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMAN  127 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999988864

>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=95.04  E-value=0.058  Score=50.90  Aligned_cols=24  Identities=17%  Similarity=0.212  Sum_probs=21.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..++.++|.+|+||||++..+..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~  119 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAY  119 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999888763

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.03  E-value=0.012  Score=50.20  Aligned_cols=23  Identities=22%  Similarity=0.255  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...|.|.|++|+||||+++.+.+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>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=95.03  E-value=0.027  Score=50.65  Aligned_cols=25  Identities=16%  Similarity=0.106  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+++|+|..|+|||||++.+..
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3457999999999999999999886

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=95.01  E-value=0.013  Score=50.17  Aligned_cols=24  Identities=8%  Similarity=0.174  Sum_probs=21.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|+.|+|||||.+.+...
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcc
Confidence            468999999999999999999873

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=94.97  E-value=0.016  Score=47.37  Aligned_cols=23  Identities=13%  Similarity=-0.015  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+|.+.|+.|+||||+++.+..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>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=94.95  E-value=0.015  Score=49.36  Aligned_cols=48  Identities=8%  Similarity=0.183  Sum_probs=31.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCC----CceeeEEEEEcCCCCCHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVK----HYFDCHAWVPGTYPYDADQ  225 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~  225 (334)
                      .-.+++|+|..|+|||||++.+.......    ..-...+|+.-...+....
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~   75 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER   75 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH
Confidence            34699999999999999999997521111    0123467776655454433

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.95  E-value=0.014  Score=50.67  Aligned_cols=24  Identities=21%  Similarity=0.264  Sum_probs=21.6

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .. .+++|+|..|+|||||.+.+..
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~G   46 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHT
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhC
Confidence            35 7999999999999999999975

>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=94.95  E-value=0.016  Score=48.87  Aligned_cols=23  Identities=13%  Similarity=-0.039  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.|.|+.|+||||+++.+..
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~   47 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEH   47 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999876

>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=94.92  E-value=0.014  Score=48.68  Aligned_cols=24  Identities=13%  Similarity=-0.051  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+|.|.|+.|+||||+++.+.+.
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHT
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH
Confidence            358999999999999999999883

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=94.92  E-value=0.075  Score=48.26  Aligned_cols=108  Identities=10%  Similarity=0.046  Sum_probs=58.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccc--hhhHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIM--DKNYEMKKIILHE  257 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~--~~~~~~l~~~l~~  257 (334)
                      .+++|+|..|.|||||.+.+..-....   ...+.+.-...+...           .........  ...  .....+..
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~---~g~i~i~~~~e~~~~-----------~~~~~i~~~~ggg~--~~r~~la~  235 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKE---ERIISIEDTEEIVFK-----------HHKNYTQLFFGGNI--TSADCLKS  235 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTT---SCEEEEESSCCCCCS-----------SCSSEEEEECBTTB--CHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCC---CcEEEECCeeccccc-----------cchhEEEEEeCCCh--hHHHHHHH
Confidence            479999999999999999998732111   123333222111100           000000000  111  33345556


Q ss_pred             HcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhc
Q 038944          258 YLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       258 ~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~  306 (334)
                      .|..+.=+|+||.+-+.+.++.+... ..+  +.-+|+||...++...+
T Consensus       236 aL~~~p~ilildE~~~~e~~~~l~~~-~~g--~~tvi~t~H~~~~~~~~  281 (330)
T 2pt7_A          236 CLRMRPDRIILGELRSSEAYDFYNVL-CSG--HKGTLTTLHAGSSEEAF  281 (330)
T ss_dssp             HTTSCCSEEEECCCCSTHHHHHHHHH-HTT--CCCEEEEEECSSHHHHH
T ss_pred             HhhhCCCEEEEcCCChHHHHHHHHHH-hcC--CCEEEEEEcccHHHHHh
Confidence            67667778899999887766655433 222  22267777766655443

>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=94.92  E-value=0.017  Score=48.92  Aligned_cols=23  Identities=22%  Similarity=0.271  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|+|.|+.|+||||+++.+..
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            36899999999999999999975

>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=94.91  E-value=0.025  Score=50.92  Aligned_cols=24  Identities=17%  Similarity=0.234  Sum_probs=21.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.|+|.+|+||||++..+..
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~  126 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAK  126 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHH
Confidence            467999999999999999988875

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=94.91  E-value=0.012  Score=49.89  Aligned_cols=23  Identities=13%  Similarity=-0.083  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...|.|.|++|+||||+++.+.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999987

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.91  E-value=0.012  Score=49.09  Aligned_cols=21  Identities=19%  Similarity=0.259  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +++|+|..|+|||||.+.+..
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g   23 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHh
Confidence            689999999999999998875

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=94.90  E-value=0.014  Score=50.51  Aligned_cols=23  Identities=17%  Similarity=0.072  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            35899999999999999999975

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=94.90  E-value=0.019  Score=59.45  Aligned_cols=48  Identities=15%  Similarity=0.020  Sum_probs=30.5

Q ss_pred             CCCeEEEEEeCCCCh---hHH----HHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          260 MTKRYLNVIDDVWNI---EVC----DIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       260 ~~kr~LlVlDdvw~~---~~w----~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      ..++-|++||..-..   ..-    ..+...+.. ..|+.||++|...+++..+..
T Consensus       739 a~~~sLlLLDEp~~GlD~~~~~~i~~~il~~l~~-~~g~~vl~aTH~~el~~lad~  793 (934)
T 3thx_A          739 ATKDSLIIIDELGRGTSTYDGFGLAWAISEYIAT-KIGAFCMFATHFHELTALANQ  793 (934)
T ss_dssp             CCTTCEEEEESCSCSSCHHHHHHHHHHHHHHHHH-TTCCEEEEEESCGGGGGGGGT
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHHHHHHHHh-cCCCEEEEEcCcHHHHHHhcc
Confidence            466789999999542   111    222222321 248899999999998876543

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.89  E-value=0.013  Score=50.15  Aligned_cols=22  Identities=18%  Similarity=0.067  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|+|||||.+.+..
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~G   52 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGL   52 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            5899999999999999999975

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.89  E-value=0.026  Score=51.93  Aligned_cols=24  Identities=21%  Similarity=0.263  Sum_probs=21.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++|+|..|+||||+++.+..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHh
Confidence            457999999999999999998864

>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=94.79  E-value=0.029  Score=53.68  Aligned_cols=24  Identities=17%  Similarity=0.254  Sum_probs=21.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|+|..|+|||||++.+..
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHH
Confidence            457999999999999999998865

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.79  E-value=0.0098  Score=50.93  Aligned_cols=23  Identities=17%  Similarity=0.234  Sum_probs=16.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHH-c
Q 038944          179 LSVVVILDSIGLDKAAFAGEAY-N  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~-~  201 (334)
                      -.+++|+|+.|+|||||++.+. .
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~   50 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEK   50 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC-
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            3589999999999999999998 5

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.78  E-value=0.018  Score=51.72  Aligned_cols=24  Identities=21%  Similarity=0.263  Sum_probs=21.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++|+|..|+||||+++.+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357999999999999999998864

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=94.78  E-value=0.016  Score=48.88  Aligned_cols=21  Identities=19%  Similarity=0.243  Sum_probs=19.1

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999976

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=94.76  E-value=0.017  Score=47.52  Aligned_cols=24  Identities=8%  Similarity=0.145  Sum_probs=21.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++.|+|..|+|||||+..+...
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHh
Confidence            579999999999999999998863

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.70  E-value=0.014  Score=49.46  Aligned_cols=22  Identities=23%  Similarity=0.147  Sum_probs=20.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|+|||||.+.+..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~G   44 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAV   44 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999875

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.68  E-value=0.016  Score=50.07  Aligned_cols=23  Identities=13%  Similarity=0.300  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999986

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.67  E-value=0.016  Score=50.91  Aligned_cols=23  Identities=26%  Similarity=0.218  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999975

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.64  E-value=0.014  Score=50.98  Aligned_cols=22  Identities=9%  Similarity=0.128  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|+|+.|+||||+++.+..
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

>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=94.64  E-value=0.018  Score=48.58  Aligned_cols=21  Identities=14%  Similarity=0.166  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999976

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=94.61  E-value=0.019  Score=47.93  Aligned_cols=21  Identities=19%  Similarity=0.139  Sum_probs=20.0

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +|+|.|+.|+||||+++.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            899999999999999999976

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.61  E-value=0.017  Score=51.18  Aligned_cols=22  Identities=23%  Similarity=0.291  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|+.|+|||||.+.+..
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            5899999999999999999975

>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=94.59  E-value=0.043  Score=51.63  Aligned_cols=24  Identities=13%  Similarity=0.059  Sum_probs=21.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.++|.+|+||||++..+..
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~  120 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLAL  120 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999988864

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.59  E-value=0.017  Score=49.95  Aligned_cols=22  Identities=14%  Similarity=0.229  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5899999999999999999975

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.58  E-value=0.019  Score=50.07  Aligned_cols=22  Identities=14%  Similarity=0.170  Sum_probs=20.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5899999999999999999987

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.58  E-value=0.017  Score=50.51  Aligned_cols=23  Identities=17%  Similarity=0.186  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999975

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.54  E-value=0.017  Score=49.01  Aligned_cols=23  Identities=9%  Similarity=0.069  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...|.|.|++|+||||+++.+.+
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999999977

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.53  E-value=0.02  Score=49.70  Aligned_cols=23  Identities=13%  Similarity=0.059  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999974

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=94.53  E-value=0.12  Score=47.85  Aligned_cols=53  Identities=13%  Similarity=-0.108  Sum_probs=33.4

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCC-CCceeeEEEEEcCCC
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYV-KHYFDCHAWVPGTYP  220 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~  220 (334)
                      -++++.|..=.. -.-++|+|.+|+|||+|++.+.+.... ...+.| +++-+.+.
T Consensus       163 iraID~l~Pigr-GQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~-V~~lIGER  216 (427)
T 3l0o_A          163 TRLIDLFAPIGK-GQRGMIVAPPKAGKTTILKEIANGIAENHPDTIR-IILLIDER  216 (427)
T ss_dssp             HHHHHHHSCCBT-TCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSEE-EEEECSCC
T ss_pred             chhhhhcccccC-CceEEEecCCCCChhHHHHHHHHHHhhcCCCeEE-EEEEeccC
Confidence            356777764221 236799999999999999988773111 122343 45666654

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.51  E-value=0.076  Score=50.72  Aligned_cols=109  Identities=14%  Similarity=0.065  Sum_probs=58.6

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHH-HHHHccCCCCCcee-eEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--c
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFA-GEAYNSSYVKHYFD-CHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--E  242 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~-~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~  242 (334)
                      .++.|..=. .-.-++|+|..|+|||+|| ..+.+..    +-+ .++++-+.+.. .+.++..++.+.-.......  .
T Consensus       152 aID~l~Pig-rGQR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~a  226 (502)
T 2qe7_A          152 AIDSMIPIG-RGQRELIIGDRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTA  226 (502)
T ss_dssp             HHHHSSCCB-TTCBCEEEECSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEE
T ss_pred             ecccccccc-cCCEEEEECCCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEE
Confidence            455554311 1124789999999999995 6777743    234 34677777765 45566666655322111100  0


Q ss_pred             cchhh--HH----HHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHH
Q 038944          243 IMDKN--YE----MKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       243 ~~~~~--~~----~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                      ..+..  ..    ...-.+-+++  +|+..||++||+-.- ..+..+.
T Consensus       227 tad~p~~~r~~a~~~a~tiAEyfrd~G~dVLl~~Dsltr~A~A~REis  274 (502)
T 2qe7_A          227 SASEPAPLLYLAPYAGCAMGEYFMYKGKHALVVYDDLSKQAAAYRELS  274 (502)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEecHHHHHHHHHHHH
Confidence            11110  00    1112233333  689999999998432 4444443

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.51  E-value=0.019  Score=50.56  Aligned_cols=23  Identities=26%  Similarity=0.238  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHc
Confidence            45899999999999999999975

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.49  E-value=0.019  Score=49.30  Aligned_cols=24  Identities=13%  Similarity=0.119  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999863

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.48  E-value=0.019  Score=50.60  Aligned_cols=23  Identities=17%  Similarity=0.148  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            35899999999999999999975

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.46  E-value=0.021  Score=50.33  Aligned_cols=23  Identities=17%  Similarity=0.173  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999987

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.45  E-value=0.02  Score=49.88  Aligned_cols=22  Identities=18%  Similarity=0.203  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            5899999999999999999975

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.41  E-value=0.017  Score=49.21  Aligned_cols=22  Identities=18%  Similarity=0.208  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~G   57 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTIST   57 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999976

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.39  E-value=0.021  Score=50.07  Aligned_cols=23  Identities=9%  Similarity=-0.003  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999975

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.37  E-value=0.021  Score=50.48  Aligned_cols=23  Identities=22%  Similarity=0.177  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999975

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=94.37  E-value=0.1  Score=49.96  Aligned_cols=98  Identities=14%  Similarity=0.104  Sum_probs=54.2

Q ss_pred             EEEEEccCCccHHHHH-HHHHccCCCCCcee-eEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchh----hH--H
Q 038944          181 VVVILDSIGLDKAAFA-GEAYNSSYVKHYFD-CHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDK----NY--E  249 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~-~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~----~~--~  249 (334)
                      -++|+|..|+|||+|| ..+.+..  .  -+ .++++-+.+.. .+.++..++.+.-.......  ...+.    .+  -
T Consensus       177 R~~I~g~~g~GKT~Lal~~I~~~~--~--~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~  252 (515)
T 2r9v_A          177 RELIIGDRQTGKTAIAIDTIINQK--G--QGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIAP  252 (515)
T ss_dssp             BEEEEEETTSSHHHHHHHHHHTTT--T--TTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHHH
T ss_pred             EEEEEcCCCCCccHHHHHHHHHhh--c--CCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHHH
Confidence            5789999999999995 6777743  2  34 34677777765 45566666654211100000  00000    00  0


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCCC-hhHHHHHHh
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVWN-IEVCDIIRE  282 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw~-~~~w~~l~~  282 (334)
                      ...-.+-+++  +|+..||++||+-. ...+..+..
T Consensus       253 ~~a~tiAEyfrd~G~dVLli~DslTr~A~A~REisl  288 (515)
T 2r9v_A          253 YAGCAMGEYFAYSGRDALVVYDDLSKHAVAYRQLSL  288 (515)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEEETHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcEEEEeccHHHHHHHHHHHhh
Confidence            1122233333  68999999999843 245555443

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.35  E-value=0.021  Score=50.08  Aligned_cols=23  Identities=17%  Similarity=0.248  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999975

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.33  E-value=0.024  Score=46.86  Aligned_cols=24  Identities=21%  Similarity=0.304  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|+|..|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            457899999999999999998864

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.30  E-value=0.036  Score=44.37  Aligned_cols=23  Identities=4%  Similarity=0.107  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++|+|.+|+|||||...+...
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            56899999999999999999864

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.29  E-value=0.022  Score=50.13  Aligned_cols=23  Identities=9%  Similarity=0.098  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999975

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=94.29  E-value=0.022  Score=49.61  Aligned_cols=22  Identities=9%  Similarity=0.229  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        27 e~~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999976

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.29  E-value=0.026  Score=48.41  Aligned_cols=25  Identities=12%  Similarity=-0.035  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+|+|.|+.|+||||+++.+..
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4566899999999999999999886

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=94.28  E-value=0.039  Score=51.14  Aligned_cols=35  Identities=14%  Similarity=0.231  Sum_probs=26.0

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++-+.-.-+.-.+++|+|++|+|||||++.+..
T Consensus       157 ~~l~~~~~~i~~~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          157 DFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             HHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHhcccccCCCCEEEEECCCCCCHHHHHHHHHh
Confidence            33333333334456999999999999999999987

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.26  E-value=0.031  Score=44.05  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +-|.++|.+|+|||||...+.+.
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999998764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=94.25  E-value=0.023  Score=49.61  Aligned_cols=22  Identities=14%  Similarity=0.267  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|+|||||.+.+..
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~G   53 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLG   53 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5899999999999999999986

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.24  E-value=0.025  Score=51.54  Aligned_cols=22  Identities=18%  Similarity=0.220  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|.|+.|+||||||..+..
T Consensus         8 ~lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHH
Confidence            5899999999999999999987

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=94.24  E-value=0.027  Score=48.22  Aligned_cols=24  Identities=21%  Similarity=0.118  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|.+.|+.|+||||+|+.+.+.
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            457999999999999999999873

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=94.24  E-value=0.13  Score=47.08  Aligned_cols=25  Identities=16%  Similarity=0.231  Sum_probs=22.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....++++|.+|+|||||...+...
T Consensus       166 ~~~~v~lvG~~gvGKSTLin~L~~~  190 (357)
T 2e87_A          166 EIPTVVIAGHPNVGKSTLLKALTTA  190 (357)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHCSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999998764

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=94.23  E-value=0.025  Score=47.71  Aligned_cols=21  Identities=14%  Similarity=0.071  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|.|++|+||||+++.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999977

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.22  E-value=0.023  Score=50.40  Aligned_cols=23  Identities=9%  Similarity=-0.021  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999975

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.21  E-value=0.025  Score=48.15  Aligned_cols=21  Identities=14%  Similarity=0.177  Sum_probs=19.4

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.|.|+.|+||||+++.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999976

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=94.20  E-value=0.035  Score=45.30  Aligned_cols=26  Identities=12%  Similarity=0.065  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .....|.|+|.+|+|||||...+.+.
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            44567899999999999999998864

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.19  E-value=0.03  Score=48.57  Aligned_cols=24  Identities=25%  Similarity=0.357  Sum_probs=21.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++.+.|.||+||||++..+..
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHH
Confidence            467889999999999999999874

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=94.19  E-value=0.026  Score=48.70  Aligned_cols=23  Identities=17%  Similarity=0.127  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|+|.|++|+||||+++.+..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999986

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=94.19  E-value=0.15  Score=48.75  Aligned_cols=108  Identities=11%  Similarity=-0.013  Sum_probs=58.6

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHH-HHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--cc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFA-GEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EI  243 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~  243 (334)
                      .++.|..=.. -.-++|.|..|+|||+|+ ..+.|.  ....+ .++++-+.+.. .+.++..++.+.-.......  ..
T Consensus       152 aID~l~Pigr-GQR~~Ifg~~g~GKT~l~l~~I~n~--~~~dv-~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~at  227 (513)
T 3oaa_A          152 AVDSMIPIGR-GQRELIIGDRQTGKTALAIDAIINQ--RDSGI-KCIYVAIGQKASTISNVVRKLEEHGALANTIVVVAT  227 (513)
T ss_dssp             HHHHHSCCBT-TCBCEEEESSSSSHHHHHHHHHHTT--SSSSC-EEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEEC
T ss_pred             eecccccccc-CCEEEeecCCCCCcchHHHHHHHhh--ccCCc-eEEEEEecCChHHHHHHHHHHhhcCcccceEEEEEC
Confidence            5555543111 124789999999999996 677773  12222 35788888765 45566666554321111000  00


Q ss_pred             chh--------h--HHHHHHHHHHHcCCCeEEEEEeCCCCh-hHHHHHH
Q 038944          244 MDK--------N--YEMKKIILHEYLMTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       244 ~~~--------~--~~~l~~~l~~~L~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                      .+.        .  .=.+++.++.  +|+..||++||+-.- ..+.++.
T Consensus       228 ad~p~~~r~~a~~~a~tiAEyfrd--~G~dVLli~Dsltr~A~A~REis  274 (513)
T 3oaa_A          228 ASESAALQYLAPYAGCAMGEYFRD--RGEDALIIYDDLSKQAVAYRQIS  274 (513)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEETHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHh--cCCCEEEEecChHHHHHHHHHHH
Confidence            000        0  0023344443  699999999999432 4444444

>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=94.14  E-value=0.056  Score=54.76  Aligned_cols=48  Identities=13%  Similarity=0.174  Sum_probs=37.7

Q ss_pred             CCCeeechhhHHHHHHHHhcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|.+..++.+...+...       ......+.++|.+|+|||++|+.+.+.
T Consensus       457 ~~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~  511 (758)
T 1r6b_X          457 KMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHH
Confidence            346889999888887776531       234457899999999999999999883

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.13  E-value=0.028  Score=49.30  Aligned_cols=115  Identities=10%  Similarity=0.066  Sum_probs=57.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEE-cCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVP-GTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILH  256 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~  256 (334)
                      .-.+++|+|+.|+|||||.+.+..-.  ...+...+++. .+-.+-.... ..++.+-   .   -..+..  .+...+.
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~--~~~~~G~I~~~g~~i~~~~~~~-~~~v~q~---~---~gl~~~--~l~~~la   92 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYI--NQTKSYHIITIEDPIEYVFKHK-KSIVNQR---E---VGEDTK--SFADALR   92 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHH--HHHCCCEEEEEESSCCSCCCCS-SSEEEEE---E---BTTTBS--CHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhC--CCCCCCEEEEcCCcceeecCCc-ceeeeHH---H---hCCCHH--HHHHHHH
Confidence            34699999999999999999987521  11112222221 1100000000 0000000   0   000111  3344455


Q ss_pred             HHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhhc
Q 038944          257 EYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       257 ~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~  306 (334)
                      ..|..+.=+|++|..-+.+....+....   ..|.-|++||...+++..+
T Consensus        93 ~aL~~~p~illlDEp~D~~~~~~~l~~~---~~g~~vl~t~H~~~~~~~~  139 (261)
T 2eyu_A           93 AALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTAIDTI  139 (261)
T ss_dssp             HHHHHCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEECCSSHHHHH
T ss_pred             HHHhhCCCEEEeCCCCCHHHHHHHHHHH---ccCCEEEEEeCcchHHHHH
Confidence            5554455578889997665444433332   2366688888877655433

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=94.11  E-value=0.027  Score=49.72  Aligned_cols=21  Identities=14%  Similarity=0.455  Sum_probs=19.4

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|+|..|+|||||.+.++.
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999985

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=94.11  E-value=0.028  Score=49.98  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5789999999999999999987

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=94.10  E-value=0.038  Score=47.39  Aligned_cols=25  Identities=16%  Similarity=0.247  Sum_probs=22.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-..|.|.|+.|+||||+++.+.+.
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999884

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=94.08  E-value=0.025  Score=46.25  Aligned_cols=22  Identities=14%  Similarity=0.294  Sum_probs=19.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||.+.+...
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            4789999999999999998873

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.06  E-value=0.026  Score=46.75  Aligned_cols=24  Identities=21%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            356899999999999999999874

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.06  E-value=0.028  Score=47.49  Aligned_cols=115  Identities=13%  Similarity=-0.055  Sum_probs=59.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc-----------------
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS-----------------  241 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~-----------------  241 (334)
                      -.++.|+|.+|+|||||++.+.....  ..=....|+...  .....+...+. .++......                 
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~--~~~~~v~~~~~~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGL--RDGDPCIYVTTE--ESRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEKED   97 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHH--HHTCCEEEEESS--SCHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC----C
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH--HCCCeEEEEEcc--cCHHHHHHHHH-HhcchHHHHhhCCEEEEeccccccCc
Confidence            35899999999999999999875211  111134455433  34455544433 333221100                 


Q ss_pred             ----ccchhhHHHHHHHHHHHc---CCCeEEEEEeCCC-----ChhHHHHHHhhCCC--CCCCeEEEEecCCh
Q 038944          242 ----EIMDKNYEMKKIILHEYL---MTKRYLNVIDDVW-----NIEVCDIIREILPD--NQNRSRVLITLTEI  300 (334)
Q Consensus       242 ----~~~~~~~~~l~~~l~~~L---~~kr~LlVlDdvw-----~~~~w~~l~~~l~~--~~~gsrIivTTr~~  300 (334)
                          ...+..  ++...+.+.+   .-+..+||||.+-     +......+...+..  ...|.-||+||...
T Consensus        98 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~  168 (235)
T 2w0m_A           98 QWSLVNLTPE--ELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYA  168 (235)
T ss_dssp             TTBCSSCCHH--HHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC--
T ss_pred             eeeecCCCHH--HHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccC
Confidence                001112  4444454443   2234599999985     33223333322211  22477788888876

>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=94.05  E-value=0.025  Score=48.41  Aligned_cols=26  Identities=23%  Similarity=0.216  Sum_probs=22.7

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-.+|+|.|..|+|||||++.+...
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc
Confidence            34579999999999999999999873

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=94.04  E-value=0.029  Score=47.38  Aligned_cols=76  Identities=13%  Similarity=0.182  Sum_probs=43.2

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc-------cccchhhHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL-------SEIMDKNYEMKKI  253 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~-------~~~~~~~~~~l~~  253 (334)
                      +|.|.|++|+||+|.|+.+.++      |.. ..+      +..+++++-+..-+.-...       ......+  -...
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~------~g~-~~i------stGdllR~~i~~~t~lg~~~~~~~~~G~lvpd~--iv~~   66 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKE------KGF-VHI------STGDILREAVQKGTPLGKKAKEYMERGELVPDD--LIIA   66 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH------HCC-EEE------EHHHHHHHHHHHTCHHHHHHHHHHHHTCCCCHH--HHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH------HCC-eEE------cHHHHHHHHHHhcChhhhhHHHHHhcCCcCCHH--HHHH
Confidence            6889999999999999999873      221 112      3456666544321100000       0111223  4556


Q ss_pred             HHHHHcCCCeEEEEEeCCC
Q 038944          254 ILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L~~kr~LlVlDdvw  272 (334)
                      .+.+.+..... +|||..=
T Consensus        67 lv~~~l~~~~~-~ilDGfP   84 (206)
T 3sr0_A           67 LIEEVFPKHGN-VIFDGFP   84 (206)
T ss_dssp             HHHHHCCSSSC-EEEESCC
T ss_pred             HHHHhhccCCc-eEecCCc
Confidence            67777754443 5789874

>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=94.04  E-value=0.32  Score=40.48  Aligned_cols=24  Identities=21%  Similarity=0.282  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           25 LIKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHCS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999998874

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.04  E-value=0.05  Score=45.92  Aligned_cols=37  Identities=16%  Similarity=0.189  Sum_probs=27.2

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...+..++.. -+.-..+.|+|++|+||||+|..+.+.
T Consensus        45 ~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           45 LGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             HHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHHHHHH
Confidence            5556666654 223346999999999999999888873

>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=93.99  E-value=0.03  Score=50.35  Aligned_cols=24  Identities=4%  Similarity=0.129  Sum_probs=21.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|+|..|.|||||++.+..
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhh
Confidence            346899999999999999999875

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=93.97  E-value=0.036  Score=50.42  Aligned_cols=23  Identities=13%  Similarity=0.251  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|+|+.|+|||||+..+..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~   62 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAA   62 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=93.95  E-value=0.028  Score=50.77  Aligned_cols=25  Identities=16%  Similarity=0.319  Sum_probs=22.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++++.|+|+.|.|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            4789999999999999999999853

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=93.93  E-value=0.048  Score=48.76  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+++++|.+|+||||++..+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~  120 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAY  120 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999988864

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=93.93  E-value=0.081  Score=50.60  Aligned_cols=93  Identities=11%  Similarity=0.007  Sum_probs=53.2

Q ss_pred             EEEEEccCCccHHHHH-HHHHccCCCCCcee-eEEEEEcCCCC-CHHHHHHHHHHHhCC--------CCCcccc--c---
Q 038944          181 VVVILDSIGLDKAAFA-GEAYNSSYVKHYFD-CHAWVPGTYPY-DADQMLDIVIKFLMP--------SSRLSEI--M---  244 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~-~~~wv~vs~~~-~~~~il~~il~~~~~--------~~~~~~~--~---  244 (334)
                      -++|+|..|+|||+|| ..+.+..  .  -+ .++++-+.+.. .+.++..++.+.-..        ..+.+..  .   
T Consensus       165 R~~Ifg~~g~GKT~Lal~~I~~~~--~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~  240 (507)
T 1fx0_A          165 RELIIGDRQTGKTAVATDTILNQQ--G--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAP  240 (507)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHTCC--T--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHH
T ss_pred             EEEEecCCCCCccHHHHHHHHHhh--c--CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHHH
Confidence            4789999999999995 6787743  2  33 35677777664 344555555432110        0000000  0   


Q ss_pred             -hhhHHHHHHHHHHHcCCCeEEEEEeCCCC-hhHHHHHH
Q 038944          245 -DKNYEMKKIILHEYLMTKRYLNVIDDVWN-IEVCDIIR  281 (334)
Q Consensus       245 -~~~~~~l~~~l~~~L~~kr~LlVlDdvw~-~~~w~~l~  281 (334)
                       .-.  ..++.++.  +|+..||++||+-. ...+..+.
T Consensus       241 ~~a~--tiAEyfrd--~G~dVLli~Dsltr~A~A~REis  275 (507)
T 1fx0_A          241 YTGA--ALAEYFMY--RERHTLIIYDDLSKQAQAYRQMS  275 (507)
T ss_dssp             HHHH--HHHHHHHH--TTCEEEEEEECHHHHHHHHHHHH
T ss_pred             HHHH--HHHHHHHH--cCCcEEEEEecHHHHHHHHHHHH
Confidence             011  23444444  69999999999843 24555554

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=93.88  E-value=0.034  Score=43.84  Aligned_cols=22  Identities=18%  Similarity=0.301  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999999764

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=93.88  E-value=0.072  Score=44.51  Aligned_cols=87  Identities=7%  Similarity=-0.039  Sum_probs=46.0

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKIILHE  257 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~~l~~  257 (334)
                      .|.|=|.-|+||||.++.+.+.  .+..-....+..-+......+.++.++..-.......   ...+..  +....+..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~--L~~~g~~v~~treP~~t~~~~~ir~~l~~~~~~~~~~~ll~~a~r~--~~~~~I~~   77 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQY--LEKRGKKVILKREPGGTETGEKIRKILLEEEVTPKAELFLFLASRN--LLVTEIKQ   77 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCSSHHHHHHHHHHHHSCCCHHHHHHHHHHHHH--HHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEECCCCCcHHHHHHHHhhcccCChHHHHHHHHHHHH--HHHHHHHH
Confidence            3667799999999999999873  3222222333333333445555666654322110000   011112  44556666


Q ss_pred             HcCCCeEEEEEeCCC
Q 038944          258 YLMTKRYLNVIDDVW  272 (334)
Q Consensus       258 ~L~~kr~LlVlDdvw  272 (334)
                      .|...+ .+|.|--.
T Consensus        78 ~L~~g~-~Vi~DRy~   91 (197)
T 3hjn_A           78 YLSEGY-AVLLDRYT   91 (197)
T ss_dssp             HHTTTC-EEEEESCH
T ss_pred             HHHCCC-eEEecccc
Confidence            675443 56777654

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.88  E-value=0.06  Score=49.05  Aligned_cols=33  Identities=18%  Similarity=0.133  Sum_probs=25.4

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHH
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +++-+.-.-....+++|+|.+|+|||||.+.+.
T Consensus        44 ~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~   76 (337)
T 2qm8_A           44 LIDAVLPQTGRAIRVGITGVPGVGKSTTIDALG   76 (337)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHH
T ss_pred             HHHhCCcccCCCeEEEEECCCCCCHHHHHHHHH
Confidence            444443333456899999999999999999987

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.86  E-value=0.04  Score=44.88  Aligned_cols=24  Identities=4%  Similarity=0.073  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|+++|.+|+|||||...+...
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            457999999999999999999873

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=93.84  E-value=0.035  Score=52.40  Aligned_cols=24  Identities=17%  Similarity=0.250  Sum_probs=20.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|.|+|.+|+||||++..+..
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~  121 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLAR  121 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356999999999999999988865

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.82  E-value=0.031  Score=49.11  Aligned_cols=22  Identities=23%  Similarity=0.262  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999985

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=93.82  E-value=0.056  Score=51.06  Aligned_cols=91  Identities=14%  Similarity=0.122  Sum_probs=51.2

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCC--------Ccee-eEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc---ccchh-
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVK--------HYFD-CHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS---EIMDK-  246 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~--------~~F~-~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~---~~~~~-  246 (334)
                      -++|.|..|+|||+|+..+.+.....        ++=+ .++++-+.+.. .+.++..++.+. +.-....   ...+. 
T Consensus       149 r~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~-g~~~rtvvv~~t~d~p  227 (464)
T 3gqb_B          149 KLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERT-GALSRSVLFLNKADDP  227 (464)
T ss_dssp             BCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHT-SGGGGEEEEEEETTSC
T ss_pred             EEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhc-ccccceEEEEECCCCC
Confidence            46788999999999999998865441        1111 45667777654 455666665442 1000000   00000 


Q ss_pred             --h---HHHHHHHHHHHc---CCCeEEEEEeCCC
Q 038944          247 --N---YEMKKIILHEYL---MTKRYLNVIDDVW  272 (334)
Q Consensus       247 --~---~~~l~~~l~~~L---~~kr~LlVlDdvw  272 (334)
                        .   .-...-.+-+++   +|+..|+++||+-
T Consensus       228 ~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlT  261 (464)
T 3gqb_B          228 TIERILTPRMALTVAEYLAFEHDYHVLVILTDMT  261 (464)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence              0   001223344554   4899999999984

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=93.80  E-value=0.035  Score=50.25  Aligned_cols=22  Identities=9%  Similarity=0.181  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|+|+.|+||||||+.+..
T Consensus         6 ~~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999987

>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=93.79  E-value=0.034  Score=52.16  Aligned_cols=24  Identities=17%  Similarity=0.232  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++|+|..|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            457999999999999999999986

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.73  E-value=0.05  Score=53.69  Aligned_cols=43  Identities=12%  Similarity=0.183  Sum_probs=35.1

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..++.+...+..+    ..+.|+|.+|+||||||+.+..-
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~   83 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAEL   83 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHT
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhcc
Confidence            35788888887777666654    37899999999999999999873

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.72  E-value=0.026  Score=50.74  Aligned_cols=23  Identities=9%  Similarity=0.170  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||++.+..
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCchHHHHHHHHHc
Confidence            46899999999999999999975

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=93.71  E-value=0.021  Score=51.00  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=18.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..+|+|.|..|+||||+|+.+.+
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999998876

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=93.70  E-value=0.071  Score=50.40  Aligned_cols=91  Identities=11%  Similarity=0.098  Sum_probs=51.5

Q ss_pred             EEEEccCCccHHHHHHHHHccCCCC--CceeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchhh--H----HH
Q 038944          182 VVILDSIGLDKAAFAGEAYNSSYVK--HYFDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDKN--Y----EM  250 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~~~~~--~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~~--~----~~  250 (334)
                      ++|.|..|+|||+|+..+.+.....  .+=-.++++-+.+.. .+.++..++.+.-..+....  ...+..  .    -.
T Consensus       154 ~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~a~~  233 (465)
T 3vr4_D          154 LPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPR  233 (465)
T ss_dssp             CCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHHHHH
T ss_pred             EEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHHHHH
Confidence            6788999999999999998864431  111156677777654 45566666554310100000  001100  0    01


Q ss_pred             HHHHHHHHc---CCCeEEEEEeCCC
Q 038944          251 KKIILHEYL---MTKRYLNVIDDVW  272 (334)
Q Consensus       251 l~~~l~~~L---~~kr~LlVlDdvw  272 (334)
                      ..-.+-+++   +|+..|+++||+-
T Consensus       234 ~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          234 MALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHhcCCeEEEEEcChH
Confidence            223344554   4899999999994

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.67  E-value=0.16  Score=45.71  Aligned_cols=53  Identities=15%  Similarity=0.081  Sum_probs=36.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      ..-.++.|.|.+|+|||||+..+..+.....  ..++|++.-  .+...+...++..
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~  118 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVT  118 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHH
Confidence            3446899999999999999988875422222  456666543  5667777776654

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=93.66  E-value=0.064  Score=48.88  Aligned_cols=34  Identities=18%  Similarity=0.091  Sum_probs=25.1

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.+-+.....+..+++|+|.+|+|||||+..+..
T Consensus        45 ~~~~l~~~~~~~~~i~i~G~~g~GKSTl~~~l~~   78 (341)
T 2p67_A           45 LLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGM   78 (341)
T ss_dssp             HHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             HHHhCCcccCCCEEEEEEcCCCCCHHHHHHHHHH
Confidence            3333333334578999999999999999998853

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=93.65  E-value=0.036  Score=43.97  Aligned_cols=24  Identities=8%  Similarity=0.116  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            345789999999999999998764

>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=93.62  E-value=0.037  Score=52.02  Aligned_cols=26  Identities=35%  Similarity=0.392  Sum_probs=22.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....+|.|+|++|+||||+|+.+...
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            34679999999999999999999873

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=93.61  E-value=0.038  Score=44.23  Aligned_cols=24  Identities=29%  Similarity=0.322  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            346899999999999999998764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=93.59  E-value=0.066  Score=51.54  Aligned_cols=24  Identities=13%  Similarity=0.167  Sum_probs=20.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|+|+|.+|+||||++..+..
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~  123 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAY  123 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999988873

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.56  E-value=0.062  Score=43.12  Aligned_cols=25  Identities=20%  Similarity=0.276  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +...|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999998764

>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=93.56  E-value=0.044  Score=48.96  Aligned_cols=24  Identities=13%  Similarity=0.059  Sum_probs=21.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+++++|.+|+||||++..+..
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~  120 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLAL  120 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999998864

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=93.55  E-value=0.036  Score=49.43  Aligned_cols=23  Identities=13%  Similarity=0.121  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~G   86 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMG   86 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            45899999999999999999986

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=93.53  E-value=0.063  Score=44.50  Aligned_cols=34  Identities=15%  Similarity=0.040  Sum_probs=24.4

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++.+.-.... .-|.++|.+|+|||||...+.+.
T Consensus        15 ~l~~~~~~~~~-~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           15 VLQFLGLYKKT-GKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             HHHHHTCTTCC-EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             HHHHhhccCCC-cEEEEECCCCCCHHHHHHHHhcC
Confidence            44555333333 45789999999999999998753

>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=93.53  E-value=0.052  Score=43.15  Aligned_cols=24  Identities=17%  Similarity=0.069  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            346899999999999999988764

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=93.52  E-value=0.042  Score=43.41  Aligned_cols=23  Identities=22%  Similarity=0.268  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.++|.+|+|||||...+.+.
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            45889999999999999998764

>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=93.50  E-value=0.043  Score=49.43  Aligned_cols=23  Identities=13%  Similarity=0.076  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|+|+.|+||||||..+..
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~   25 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAK   25 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHHH
Confidence            36899999999999999999976

>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=93.49  E-value=0.04  Score=48.93  Aligned_cols=24  Identities=17%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.++.|+|.+|+|||||+..+...
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~~   58 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQALQ   58 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            458999999999999999988763

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.47  E-value=0.048  Score=46.89  Aligned_cols=24  Identities=17%  Similarity=0.171  Sum_probs=21.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|.|.|..|+||||+++.+.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999999874

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=93.47  E-value=0.039  Score=45.07  Aligned_cols=23  Identities=13%  Similarity=-0.135  Sum_probs=19.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .--|.|+|.+|+|||||.+.+.+
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~   36 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYS   36 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            34688999999999999988875

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=93.45  E-value=0.042  Score=48.45  Aligned_cols=23  Identities=17%  Similarity=0.081  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.++.|+|.+|+|||||+..+..
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            35899999999999999988874

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.45  E-value=0.053  Score=44.36  Aligned_cols=25  Identities=8%  Similarity=0.026  Sum_probs=21.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|.|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4557899999999999999998874

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=93.41  E-value=0.041  Score=44.94  Aligned_cols=23  Identities=17%  Similarity=0.261  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.++|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46789999999999999999764

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=93.39  E-value=0.042  Score=50.59  Aligned_cols=23  Identities=9%  Similarity=0.047  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHhc
Confidence            45899999999999999999975

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=93.39  E-value=0.057  Score=42.73  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=19.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||...+.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5789999999999999998764

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.38  E-value=0.044  Score=43.57  Aligned_cols=23  Identities=13%  Similarity=0.164  Sum_probs=20.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.++|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998764

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.35  E-value=0.064  Score=43.69  Aligned_cols=25  Identities=12%  Similarity=0.210  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|.|+|.+|+|||||...+.+.
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHcC
Confidence            3457899999999999999998875

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.32  E-value=0.047  Score=47.56  Aligned_cols=22  Identities=18%  Similarity=0.184  Sum_probs=19.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+|.|-||+||||+|..+..
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~   23 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTS   23 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEEecCCCCcHHHHHHHHHH
Confidence            6888899999999999987764

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.31  E-value=0.06  Score=44.06  Aligned_cols=25  Identities=16%  Similarity=0.276  Sum_probs=21.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|.|+|.+|+|||||...+.+.
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999999864

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=93.31  E-value=0.05  Score=48.13  Aligned_cols=23  Identities=13%  Similarity=0.161  Sum_probs=20.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|+|.|-||+||||+|..+..
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~   24 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHH
Confidence            57899999999999999988764

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.29  E-value=0.046  Score=44.22  Aligned_cols=23  Identities=17%  Similarity=0.097  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999864

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=93.29  E-value=0.049  Score=44.39  Aligned_cols=22  Identities=14%  Similarity=0.170  Sum_probs=19.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..|+|..|.|||||+..++-
T Consensus        27 g~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            3889999999999999999864

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.28  E-value=0.049  Score=43.27  Aligned_cols=23  Identities=17%  Similarity=0.219  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+.+.
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            45889999999999999998765

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=93.25  E-value=0.046  Score=50.27  Aligned_cols=23  Identities=13%  Similarity=0.153  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            35899999999999999999975

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.23  E-value=0.05  Score=43.13  Aligned_cols=22  Identities=14%  Similarity=0.200  Sum_probs=19.4

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999888764

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=93.17  E-value=0.28  Score=47.41  Aligned_cols=59  Identities=10%  Similarity=0.048  Sum_probs=39.6

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCC-HHHHHHHH
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYD-ADQMLDIV  230 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~il~~i  230 (334)
                      +.++.|..=. .-.-++|.|..|+|||+|++.+.+..    +-+.++++-+.+..+ +.+++.++
T Consensus       216 rvID~l~Pig-kGqr~~I~g~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          216 RVIDTFFPQA-KGGTAAIPGPAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             HHHHHHSCEE-TTCEEEECSCCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHT
T ss_pred             chhhccCCcc-cCCeEEeecCCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHH
Confidence            3555554311 12368999999999999999998742    235778888887764 44555554

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.17  E-value=0.052  Score=43.67  Aligned_cols=25  Identities=24%  Similarity=0.371  Sum_probs=21.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3557899999999999999888764

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.16  E-value=0.047  Score=43.32  Aligned_cols=21  Identities=29%  Similarity=0.302  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -|.++|.+|+|||||...+.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            478999999999999998865

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=93.16  E-value=0.048  Score=43.01  Aligned_cols=23  Identities=30%  Similarity=0.317  Sum_probs=19.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999888754

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.12  E-value=0.059  Score=49.36  Aligned_cols=25  Identities=20%  Similarity=0.086  Sum_probs=22.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....+++|+|.+|+|||||...+..
T Consensus        72 ~~~~~v~lvG~pgaGKSTLln~L~~   96 (349)
T 2www_A           72 PLAFRVGLSGPPGAGKSTFIEYFGK   96 (349)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cCceEEEEEcCCCCCHHHHHHHHHH
Confidence            3478999999999999999999875

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=93.12  E-value=0.1  Score=45.85  Aligned_cols=36  Identities=8%  Similarity=0.038  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-+..||....+.-.-+.++|++|+|||++|..+.+
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            345666655434456799999999999999999987

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.09  E-value=0.063  Score=44.94  Aligned_cols=26  Identities=8%  Similarity=0.031  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .....|.++|.+|+|||||...+.+.
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34567899999999999999998875

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=93.09  E-value=0.11  Score=45.20  Aligned_cols=37  Identities=16%  Similarity=0.196  Sum_probs=27.3

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ++...+.........|.++|.+|+|||||...+....
T Consensus        24 ~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           24 EFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444444444455678999999999999999988653

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.08  E-value=0.05  Score=49.93  Aligned_cols=23  Identities=17%  Similarity=0.081  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999975

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.06  E-value=0.065  Score=42.58  Aligned_cols=22  Identities=23%  Similarity=0.335  Sum_probs=19.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      --|.|+|.+|+|||||...+..
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            4588999999999999998864

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=93.05  E-value=0.052  Score=44.21  Aligned_cols=24  Identities=13%  Similarity=0.066  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            7 KCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcC
Confidence            446789999999999999988764

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=93.05  E-value=0.05  Score=50.03  Aligned_cols=23  Identities=17%  Similarity=0.162  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...++|+|..|.|||||++.+..
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~g  192 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAA  192 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=93.01  E-value=0.056  Score=43.34  Aligned_cols=24  Identities=21%  Similarity=0.321  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            456899999999999999998764

>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=93.00  E-value=0.057  Score=48.53  Aligned_cols=24  Identities=17%  Similarity=0.155  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++|.|+|+.|+||||||..+..
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~   32 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRK   32 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHH
Confidence            356899999999999999999986

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=93.00  E-value=0.057  Score=42.87  Aligned_cols=23  Identities=9%  Similarity=0.225  Sum_probs=20.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            45899999999999999988764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=92.98  E-value=0.058  Score=43.32  Aligned_cols=25  Identities=16%  Similarity=0.258  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcC
Confidence            4557899999999999999998764

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=92.96  E-value=0.071  Score=43.19  Aligned_cols=23  Identities=17%  Similarity=0.271  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+.+.
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35789999999999999999864

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=92.95  E-value=0.048  Score=48.84  Aligned_cols=22  Identities=14%  Similarity=0.434  Sum_probs=19.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++| +|+|..|+|||||.+.++.
T Consensus        19 ~~I-~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           19 FTL-MVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEE-EEEEETTSSHHHHHHHHHC
T ss_pred             EEE-EEECCCCCCHHHHHHHHhC
Confidence            444 9999999999999999875

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=92.94  E-value=0.11  Score=41.72  Aligned_cols=25  Identities=20%  Similarity=0.262  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            8 ETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            4567899999999999999998765

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=92.94  E-value=0.059  Score=42.71  Aligned_cols=23  Identities=13%  Similarity=0.143  Sum_probs=20.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            45889999999999999988764

>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=92.93  E-value=0.055  Score=42.80  Aligned_cols=21  Identities=5%  Similarity=-0.024  Sum_probs=18.7

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.+.
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999988753

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=92.93  E-value=0.12  Score=45.17  Aligned_cols=35  Identities=14%  Similarity=0.191  Sum_probs=26.1

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +...+.........|.++|.+|+|||||...+...
T Consensus        28 ~~~~~~~~~~~~~~I~vvG~~g~GKSSLin~l~~~   62 (270)
T 1h65_A           28 LLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   62 (270)
T ss_dssp             HHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHhhcCCCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            33334444444567899999999999999999865

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=92.92  E-value=0.072  Score=43.06  Aligned_cols=25  Identities=16%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..--|.|+|.+|+|||||...+.+.
T Consensus        17 ~~~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           17 PTYKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3457899999999999999998864

>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=92.92  E-value=0.1  Score=44.27  Aligned_cols=52  Identities=6%  Similarity=-0.111  Sum_probs=31.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      -..|.|-|..|+||||+++.+.+...- ..+++. ...-+......+.+++++.
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~-~~~~v~-~~~~p~~~~~g~~i~~~l~   57 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRE-RGIEVQ-LTREPGGTPLAERIRELLL   57 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHT-TTCCEE-EEESSCSSHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHH-cCCCcc-cccCCCCCHHHHHHHHHHh
Confidence            368899999999999999999873221 234442 2222222223445666654

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=92.92  E-value=0.12  Score=49.47  Aligned_cols=114  Identities=12%  Similarity=0.061  Sum_probs=59.8

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHH-HHHHHccCCC----CCcee-eEEEEEcCCCC-CHHHHHHHHHHHhCCCCC
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAF-AGEAYNSSYV----KHYFD-CHAWVPGTYPY-DADQMLDIVIKFLMPSSR  239 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtL-a~~v~~~~~~----~~~F~-~~~wv~vs~~~-~~~~il~~il~~~~~~~~  239 (334)
                      +.++.|..=.. -.-++|+|..|+|||+| ...+.+....    .++-+ .++++-+.+.. .+.++.+++.+.-.....
T Consensus       151 raID~l~Pigr-GQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~t  229 (510)
T 2ck3_A          151 KAVDSLVPIGR-GQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYT  229 (510)
T ss_dssp             HHHHHHSCCBT-TCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGE
T ss_pred             eeecccccccc-CCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccc
Confidence            35666653111 12478999999999999 4566663221    12234 46778888765 455666666542111100


Q ss_pred             cc--ccchh----hH--HHHHHHHHHHc--CCCeEEEEEeCCCCh-hHHHHHH
Q 038944          240 LS--EIMDK----NY--EMKKIILHEYL--MTKRYLNVIDDVWNI-EVCDIIR  281 (334)
Q Consensus       240 ~~--~~~~~----~~--~~l~~~l~~~L--~~kr~LlVlDdvw~~-~~w~~l~  281 (334)
                      ..  ...+.    .+  -...-.+-+++  +|+..||++||+-.- ..+..+.
T Consensus       230 vvV~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dsltr~A~A~REis  282 (510)
T 2ck3_A          230 IVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMS  282 (510)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHHHHHHHHHHHH
T ss_pred             eEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHHHHHHHHHHHH
Confidence            00  00000    00  01122233333  689999999999432 4555544

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.92  E-value=0.056  Score=43.93  Aligned_cols=22  Identities=5%  Similarity=0.098  Sum_probs=19.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||...+.+.
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4789999999999999998864

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=92.91  E-value=0.059  Score=43.16  Aligned_cols=24  Identities=13%  Similarity=0.299  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998864

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=92.89  E-value=0.04  Score=48.13  Aligned_cols=24  Identities=17%  Similarity=0.245  Sum_probs=21.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +...|.|.|..|+||||+++.+.+
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~   46 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQ   46 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998877

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=92.89  E-value=0.074  Score=42.91  Aligned_cols=24  Identities=13%  Similarity=0.119  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            457889999999999999988854

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=92.89  E-value=0.06  Score=44.05  Aligned_cols=24  Identities=17%  Similarity=0.113  Sum_probs=20.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            446899999999999999777654

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=92.89  E-value=0.056  Score=49.72  Aligned_cols=23  Identities=17%  Similarity=0.027  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAG   51 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHHC
Confidence            35899999999999999999975

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=92.85  E-value=0.062  Score=43.14  Aligned_cols=24  Identities=13%  Similarity=0.039  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            346889999999999999988754

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=92.85  E-value=0.057  Score=49.73  Aligned_cols=23  Identities=13%  Similarity=0.099  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAG   51 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            35899999999999999999975

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.85  E-value=0.12  Score=57.43  Aligned_cols=86  Identities=13%  Similarity=-0.009  Sum_probs=53.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      ..-+++-|+|++|+|||+||..+.....  .+=..++|+++...++...     ++.++......   .....+  ++..
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~ea~--~~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E--~~l~ 1495 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGE--QALE 1495 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHH--TTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHH--HHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHH--HcCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHH--HHHH
Confidence            3457999999999999999988866322  1112567888888877655     44454322111   011112  4445


Q ss_pred             HHHHHc-CCCeEEEEEeCC
Q 038944          254 ILHEYL-MTKRYLNVIDDV  271 (334)
Q Consensus       254 ~l~~~L-~~kr~LlVlDdv  271 (334)
                      .++... ..+--+||+|.+
T Consensus      1496 ~~~~lvr~~~~~lVVIDsi 1514 (2050)
T 3cmu_A         1496 ICDALARSGAVDVIVVDSV 1514 (2050)
T ss_dssp             HHHHHHHHTCCSEEEESCG
T ss_pred             HHHHHHhcCCCCEEEEcCh
Confidence            555443 345669999998

>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=92.82  E-value=0.058  Score=50.00  Aligned_cols=23  Identities=17%  Similarity=0.140  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaG   51 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAG   51 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHHc
Confidence            35899999999999999999975

>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=92.79  E-value=0.083  Score=44.39  Aligned_cols=25  Identities=8%  Similarity=-0.065  Sum_probs=22.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..+|+|+||+|+||+|+|..+-+
T Consensus         9 ~~~~II~itGk~~SGKd~va~~l~~   33 (202)
T 3ch4_B            9 APRLVLLFSGKRKSGKDFVTEALQS   33 (202)
T ss_dssp             CCSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCChHHHHHHHHH
Confidence            3567999999999999999998865

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=92.78  E-value=0.063  Score=43.49  Aligned_cols=24  Identities=13%  Similarity=0.235  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999998764

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=92.78  E-value=0.059  Score=49.84  Aligned_cols=22  Identities=14%  Similarity=0.170  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaG   51 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAG   51 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCcHHHHHHHHHHc
Confidence            5899999999999999999975

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=92.77  E-value=0.065  Score=42.64  Aligned_cols=24  Identities=17%  Similarity=0.034  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            356899999999999999998754

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=92.73  E-value=0.065  Score=43.88  Aligned_cols=24  Identities=21%  Similarity=0.174  Sum_probs=20.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhC
Confidence            346889999999999999888754

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.72  E-value=0.039  Score=45.93  Aligned_cols=25  Identities=12%  Similarity=-0.055  Sum_probs=21.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-..++|+|..|+|||||.+.+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999988763

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=92.71  E-value=0.061  Score=49.72  Aligned_cols=23  Identities=17%  Similarity=0.107  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaG   59 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAG   59 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            35899999999999999999974

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=92.71  E-value=0.055  Score=43.54  Aligned_cols=24  Identities=8%  Similarity=-0.002  Sum_probs=20.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.++|.+|+|||||...+.+.
T Consensus         7 ~~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            7 ELRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEEECCGGGCHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            345789999999999999988764

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.70  E-value=0.064  Score=44.05  Aligned_cols=23  Identities=13%  Similarity=0.055  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..|.++|.+|+|||||...+.+.
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            36799999999999999988864

>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=92.69  E-value=0.061  Score=44.34  Aligned_cols=24  Identities=4%  Similarity=0.129  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.++|.+|+|||||.+.+.+.
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhc
Confidence            446899999999999999987763

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=92.68  E-value=0.066  Score=42.88  Aligned_cols=23  Identities=13%  Similarity=0.124  Sum_probs=20.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|..|+|||||...+..+
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999998754

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=92.64  E-value=0.051  Score=49.76  Aligned_cols=22  Identities=27%  Similarity=0.277  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|+.|.|||||.+.+..
T Consensus        27 e~~~llGpnGsGKSTLLr~iaG   48 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAG   48 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHT
T ss_pred             CEEEEECCCCccHHHHHHHHHc
Confidence            5899999999999999999985

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.61  E-value=0.069  Score=43.13  Aligned_cols=23  Identities=9%  Similarity=0.023  Sum_probs=19.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.++|.+|+|||||...+.+.
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            45889999999999999888754

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=92.60  E-value=0.069  Score=43.12  Aligned_cols=24  Identities=25%  Similarity=0.313  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhC
Confidence            456889999999999999998764

>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=92.60  E-value=0.083  Score=43.63  Aligned_cols=25  Identities=28%  Similarity=0.393  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            4557899999999999999988764

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=92.59  E-value=0.068  Score=43.73  Aligned_cols=24  Identities=17%  Similarity=0.263  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|..|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999988764

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=92.58  E-value=0.068  Score=44.08  Aligned_cols=25  Identities=24%  Similarity=0.297  Sum_probs=21.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|.+|+|||||...+...
T Consensus        13 ~~~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           13 ALHKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3457899999999999999988754

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=92.58  E-value=0.21  Score=42.29  Aligned_cols=22  Identities=14%  Similarity=0.172  Sum_probs=18.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||+|.....++
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4778999999999999887653

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=92.54  E-value=0.071  Score=42.90  Aligned_cols=24  Identities=17%  Similarity=0.265  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+...
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            346889999999999999988764

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.53  E-value=0.071  Score=42.93  Aligned_cols=23  Identities=9%  Similarity=-0.025  Sum_probs=20.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999988864

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.52  E-value=0.068  Score=45.60  Aligned_cols=48  Identities=15%  Similarity=0.081  Sum_probs=29.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~i  230 (334)
                      -.++.|.|.+|+|||||+..+.....  ..=...+|++...  ....+...+
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~--~~~~~v~~~~~e~--~~~~~~~~~   70 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGL--KMGEPGIYVALEE--HPVQVRQNM   70 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHH--HTTCCEEEEESSS--CHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEEccC--CHHHHHHHH
Confidence            45899999999999999877654211  1112456665443  344554443

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=92.49  E-value=0.066  Score=43.48  Aligned_cols=24  Identities=17%  Similarity=0.181  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        11 ~~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           11 LIKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998864

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=92.49  E-value=0.53  Score=45.10  Aligned_cols=56  Identities=7%  Similarity=-0.060  Sum_probs=37.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      ..-.++.|.|.+|+|||||+..+..+.... +=..++|++.  +-+..++...++....
T Consensus       240 ~~G~l~li~G~pG~GKT~lal~~a~~~a~~-~g~~vl~~s~--E~s~~~l~~r~~~~~~  295 (503)
T 1q57_A          240 RGGEVIMVTSGSGMVMSTFVRQQALQWGTA-MGKKVGLAML--EESVEETAEDLIGLHN  295 (503)
T ss_dssp             CTTCEEEEEESSCHHHHHHHHHHHHHHTTT-SCCCEEEEES--SSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEeecCCCCchHHHHHHHHHHHHh-cCCcEEEEec--cCCHHHHHHHHHHHHc
Confidence            344688999999999999998887642222 1124566654  4456788877765543

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=92.45  E-value=0.054  Score=44.82  Aligned_cols=23  Identities=22%  Similarity=0.341  Sum_probs=20.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ...-|.|+|.+|+|||||...+.
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            35678999999999999999884

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=92.44  E-value=0.046  Score=50.19  Aligned_cols=23  Identities=22%  Similarity=0.107  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        31 Ge~~~llGpnGsGKSTLLr~iaG   53 (353)
T 1oxx_K           31 GERFGILGPSGAGKTTFMRIIAG   53 (353)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999975

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=92.44  E-value=0.09  Score=42.93  Aligned_cols=25  Identities=12%  Similarity=0.190  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|..|+|||||...+.++
T Consensus        15 ~~~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           15 YLFKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3456899999999999999998865

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=92.42  E-value=0.059  Score=45.35  Aligned_cols=22  Identities=9%  Similarity=0.055  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|+.|+||||+++.+..
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999876

>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=92.42  E-value=0.08  Score=49.34  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|.|+.|+||||||..+..
T Consensus         2 ~~~i~i~GptgsGKttla~~La~   24 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQ   24 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHH
T ss_pred             CcEEEEECcchhhHHHHHHHHHH
Confidence            36899999999999999998875

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.41  E-value=0.075  Score=42.69  Aligned_cols=24  Identities=13%  Similarity=0.163  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.++|.+|+|||||...+.+.
T Consensus        10 ~~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           10 AFKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            446899999999999999988764

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.34  E-value=0.071  Score=48.81  Aligned_cols=23  Identities=22%  Similarity=0.349  Sum_probs=21.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|+|..|+|||||.+.+.+.
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~   94 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNG   94 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999985

>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=92.33  E-value=0.076  Score=43.54  Aligned_cols=24  Identities=17%  Similarity=0.207  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999998764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.33  E-value=0.059  Score=49.57  Aligned_cols=23  Identities=17%  Similarity=0.291  Sum_probs=20.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|+|..|.|||||++.+..-
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~  198 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQE  198 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            48999999999999999999873

>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=92.31  E-value=0.083  Score=47.24  Aligned_cols=25  Identities=8%  Similarity=0.170  Sum_probs=21.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....++|+|.+|+|||||...+...
T Consensus         7 r~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            7 YCGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHCC
Confidence            3568999999999999999999764

>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=92.31  E-value=0.08  Score=43.69  Aligned_cols=24  Identities=13%  Similarity=0.220  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456899999999999999998764

>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=92.30  E-value=0.075  Score=43.71  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999988764

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=92.29  E-value=0.087  Score=43.15  Aligned_cols=26  Identities=12%  Similarity=-0.010  Sum_probs=22.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .....|.|+|.+|+|||||...+.+.
T Consensus        15 ~~~~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           15 KTKLQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             -CEEEEEEECCTTSCHHHHHHHHSCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            34678999999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.23  E-value=0.074  Score=43.47  Aligned_cols=24  Identities=13%  Similarity=0.086  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+...
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            446889999999999999999875

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=92.21  E-value=0.074  Score=43.97  Aligned_cols=24  Identities=25%  Similarity=0.225  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhC
Confidence            457899999999999999998865

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=92.19  E-value=0.095  Score=45.89  Aligned_cols=24  Identities=13%  Similarity=0.163  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|+++|.+|+|||||...+...
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999998864

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=92.18  E-value=0.13  Score=48.88  Aligned_cols=91  Identities=14%  Similarity=0.094  Sum_probs=52.0

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCc--eeeEEEEEcCCCC-CHHHHHHHHHHHhCCCCCcc--ccchhh------HH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHY--FDCHAWVPGTYPY-DADQMLDIVIKFLMPSSRLS--EIMDKN------YE  249 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~-~~~~il~~il~~~~~~~~~~--~~~~~~------~~  249 (334)
                      -++|.|..|+|||+|+..+.++......  =+.++++-+.+.. .+.++..++.+.-..+....  ...+..      --
T Consensus       154 r~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~r~~~~  233 (469)
T 2c61_A          154 KLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTP  233 (469)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHHHHHHH
Confidence            4677899999999999999886443211  1356677777654 45667777665311110000  001110      00


Q ss_pred             HHHHHHHHHc---CCCeEEEEEeCC
Q 038944          250 MKKIILHEYL---MTKRYLNVIDDV  271 (334)
Q Consensus       250 ~l~~~l~~~L---~~kr~LlVlDdv  271 (334)
                      ...-.+-+++   +|+..|+++||+
T Consensus       234 ~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          234 RMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             HHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEeCH
Confidence            1223334444   479999999997

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=92.18  E-value=0.075  Score=45.63  Aligned_cols=23  Identities=17%  Similarity=0.134  Sum_probs=20.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.-++|.|++|+||||+|+.+.+
T Consensus         8 ~~~~~~~G~pGsGKsT~a~~L~~   30 (230)
T 3gmt_A            8 HMRLILLGAPGAGKGTQANFIKE   30 (230)
T ss_dssp             -CEEEEECCTTSCHHHHHHHHHH
T ss_pred             ccceeeECCCCCCHHHHHHHHHH
Confidence            35689999999999999999876

>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=92.17  E-value=0.099  Score=44.26  Aligned_cols=25  Identities=8%  Similarity=0.215  Sum_probs=21.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|.|+|.+|+|||||...+...
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999998764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=92.16  E-value=0.08  Score=42.96  Aligned_cols=26  Identities=8%  Similarity=0.001  Sum_probs=22.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccC
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ...-|.|+|.+|+|||||...+.+..
T Consensus        17 ~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           17 RELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            35678999999999999999998653

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.16  E-value=0.19  Score=40.73  Aligned_cols=24  Identities=13%  Similarity=-0.032  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            567899999999999999998853

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=92.15  E-value=0.091  Score=47.11  Aligned_cols=26  Identities=12%  Similarity=0.221  Sum_probs=23.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++...|+|+|.+|+|||||...+...
T Consensus         8 ~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            8 MKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            45789999999999999999998864

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=92.14  E-value=0.084  Score=44.23  Aligned_cols=22  Identities=14%  Similarity=0.102  Sum_probs=20.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|.|.|+.|+||||+++.+.+
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~   28 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAE   28 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHH
Confidence            5899999999999999999987

>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=92.13  E-value=0.084  Score=43.25  Aligned_cols=24  Identities=8%  Similarity=0.038  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.++|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999998875

>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=92.11  E-value=0.1  Score=43.53  Aligned_cols=24  Identities=8%  Similarity=0.008  Sum_probs=20.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            456889999999999999988764

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=92.10  E-value=0.08  Score=44.21  Aligned_cols=24  Identities=13%  Similarity=0.066  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+...
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998865

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=92.09  E-value=0.08  Score=49.24  Aligned_cols=23  Identities=17%  Similarity=0.128  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhC
Confidence            45899999999999999999975

>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=92.09  E-value=0.086  Score=42.99  Aligned_cols=24  Identities=8%  Similarity=0.185  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998764

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.09  E-value=0.079  Score=43.42  Aligned_cols=24  Identities=17%  Similarity=0.148  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            8 DYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCcHHHHHHHHHcC
Confidence            456899999999999999998763

>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=92.08  E-value=0.14  Score=51.93  Aligned_cols=55  Identities=24%  Similarity=0.196  Sum_probs=38.8

Q ss_pred             CCCCCeeechhhHHHHHHHHhcC-----------CCCceEEEEEccCCccHHHHHHHHHccCCCCCce
Q 038944          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYF  209 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  209 (334)
                      ..-.++.|.++.++.|.+.+.-.           -...+=+-++|++|.|||.||+.+.+  .....|
T Consensus       474 v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~--e~~~~f  539 (806)
T 3cf2_A          474 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQANF  539 (806)
T ss_dssp             CCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHH--TTTCEE
T ss_pred             CCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHH--HhCCce
Confidence            34456788888888887765421           12334567899999999999999999  444433

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.08  E-value=0.079  Score=43.35  Aligned_cols=24  Identities=13%  Similarity=0.202  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            346889999999999999998875

>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=92.07  E-value=0.087  Score=43.03  Aligned_cols=24  Identities=8%  Similarity=-0.015  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999998864

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=92.07  E-value=0.058  Score=55.66  Aligned_cols=23  Identities=13%  Similarity=0.091  Sum_probs=20.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .-.+++|+|+.|.|||||.+.+.
T Consensus       672 ~g~i~~ItGPNGaGKSTlLr~i~  694 (918)
T 3thx_B          672 SERVMIITGPNMGGKSSYIKQVA  694 (918)
T ss_dssp             SCCEEEEESCCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCchHHHHHHHH
Confidence            34699999999999999999874

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=92.05  E-value=0.16  Score=47.69  Aligned_cols=24  Identities=8%  Similarity=0.159  Sum_probs=21.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|+|+.|+|||||.+.+..
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg  189 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQ  189 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHh
Confidence            356999999999999999998875

>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=92.03  E-value=0.13  Score=44.27  Aligned_cols=52  Identities=12%  Similarity=-0.014  Sum_probs=32.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVI  231 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il  231 (334)
                      -..|.|.|..|+||||+++.+.+... ..++.+.....-+......+.+++++
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~-~~~~~~~~~~rep~~t~~g~~ir~~l   78 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQ-QNGIDHITRTREPGGTLLAEKLRALV   78 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHH-HTTCCCEEEEESSCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-hcCCCeeeeecCCCCCHHHHHHHHHH
Confidence            46899999999999999999987321 12355344443333323344455555

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.00  E-value=0.072  Score=50.08  Aligned_cols=21  Identities=19%  Similarity=0.499  Sum_probs=19.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|+|..|+|||||.+.++.-
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            999999999999999999763

>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=91.99  E-value=0.085  Score=43.48  Aligned_cols=23  Identities=22%  Similarity=0.267  Sum_probs=19.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..-|.|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            35689999999999999988764

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=91.99  E-value=0.089  Score=43.03  Aligned_cols=24  Identities=17%  Similarity=0.249  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            346889999999999999988764

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=91.98  E-value=0.085  Score=43.44  Aligned_cols=24  Identities=8%  Similarity=0.011  Sum_probs=20.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999988764

>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=91.97  E-value=0.082  Score=44.03  Aligned_cols=24  Identities=17%  Similarity=0.321  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456899999999999999988754

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=91.95  E-value=0.092  Score=42.81  Aligned_cols=24  Identities=4%  Similarity=0.170  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|..|+|||||...+...
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998754

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=91.93  E-value=0.071  Score=51.95  Aligned_cols=23  Identities=17%  Similarity=0.036  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.++.|+|+.|+|||||++.+..
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~  391 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAA  391 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHH
Confidence            46899999999999999999987

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=91.92  E-value=0.092  Score=42.77  Aligned_cols=24  Identities=13%  Similarity=0.200  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        15 ~~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           15 TLKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999998764

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=91.91  E-value=0.14  Score=41.70  Aligned_cols=35  Identities=17%  Similarity=-0.030  Sum_probs=24.8

Q ss_pred             HHHHHhcCC-CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          168 LLDLLIEGP-PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       168 l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.++|.--. .+..-|.|+|.+|+|||||...+..+
T Consensus        10 ~~~~l~~f~~~~~~~i~v~G~~~~GKssli~~l~~~   45 (189)
T 2x77_A           10 LKQTLGLLPADRKIRVLMLGLDNAGKTSILYRLHLG   45 (189)
T ss_dssp             HHHHHHTSCTTSCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             HHHHhhhccCCCceEEEEECCCCCCHHHHHHHHHcC
Confidence            445443322 33456899999999999999988653

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=91.89  E-value=0.091  Score=43.49  Aligned_cols=24  Identities=13%  Similarity=0.231  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            8 LFKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            456899999999999999998764

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=91.89  E-value=0.092  Score=43.30  Aligned_cols=25  Identities=12%  Similarity=0.203  Sum_probs=21.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|+|.+|+|||||...+...
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhC
Confidence            3567899999999999999998764

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=91.88  E-value=0.088  Score=43.56  Aligned_cols=24  Identities=17%  Similarity=0.264  Sum_probs=20.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456889999999999999988754

>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=91.87  E-value=0.1  Score=50.54  Aligned_cols=23  Identities=13%  Similarity=0.121  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.++|++|.||||+|+.+..
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~   57 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTR   57 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999976

>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=91.85  E-value=0.067  Score=43.18  Aligned_cols=24  Identities=17%  Similarity=0.032  Sum_probs=20.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...-|.|+|.+|+|||||...+.+
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            356788999999999999998874

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=91.80  E-value=0.097  Score=42.40  Aligned_cols=24  Identities=13%  Similarity=-0.032  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|..|+|||||...+.+.
T Consensus        21 ~~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           21 EHKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            356899999999999999998864

>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=91.80  E-value=0.086  Score=43.37  Aligned_cols=24  Identities=4%  Similarity=-0.090  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+...
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhC
Confidence            456899999999999999998753

>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=91.78  E-value=0.092  Score=43.47  Aligned_cols=23  Identities=17%  Similarity=0.133  Sum_probs=18.8

Q ss_pred             ceEEEEE-ccCCccHHHHHHHHHc
Q 038944          179 LSVVVIL-DSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~Iv-G~gGvGKTtLa~~v~~  201 (334)
                      .++|+|+ +-||+||||+|..+..
T Consensus         1 M~vi~v~s~kgG~GKTt~a~~la~   24 (206)
T 4dzz_A            1 MKVISFLNPKGGSGKTTAVINIAT   24 (206)
T ss_dssp             CEEEEECCSSTTSSHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCccHHHHHHHHHH
Confidence            3688888 5689999999988764

>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=91.76  E-value=0.092  Score=46.98  Aligned_cols=31  Identities=19%  Similarity=0.377  Sum_probs=25.7

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHH
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +++|.+.+..     .+++++|..|+|||||.+.+.
T Consensus       156 i~~L~~~l~G-----~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          156 IDELVDYLEG-----FICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             HHHHHHHTTT-----CEEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHhhccC-----cEEEEECCCCCCHHHHHHHHH
Confidence            5666666643     488999999999999999998

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=91.76  E-value=0.11  Score=44.37  Aligned_cols=25  Identities=16%  Similarity=0.211  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|+++|.+|+|||||...+...
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCC
Confidence            4567899999999999999999874

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.72  E-value=0.099  Score=43.46  Aligned_cols=23  Identities=9%  Similarity=-0.005  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|.+|+|||||...+.+.
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcC
Confidence            46899999999999999988864

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=91.72  E-value=0.093  Score=43.97  Aligned_cols=24  Identities=17%  Similarity=0.090  Sum_probs=20.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC-
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            456889999999999999998764

>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=91.69  E-value=0.14  Score=48.68  Aligned_cols=36  Identities=11%  Similarity=0.112  Sum_probs=25.8

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+..+...+..++   ..+.|.|.+|+||||++..+...
T Consensus        33 av~~~~~~i~~~~---~~~li~G~aGTGKT~ll~~~~~~   68 (459)
T 3upu_A           33 AFNIVMKAIKEKK---HHVTINGPAGTGATTLTKFIIEA   68 (459)
T ss_dssp             HHHHHHHHHHSSS---CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCC---CEEEEEeCCCCCHHHHHHHHHHH
Confidence            3344444454433   38999999999999999888763

>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=91.68  E-value=0.1  Score=43.74  Aligned_cols=23  Identities=26%  Similarity=0.111  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -+.+.|.|..|+||||||..+..
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~   56 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQ   56 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999999987

>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=91.67  E-value=0.12  Score=49.88  Aligned_cols=45  Identities=11%  Similarity=0.073  Sum_probs=30.2

Q ss_pred             eeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          158 TVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -+.+.+-.+.+.+..-...++..+|.+.|+.|+||||+|+.+...
T Consensus       374 ~f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~  418 (511)
T 1g8f_A          374 WFSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLST  418 (511)
T ss_dssp             TTSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHH
T ss_pred             cccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHH
Confidence            334444444444433222234578999999999999999999884

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=91.66  E-value=0.097  Score=44.84  Aligned_cols=24  Identities=8%  Similarity=-0.079  Sum_probs=18.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -..|.|-|+.|+||||+++.+.+.
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~   48 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDR   48 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999873

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=91.63  E-value=0.099  Score=48.01  Aligned_cols=23  Identities=9%  Similarity=0.226  Sum_probs=21.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|+|.+|+|||||.+.+...
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~  238 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGL  238 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CEEEEECCCCccHHHHHHHHhcc
Confidence            48999999999999999999874

>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=91.60  E-value=0.12  Score=42.90  Aligned_cols=24  Identities=8%  Similarity=0.005  Sum_probs=20.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        30 ~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           30 AIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            346789999999999999888764

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=91.58  E-value=0.087  Score=43.24  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=19.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|..|+|||||...+.+.
T Consensus        27 ~ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           27 LQVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHCC-
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45889999999999999998764

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=91.56  E-value=0.078  Score=50.45  Aligned_cols=23  Identities=17%  Similarity=0.135  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||++.+..
T Consensus       138 Ge~v~IvGpnGsGKSTLlr~L~G  160 (460)
T 2npi_A          138 GPRVVIVGGSQTGKTSLSRTLCS  160 (460)
T ss_dssp             CCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999876

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=91.51  E-value=0.1  Score=42.65  Aligned_cols=24  Identities=13%  Similarity=0.106  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           18 MLKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            347899999999999999998864

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.46  E-value=0.11  Score=43.11  Aligned_cols=24  Identities=8%  Similarity=0.254  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+...
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            457899999999999999988754

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=91.44  E-value=0.11  Score=43.04  Aligned_cols=24  Identities=13%  Similarity=0.166  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhC
Confidence            457899999999999999988764

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=91.42  E-value=0.11  Score=42.90  Aligned_cols=23  Identities=13%  Similarity=0.008  Sum_probs=20.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|.+|+|||||...+.+.
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999998764

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=91.39  E-value=0.11  Score=43.17  Aligned_cols=24  Identities=8%  Similarity=-0.046  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         9 ~~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A            9 FIKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456899999999999999888754

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=91.34  E-value=0.15  Score=43.14  Aligned_cols=52  Identities=10%  Similarity=-0.051  Sum_probs=32.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      ..|.+-|..|+||||+++.+.+.-.- ..+....+..-+......+.+++++.
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~-~~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQ-LGIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHH-TTCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH-cCCCcceeeeCCCCCHHHHHHHHHHh
Confidence            57899999999999999999874221 22322333333333345566666665

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=91.34  E-value=0.27  Score=47.68  Aligned_cols=58  Identities=10%  Similarity=0.081  Sum_probs=38.8

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHH
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDI  229 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~  229 (334)
                      +.++.|..=. .-.-++|.|..|+|||+|+..+.+..    +-+.++++-+.+.. .+.+++.+
T Consensus       221 rvID~l~Pig-rGqr~~Ifgg~g~GKT~L~~~ia~~~----~~~v~V~~~iGER~~Ev~e~~~~  279 (600)
T 3vr4_A          221 RVIDTFFPVT-KGGAAAVPGPFGAGKTVVQHQIAKWS----DVDLVVYVGCGERGNEMTDVVNE  279 (600)
T ss_dssp             HHHHHHSCCB-TTCEEEEECCTTSCHHHHHHHHHHHS----SCSEEEEEEEEECHHHHHHHHHH
T ss_pred             hhhhccCCcc-CCCEEeeecCCCccHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHH
Confidence            4566665421 12368999999999999999998853    23567788787663 34444444

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=91.32  E-value=0.099  Score=46.64  Aligned_cols=26  Identities=15%  Similarity=0.187  Sum_probs=23.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+..|+|+|..|+|||||...+...
T Consensus        22 ~~~~~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B           22 LDLPQIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             TCCCEEEEEECSSSSHHHHHHHHHTS
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHCC
Confidence            45778999999999999999999764

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=91.29  E-value=0.089  Score=44.13  Aligned_cols=26  Identities=8%  Similarity=-0.017  Sum_probs=22.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccC
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ....|.|+|..|+|||||...+....
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            45678999999999999999998764

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=91.28  E-value=0.11  Score=50.58  Aligned_cols=127  Identities=14%  Similarity=0.200  Sum_probs=63.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCC--CC-cee-eEEEEEcCC----CCCHHHHHHHH--------------HHHhCCC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYV--KH-YFD-CHAWVPGTY----PYDADQMLDIV--------------IKFLMPS  237 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~--~~-~F~-~~~wv~vs~----~~~~~~il~~i--------------l~~~~~~  237 (334)
                      .+++|+|..|.|||||++.++.-..-  .. .+. ...+|.-..    ..++..++...              ++.++..
T Consensus       313 e~~~i~G~NGsGKSTLlk~l~Gl~~p~~G~i~~~~~i~~v~Q~~~~~~~~tv~~~~~~~~~~~~~~~~~~~~~l~~~~l~  392 (538)
T 1yqt_A          313 EVIGIVGPNGIGKTTFVKMLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELLKPLGII  392 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCCSBCCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHTCHHHHHHTTTTTTCG
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECceEEEEecCCcCCCCCcHHHHHHhhhccCCCHHHHHHHHHHHcCCh
Confidence            58999999999999999999873211  11 112 133432211    12344433222              1111111


Q ss_pred             CCc---cccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh---hHHHHHHhhCCC--CCCCeEEEEecCChHHHhhcc
Q 038944          238 SRL---SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI---EVCDIIREILPD--NQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       238 ~~~---~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~---~~w~~l~~~l~~--~~~gsrIivTTr~~~va~~~~  307 (334)
                      ...   ....+-. +.-.-.|-..|..+.-+|+||.--+.   ..-..+...+..  ...|.-||++|.+.+.+..++
T Consensus       393 ~~~~~~~~~LSGG-e~qrv~lAraL~~~p~lLlLDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vsHd~~~~~~~~  469 (538)
T 1yqt_A          393 DLYDREVNELSGG-ELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDVLMIDYVS  469 (538)
T ss_dssp             GGTTSBGGGCCHH-HHHHHHHHHHHTSCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHHTCEEEEECSCHHHHHHHC
T ss_pred             hhhcCChhhCCHH-HHHHHHHHHHHHhCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHhC
Confidence            000   0111111 12233445556667778999998543   222222222211  122555888888877766544

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=91.25  E-value=0.1  Score=50.74  Aligned_cols=22  Identities=27%  Similarity=0.403  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|+|||||++.++.
T Consensus       295 ei~~i~G~nGsGKSTLl~~l~G  316 (538)
T 3ozx_A          295 EIIGILGPNGIGKTTFARILVG  316 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999986

>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=91.24  E-value=1.3  Score=39.86  Aligned_cols=103  Identities=10%  Similarity=-0.061  Sum_probs=60.2

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhh
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKN  247 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~  247 (334)
                      +.+.|. + .-.++.-++|..|.||++.+..+.+... ...|+....+.+....+..                       
T Consensus         9 l~~~l~-~-~~~~~yl~~G~e~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~-----------------------   62 (343)
T 1jr3_D            9 LRAQLN-E-GLRAAYLLLGNDPLLLQESQDAVRQVAA-AQGFEEHHTFSIDPNTDWN-----------------------   62 (343)
T ss_dssp             HHHHHH-H-CCCSEEEEEESCHHHHHHHHHHHHHHHH-HHTCCEEEEEECCTTCCHH-----------------------
T ss_pred             HHHHHh-c-CCCcEEEEECCcHHHHHHHHHHHHHHHH-hCCCCeeEEEEecCCCCHH-----------------------
Confidence            444444 2 3456888999999999999888866211 1123221222233333333                       


Q ss_pred             HHHHHHHHHHH-cCCCeEEEEEeCCC---ChhHHHHHHhhCCCCCCCeEEEEecC
Q 038944          248 YEMKKIILHEY-LMTKRYLNVIDDVW---NIEVCDIIREILPDNQNRSRVLITLT  298 (334)
Q Consensus       248 ~~~l~~~l~~~-L~~kr~LlVlDdvw---~~~~w~~l~~~l~~~~~gsrIivTTr  298 (334)
                        ++.+.+... +-+++-++|+|++.   +...++.+...+..-..++.+|++|.
T Consensus        63 --~l~~~~~~~plf~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~  115 (343)
T 1jr3_D           63 --AIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGN  115 (343)
T ss_dssp             --HHHHHHHHHHHCCSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEES
T ss_pred             --HHHHHhcCcCCccCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcC
Confidence              333222221 34566788889884   45788888877765556787777654

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=91.21  E-value=0.11  Score=43.72  Aligned_cols=23  Identities=22%  Similarity=0.267  Sum_probs=20.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..-|.|+|.+|+|||||...+..
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            45689999999999999988864

>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=91.18  E-value=0.099  Score=49.09  Aligned_cols=21  Identities=14%  Similarity=0.423  Sum_probs=19.1

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+|+|..|+|||||.+.+...
T Consensus        34 I~lvG~sGaGKSTLln~L~g~   54 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLT   54 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            499999999999999999864

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=91.14  E-value=0.064  Score=52.80  Aligned_cols=45  Identities=20%  Similarity=0.138  Sum_probs=29.8

Q ss_pred             CeeechhhHHHHHHHHhcCCC---------CceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDLLIEGPP---------QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~---------~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.+..+..+.-.|..+..         .-.-+-++|.+|+|||+||+.+.+
T Consensus       296 ~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~  349 (595)
T 3f9v_A          296 SIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISR  349 (595)
T ss_dssp             TTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSST
T ss_pred             hhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHH
Confidence            466776655555444433310         001478899999999999999887

>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=91.10  E-value=0.086  Score=43.03  Aligned_cols=25  Identities=16%  Similarity=0.003  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccC
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ..-|.|+|.+|+|||||...+.+..
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            3468899999999999999987653

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=91.09  E-value=0.11  Score=50.36  Aligned_cols=23  Identities=22%  Similarity=0.039  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        47 Ge~~~LvG~NGaGKSTLlk~l~G   69 (538)
T 1yqt_A           47 GMVVGIVGPNGTGKSTAVKILAG   69 (538)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999985

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=91.08  E-value=0.11  Score=50.35  Aligned_cols=24  Identities=13%  Similarity=0.145  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|+|+.|+|||||.+.+..
T Consensus        24 ~Gei~gLiGpNGaGKSTLlkiL~G   47 (538)
T 3ozx_A           24 NNTILGVLGKNGVGKTTVLKILAG   47 (538)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            346999999999999999999986

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=91.06  E-value=0.13  Score=48.97  Aligned_cols=23  Identities=9%  Similarity=0.098  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+|.++|++|+||||+++.+..
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~   61 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTR   61 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHH
Confidence            45889999999999999999876

>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=91.06  E-value=0.28  Score=41.18  Aligned_cols=50  Identities=10%  Similarity=0.148  Sum_probs=31.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      +.|+|=|..|+||||+++.+.+.  ....+++. ...-+......+.+++++.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~--L~~~~~v~-~~~eP~~t~~g~~ir~~l~   52 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHR--LVKDYDVI-MTREPGGVPTGEEIRKIVL   52 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH--HTTTSCEE-EEESSTTCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH--HHCCCCEE-EeeCCCCChHHHHHHHHHh
Confidence            46888899999999999999884  33334432 2222223334455555554

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=91.05  E-value=0.27  Score=43.29  Aligned_cols=27  Identities=7%  Similarity=0.116  Sum_probs=23.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccC
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      .....|+|+|.+|+|||||...+....
T Consensus        24 ~~~~~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B           24 LDLPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             CCCCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             CCCCeEEEEeCCCCCHHHHHHHHHCCC
Confidence            356789999999999999999998753

>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=91.02  E-value=0.16  Score=42.61  Aligned_cols=24  Identities=13%  Similarity=0.126  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        27 ~~ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           27 RCKLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            346789999999999999988764

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=91.02  E-value=0.12  Score=48.93  Aligned_cols=24  Identities=13%  Similarity=0.127  Sum_probs=21.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|..|+|||||.+.+.+-
T Consensus       157 Gq~~~IvG~sGsGKSTLl~~Iag~  180 (438)
T 2dpy_A          157 GQRMGLFAGSGVGKSVLLGMMARY  180 (438)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            358999999999999999999884

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=91.01  E-value=0.16  Score=43.36  Aligned_cols=56  Identities=4%  Similarity=-0.241  Sum_probs=33.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      ....|.|.|..|+||||+++.+.+.......+++.....-+......+.+++++..
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~~treP~~t~~g~~ir~~l~~   75 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFK   75 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEEEEESSCSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhccCceeeEeeeCCCCChHHHHHHHHHhC
Confidence            45789999999999999999998732110123333312223332344556666653

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=91.00  E-value=0.15  Score=44.11  Aligned_cols=25  Identities=12%  Similarity=0.191  Sum_probs=21.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|+|+|.+|+|||||...+...
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~~   45 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILRK   45 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhCC
Confidence            3567899999999999999998754

>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=90.99  E-value=0.07  Score=43.13  Aligned_cols=24  Identities=13%  Similarity=0.163  Sum_probs=10.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            8 LFKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEEECCCCC------------
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456899999999999999888754

>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=90.94  E-value=0.13  Score=47.42  Aligned_cols=25  Identities=8%  Similarity=0.068  Sum_probs=22.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.++++|+|.+|+|||||...+...
T Consensus       178 ~~~~V~lvG~~naGKSTLln~L~~~  202 (364)
T 2qtf_A          178 NIPSIGIVGYTNSGKTSLFNSLTGL  202 (364)
T ss_dssp             -CCEEEEECBTTSSHHHHHHHHHCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHCC
Confidence            4678999999999999999999874

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=90.94  E-value=0.12  Score=49.32  Aligned_cols=22  Identities=14%  Similarity=0.063  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|+|||||.+.+..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~G   51 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVT   51 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHhc
Confidence            7999999999999999999874

>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=90.92  E-value=0.12  Score=46.08  Aligned_cols=33  Identities=18%  Similarity=0.279  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++++..++..     .+++++|+.|+|||||.+.+...
T Consensus       160 v~~lf~~l~g-----eiv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          160 IEELKEYLKG-----KISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             HHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HHHHHHHhcC-----CeEEEECCCCCcHHHHHHHhccc
Confidence            5666666643     48999999999999999999863

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=90.92  E-value=0.13  Score=43.97  Aligned_cols=107  Identities=14%  Similarity=0.054  Sum_probs=53.0

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc-----cccchhhHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL-----SEIMDKNYEMKKIIL  255 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~-----~~~~~~~~~~l~~~l  255 (334)
                      .|.+.|.||+||||+|-.+..... ..-++.. .+.+...-+... . ..+..+......     .....+.  .+...+
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~-~~G~~V~-v~d~D~q~~~~~-~-al~~gl~~~~~~~~~~~~~~~~e~--~l~~~L   81 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQL-RQGVRVM-AGVVETHGRAET-E-ALLNGLPQQPLLRTEYRGMTLEEM--DLDALL   81 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHH-HTTCCEE-EEECCCTTCHHH-H-HHHTTSCBCCCEEEEETTEEEEEC--CHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH-HCCCCEE-EEEeCCCCChhH-H-HHhcCccccCcceeecCCcccccc--cHHHHH
Confidence            477889999999999877765311 1223333 333333222221 1 112222211000     0011111  222222


Q ss_pred             HHHcCCCeEEEEEeCCCCh--------hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          256 HEYLMTKRYLNVIDDVWNI--------EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       256 ~~~L~~kr~LlVlDdvw~~--------~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      .    .+.=++|+|++=..        ..|.++...++.   |-.|+.|+..+
T Consensus        82 ~----~~pdlvIVDElG~~~~~~~r~~~~~qDV~~~l~s---gidVitT~Nlq  127 (228)
T 2r8r_A           82 K----AAPSLVLVDELAHTNAPGSRHTKRWQDIQELLAA---GIDVYTTVNVQ  127 (228)
T ss_dssp             H----HCCSEEEESCTTCBCCTTCSSSBHHHHHHHHHHT---TCEEEEEEEGG
T ss_pred             h----cCCCEEEEeCCCCCCcccchhHHHHHHHHHHHcC---CCCEEEEcccc
Confidence            2    23448999986532        378888776543   55588887754

>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=90.90  E-value=0.16  Score=40.28  Aligned_cols=22  Identities=14%  Similarity=0.224  Sum_probs=19.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ..+..|+|..|.||||+...++
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~   44 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAIL   44 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHH
Confidence            3588999999999999998876

>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=90.87  E-value=0.24  Score=46.61  Aligned_cols=43  Identities=21%  Similarity=0.251  Sum_probs=32.0

Q ss_pred             echhhHHHHHHHHhcC---------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          160 GLDDRMEELLDLLIEG---------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++-.+.+.+.+...         ......++|+|.+|+|||||.+.+...
T Consensus       152 gv~~L~~~i~~~l~~~~~~~~~~~~~~~~~kvaivG~~gvGKSTLln~l~g~  203 (439)
T 1mky_A          152 NLDTMLETIIKKLEEKGLDLESKPEITDAIKVAIVGRPNVGKSTLFNAILNK  203 (439)
T ss_dssp             SHHHHHHHHHHHHHHTTCCSSSCCCCCSCEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHhcccccccchhccccccCceEEEECCCCCCHHHHHHHHhCC
Confidence            5666667776666521         123468999999999999999999864

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=90.85  E-value=0.14  Score=42.29  Aligned_cols=21  Identities=14%  Similarity=-0.050  Sum_probs=17.4

Q ss_pred             eEEEEEccCCccHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .++.|+|..|+||||++..+.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~   24 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFV   24 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            478899999999999984444

>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=90.79  E-value=0.13  Score=50.83  Aligned_cols=125  Identities=18%  Similarity=0.254  Sum_probs=64.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCC--CCc-ee-eEEEEEcCC----CCCHHHHH--------------HHHHHHhCCC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYV--KHY-FD-CHAWVPGTY----PYDADQML--------------DIVIKFLMPS  237 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~-F~-~~~wv~vs~----~~~~~~il--------------~~il~~~~~~  237 (334)
                      .+++|+|..|+|||||.+.+..-..-  ..- +. ...++.-..    ..++.+.+              .++++.++..
T Consensus       383 ei~~i~G~NGsGKSTLlk~l~Gl~~p~~G~I~~~~~i~~v~Q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l~~~~l~  462 (607)
T 3bk7_A          383 EVIGIVGPNGIGKTTFVKMLAGVEEPTEGKVEWDLTVAYKPQYIKAEYEGTVYELLSKIDSSKLNSNFYKTELLKPLGII  462 (607)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCCSBSCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHHCHHHHHHTHHHHTCT
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCceEEEEeeEEEEEecCccCCCCCcHHHHHHhhhccCCCHHHHHHHHHHHcCCc
Confidence            48999999999999999999863211  111 11 233442211    12333332              2334444432


Q ss_pred             CCc---cccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh---h----HHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          238 SRL---SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI---E----VCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       238 ~~~---~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~---~----~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      ...   ....+.. +.-.-.|-..|..+.-+++||.--+.   .    .++.|.. +.. ..|.-||++|.+.+.+..++
T Consensus       463 ~~~~~~~~~LSGG-e~QRv~iAraL~~~p~lLlLDEPt~~LD~~~~~~l~~~l~~-l~~-~~g~tvi~vsHd~~~~~~~a  539 (607)
T 3bk7_A          463 DLYDRNVEDLSGG-ELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRH-LME-KNEKTALVVEHDVLMIDYVS  539 (607)
T ss_dssp             TTTTSBGGGCCHH-HHHHHHHHHHHTSCCSEEEEECTTTTCCHHHHHHHHHHHHH-HHH-HTTCEEEEECSCHHHHHHHC
T ss_pred             hHhcCChhhCCHH-HHHHHHHHHHHHhCCCEEEEeCCccCCCHHHHHHHHHHHHH-HHH-hCCCEEEEEeCCHHHHHHhC
Confidence            211   0122211 12223444556666778999997543   2    2222222 211 23555888888887776544

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=90.76  E-value=0.16  Score=43.37  Aligned_cols=24  Identities=13%  Similarity=-0.039  Sum_probs=19.7

Q ss_pred             CceEEEEEc-cCCccHHHHHHHHHc
Q 038944          178 QLSVVVILD-SIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG-~gGvGKTtLa~~v~~  201 (334)
                      ..++|+|+| -||+||||+|..+..
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~   27 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAF   27 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHH
Confidence            467899985 589999999988865

>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=90.74  E-value=0.14  Score=44.62  Aligned_cols=23  Identities=9%  Similarity=0.157  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.|+++|.+|+|||||...+...
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~g~   24 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALTNA   24 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            46899999999999999999864

>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=90.66  E-value=0.072  Score=47.87  Aligned_cols=22  Identities=14%  Similarity=0.203  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|.+|+|||||.+.+..
T Consensus       174 ~~~~lvG~sG~GKSTLln~L~g  195 (307)
T 1t9h_A          174 KTTVFAGQSGVGKSSLLNAISP  195 (307)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHhcc
Confidence            4899999999999999999976

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=90.64  E-value=0.13  Score=50.66  Aligned_cols=125  Identities=16%  Similarity=0.193  Sum_probs=63.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCC--CCcee--eEEEEEcC--CCC--CHH--------------HHHHHHHHHhCCC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYV--KHYFD--CHAWVPGT--YPY--DAD--------------QMLDIVIKFLMPS  237 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F~--~~~wv~vs--~~~--~~~--------------~il~~il~~~~~~  237 (334)
                      .+++|+|..|+|||||++.+..-..-  .....  ...++.-.  ..+  ++.              ....++++.++..
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl~~p~~G~~~~~~~i~~~~q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l~~l~l~  458 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKIRGQFLNPQFQTDVVKPLRID  458 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTSSCCSBCCCCCSCCEEEECSSCCCCCCSBHHHHHHHHCSSTTTSHHHHHHTHHHHTST
T ss_pred             eEEEEECCCCCcHHHHHHHHhcCCCCCCCcCccCCcEEEecccccccCCccHHHHHHHHhhcccccHHHHHHHHHHcCCh
Confidence            57999999999999999999863211  11010  11222111  011  122              2223344444432


Q ss_pred             CCc---cccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh---h----HHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          238 SRL---SEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI---E----VCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       238 ~~~---~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~---~----~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      ...   +...+-. +.-.-.|-..|..+.=+|+||.--..   .    .++.|.... . ..|.-||++|.+.+.+..++
T Consensus       459 ~~~~~~~~~LSGG-qkQRv~iAraL~~~p~lLlLDEPT~gLD~~~~~~i~~ll~~l~-~-~~g~tviivtHdl~~~~~~a  535 (608)
T 3j16_B          459 DIIDQEVQHLSGG-ELQRVAIVLALGIPADIYLIDEPSAYLDSEQRIICSKVIRRFI-L-HNKKTAFIVEHDFIMATYLA  535 (608)
T ss_dssp             TTSSSBSSSCCHH-HHHHHHHHHHTTSCCSEEEECCTTTTCCHHHHHHHHHHHHHHH-H-HHTCEEEEECSCHHHHHHHC
T ss_pred             hhhcCChhhCCHH-HHHHHHHHHHHHhCCCEEEEECCCCCCCHHHHHHHHHHHHHHH-H-hCCCEEEEEeCCHHHHHHhC
Confidence            211   0122212 12233455667777788999997543   1    222222221 1 23556888888888776543

>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=90.63  E-value=0.17  Score=45.25  Aligned_cols=25  Identities=12%  Similarity=0.150  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ....|+|+|.+|+|||||...+...
T Consensus         6 ~~g~V~ivG~~nvGKSTLln~l~g~   30 (301)
T 1wf3_A            6 YSGFVAIVGKPNVGKSTLLNNLLGV   30 (301)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999998764

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=90.54  E-value=0.12  Score=45.34  Aligned_cols=23  Identities=13%  Similarity=0.346  Sum_probs=19.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|+|+|.+|+|||||...++..
T Consensus         9 ~~I~vvG~~g~GKSTLin~L~~~   31 (274)
T 3t5d_A            9 FTLMVVGESGLGKSTLINSLFLT   31 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHSSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            35889999999999999988754

>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=90.48  E-value=0.12  Score=44.20  Aligned_cols=21  Identities=14%  Similarity=0.189  Sum_probs=17.8

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|+|.|-||+||||+|..+..
T Consensus         2 kI~vs~kGGvGKTt~a~~LA~   22 (254)
T 3kjh_A            2 KLAVAGKGGVGKTTVAAGLIK   22 (254)
T ss_dssp             EEEEECSSSHHHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHH
Confidence            367789999999999988865

>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=90.44  E-value=0.16  Score=49.62  Aligned_cols=24  Identities=17%  Similarity=0.029  Sum_probs=21.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...+|.|.|++|+||||+|+.+.+
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~  418 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQV  418 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHH
Confidence            457899999999999999999987

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=90.43  E-value=0.14  Score=50.45  Aligned_cols=23  Identities=13%  Similarity=0.078  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||.+.+..
T Consensus       103 Gei~~LvGpNGaGKSTLLkiL~G  125 (608)
T 3j16_B          103 GQVLGLVGTNGIGKSTALKILAG  125 (608)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            45999999999999999999975

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=90.42  E-value=0.33  Score=44.11  Aligned_cols=53  Identities=17%  Similarity=0.011  Sum_probs=36.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHh
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFL  234 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~  234 (334)
                      .-.++.|.|.+|+||||||..+..+...  +=..++|++  -+-+...+...++...
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fS--lEms~~ql~~Rlls~~   97 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFS--LEMSAEQLALRALSDL   97 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEE--SSSCHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEe--CCCCHHHHHHHHHHHh
Confidence            3458899999999999999888764221  112445554  4567788888876553

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=90.39  E-value=0.17  Score=43.74  Aligned_cols=22  Identities=9%  Similarity=-0.004  Sum_probs=20.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+|.|+.|+||||+|+.+-.
T Consensus         2 ~~i~ltG~~~sGK~tv~~~l~~   23 (241)
T 1dek_A            2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999998876

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.39  E-value=0.39  Score=55.04  Aligned_cols=98  Identities=14%  Similarity=0.154  Sum_probs=58.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHccC-CCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHH
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSS-YVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  258 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~-~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~  258 (334)
                      .-+-+||.+|.||||+.+.+.+-. ++.. ......+--++..+..+++    ..+....   ..+.+.  -+...+++.
T Consensus       924 ~gvmlvGptgsGKTt~~~~La~al~~l~~-~~~~~~~inpk~~t~~el~----G~~d~~t---~eW~DG--ils~~~R~~  993 (2695)
T 4akg_A          924 QALILVGKAGCGKTATWKTVIDAMAIFDG-HANVVYVIDTKVLTKESLY----GSMLKAT---LEWRDG--LFTSILRRV  993 (2695)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHHTC-CEEEEEEECTTTSCHHHHT----TEECTTT---CCEECC--SHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhcC-CCceEEEeCCCCCCHHHhc----ceecCCC---CeEecC--hHHHHHHHH
Confidence            457899999999999998887521 1111 1233344344555654433    2222221   345555  666666665


Q ss_pred             cCC-------CeEEEEEeCCCChhHHHHHHhhCCCC
Q 038944          259 LMT-------KRYLNVIDDVWNIEVCDIIREILPDN  287 (334)
Q Consensus       259 L~~-------kr~LlVlDdvw~~~~w~~l~~~l~~~  287 (334)
                      ..+       .+.-||||+.=+....+.+...|.++
T Consensus       994 ~~~~~~~~~~~~~WivfDG~vD~~WIE~LNsVLDDN 1029 (2695)
T 4akg_A          994 NDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDN 1029 (2695)
T ss_dssp             HTCCCSSCSSEEEEEEECSCCCHHHHHTTHHHHSTT
T ss_pred             HhccccccCCCCeEEEECCCCCHHHHHHHHHHhcCC
Confidence            432       27789999887776666666666544

>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=90.37  E-value=0.16  Score=44.19  Aligned_cols=26  Identities=15%  Similarity=0.061  Sum_probs=20.4

Q ss_pred             CCceEEEEEc-cCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILD-SIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG-~gGvGKTtLa~~v~~~  202 (334)
                      ...++|+|+| -||+||||+|..+...
T Consensus        25 ~~~~vI~v~s~kGGvGKTT~a~~LA~~   51 (267)
T 3k9g_A           25 KKPKIITIASIKGGVGKSTSAIILATL   51 (267)
T ss_dssp             -CCEEEEECCSSSSSCHHHHHHHHHHH
T ss_pred             CCCeEEEEEeCCCCchHHHHHHHHHHH
Confidence            3578999975 6889999999888653

>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=90.34  E-value=0.22  Score=43.77  Aligned_cols=24  Identities=4%  Similarity=0.109  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|+++|.+|+|||||...+...
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            457899999999999999999864

---

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	334
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	8e-11

>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 = 59.4 bits (143), Expect = 8e-11
 Identities = 27/152 (17%), Positives = 49/152 (32%), Gaps = 15/152 (9%)

Query: 154 KSRDTVGLDDRMEELLDLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYNSS--YVKHYFD 210
           K       +  ++ ++  L E        + +    G  K+  A +A + S   +   +D
Sbjct: 18  KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYD 77

Query: 211 CHAWVPGTYPYDADQMLDIVIKFLMPSSRL------SEIMDKNYEMKKIILHEYLMTKRY 264
              W+  +               LM  S        S     +  +K++I +  +     
Sbjct: 78  SIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNT 137

Query: 265 LNVIDDVWNIEVCDIIREILPDNQNRSRVLIT 296
           L V DDV   E     +E       R R L+T
Sbjct: 138 LFVFDDVVQEETIRWAQE------LRLRCLVT 163

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	334
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.96
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.7
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.41
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.34
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.24
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.18
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.09
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.09
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.09
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.06
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.99
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.95
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.95
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.82
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.82
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.71
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.48
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.45
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.4
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.38
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.32
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.27
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.22
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.21
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.2
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.18
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.17
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.17
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.16
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.01
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.97
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.95
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.86
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.84
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.82
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.81
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.79
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.79
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.77
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.72
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.71
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.68
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.68
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.67
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.66
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.63
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.6
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.58
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.54
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.54
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.5
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.39
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.39
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.35
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.31
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.24
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.23
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.15
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.15
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.12
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.08
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.02
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.99
d1okkd2	207	GTPase domain of the signal recognition particle r	95.98
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.87
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.82
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.78
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.75
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.75
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.72
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.65
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.64
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.63
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.62
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.61
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.61
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.58
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.54
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.52
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.48
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.31
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.27
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.27
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.2
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.18
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.17
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.15
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.13
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.09
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.03
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.98
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.98
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.95
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.95
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.88
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.87
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.86
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.8
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.79
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.77
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.76
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.75
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.72
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.7
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.69
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.66
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.65
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.65
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.64
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.6
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	94.56
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.54
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.54
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.54
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.52
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	94.36
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.35
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.33
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.29
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.23
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.21
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.21
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.19
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.16
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.15
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.14
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.14
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	94.08
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	94.05
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.03
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.0
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	93.98
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.97
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.95
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.95
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	93.93
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.92
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.91
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.9
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	93.89
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.86
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	93.78
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	93.78
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.74
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.73
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.72
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.72
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.7
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.66
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.65
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.64
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	93.64
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.63
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.61
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.55
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.54
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.48
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.47
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.46
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.43
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.41
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.39
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.37
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	93.36
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.35
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.34
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	93.33
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.32
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.31
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.3
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	93.29
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.27
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	93.26
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.25
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.24
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.23
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.2
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.18
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.14
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	93.03
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.93
d2fh5b1	207	Signal recognition particle receptor beta-subunit	92.89
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.72
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.67
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.66
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.64
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	92.64
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.51
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.5
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	92.49
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.47
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	92.46
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.43
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.42
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.42
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.3
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	92.29
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.25
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.23
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.17
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.15
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	92.12
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.98
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	91.9
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.86
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	91.76
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	91.74
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.69
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.58
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.48
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	91.34
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	90.99
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.51
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	90.5
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	90.31
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	90.04
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	89.93
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	89.7
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.27
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	89.08
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	88.74
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	88.56
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	88.32
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	87.64
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	87.26
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	87.13
d1tuea_	205	Replication protein E1 helicase domain {Human papi	87.1
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	86.81
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	86.54
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	86.38
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	86.26
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	86.2
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.01
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	85.81
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	85.64
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	85.33
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	85.22
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	84.75
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	83.88
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	83.34
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	82.51
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	82.45
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	81.83
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	81.4
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	81.21
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	81.11
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	80.37
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	80.25

>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=99.96  E-value=1.2e-29  Score=227.27  Aligned_cols=172  Identities=16%  Similarity=0.159  Sum_probs=134.3

Q ss_pred             CCCCeeechhhHHHHHHHHhc-CCCCceEEEEEccCCccHHHHHHHHHccCC--CCCceeeEEEEEcCCCCCHHHHHHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYNSSY--VKHYFDCHAWVPGTYPYDADQMLDIV  230 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~il~~i  230 (334)
                      .++.++||+.++++|+++|.. .+....+|+|+||||+||||||+.+|++..  .+.+|++++||++++.++...+...+
T Consensus        18 ~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~   97 (277)
T d2a5yb3          18 KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFT   97 (277)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHH
T ss_pred             CCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHH
Confidence            456689999999999999975 455688999999999999999999998644  67789999999999999887776666


Q ss_pred             HHHh---CCCCCc--c---ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHH
Q 038944          231 IKFL---MPSSRL--S---EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKM  302 (334)
Q Consensus       231 l~~~---~~~~~~--~---~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~v  302 (334)
                      ...+   +.....  +   ...+..  .....+.+.|.+||||+||||||+.+.|+.+..      .|||||||||+.+|
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~------~~srilvTTR~~~v  169 (277)
T d2a5yb3          98 DILLMLKSEDDLLNFPSVEHVTSVV--LKRMICNALIDRPNTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVEI  169 (277)
T ss_dssp             HHHHHHTTTSCCTTCCCCTTCCHHH--HHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHH------TTCEEEEEESBGGG
T ss_pred             HHHHHHhcchhhcCCccchhhhhHH--HHHHHHHHHhccCCeeEecchhhHHhhhhhhcc------cCceEEEEeehHHH
Confidence            4433   322111  0   122223  456678899999999999999999999886643      48999999999999


Q ss_pred             Hhhcccc-CcccccccCC---------------CChhHHHHHHHhcc
Q 038944          303 FTFLLET-LFSLLICVSR---------------TPRDIQQAVISVVD  333 (334)
Q Consensus       303 a~~~~~~-~~~~l~~l~~---------------~~~~l~~i~~~Iv~  333 (334)
                      |..+... ..|.+.+|+.               .++..++++++||+
T Consensus       170 ~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~  216 (277)
T d2a5yb3         170 SNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIE  216 (277)
T ss_dssp             GGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHH
T ss_pred             HHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHH
Confidence            9987655 5688888882               44567888888875

>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=98.70  E-value=7.6e-08  Score=82.78  Aligned_cols=117  Identities=14%  Similarity=0.103  Sum_probs=81.5

Q ss_pred             CCCCCeeechhhHHHHHHHHhc----CCCCceEEEEEccCCccHHHHHHHHHccCCCCCcee-eEEEEEcCCCCCHHHHH
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE----GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD-CHAWVPGTYPYDADQML  227 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~il  227 (334)
                      ..+..++||+++.+.|.++|..    .......+.|+|++|+||||+|+.+.+..  ...+. ..+|+..........++
T Consensus        13 y~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~   90 (276)
T d1fnna2          13 YVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY--KDKTTARFVYINGFIYRNFTAII   90 (276)
T ss_dssp             CCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHH--TTSCCCEEEEEETTTCCSHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHH--hcccCCcEEEecchhhhhhhhhh
Confidence            3455689999999999999864    33456789999999999999999999843  22222 24577777778888999


Q ss_pred             HHHHHHhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCCh
Q 038944          228 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNI  274 (334)
Q Consensus       228 ~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~  274 (334)
                      ..+.......... ......  .+...+.+.+  .....++++|++++.
T Consensus        91 ~~~~~~~~~~~~~-~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~d~~  136 (276)
T d1fnna2          91 GEIARSLNIPFPR-RGLSRD--EFLALLVEHLRERDLYMFLVLDDAFNL  136 (276)
T ss_dssp             HHHHHHTTCCCCS-SCCCHH--HHHHHHHHHHHHTTCCEEEEEETGGGS
T ss_pred             hhhHHhhhhhhhh-hccchh--HHHHHHHHHHhhcccccccchhHHHHh
Confidence            9999887765543 122222  4445555444  345677778887653

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.41  E-value=3.3e-07  Score=79.13  Aligned_cols=117  Identities=11%  Similarity=0.048  Sum_probs=77.3

Q ss_pred             CCCCCeeechhhHHHHHHHHhc----CC---CCceEEEEEccCCccHHHHHHHHHccCC----CCCceeeEEEEEcCCCC
Q 038944          153 SKSRDTVGLDDRMEELLDLLIE----GP---PQLSVVVILDSIGLDKAAFAGEAYNSSY----VKHYFDCHAWVPGTYPY  221 (334)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----~~---~~~~vi~IvG~gGvGKTtLa~~v~~~~~----~~~~F~~~~wv~vs~~~  221 (334)
                      ..+..++||+.+.+.|.+++..    +.   ....++.++|++|+||||+++.+.+.-.    .........++......
T Consensus        13 ~~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   92 (287)
T d1w5sa2          13 YIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAP   92 (287)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCC
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeecccccc
Confidence            3456789999999999987742    21   2233566789999999999999997411    01112345677888888


Q ss_pred             CHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCC
Q 038944          222 DADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVW  272 (334)
Q Consensus       222 ~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw  272 (334)
                      .....+..+...+...... ......  .+...+.+..  .+..+++++|.+.
T Consensus        93 ~~~~~~~~~~~~~~~~~~~-~~~~~~--~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          93 NLYTILSLIVRQTGYPIQV-RGAPAL--DILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             SHHHHHHHHHHHHTCCCCC-TTCCHH--HHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             chhhHHHHHhhhccccccc-ccchHH--HHHHHHHHHHHhccCccccceeEEE
Confidence            8888888888888765432 122222  4444555444  3566777888774

>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=98.34  E-value=7.2e-07  Score=74.97  Aligned_cols=124  Identities=12%  Similarity=0.160  Sum_probs=70.9

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      .+++|.++.++.|.+|+..+.  .+.+-++|++|+||||+|+.+.+.-..........-...+...+............ 
T Consensus        14 ~divg~~~~~~~L~~~i~~~~--~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~-   90 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFA-   90 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHH-
T ss_pred             HHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhcc-
Confidence            468999999999999998765  33366899999999999999987321111111122222333322221111111000 


Q ss_pred             CCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          236 PSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                                        .......+++-++|+|++...  ..-..+...+......++++++|...
T Consensus        91 ------------------~~~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~  139 (227)
T d1sxjc2          91 ------------------STRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYA  139 (227)
T ss_dssp             ------------------HBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             ------------------ccccccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcH
Confidence                              000111344558889998543  45555666665555678887777653

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.24  E-value=1.2e-06  Score=74.54  Aligned_cols=46  Identities=13%  Similarity=0.035  Sum_probs=35.7

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.++..+.|.+++.... ..+-+-++|++|+||||+|+.+.+.
T Consensus        11 ~diig~~~~~~~L~~~~~~~~-~~~~lll~Gp~G~GKTt~~~~la~~   56 (252)
T d1sxje2          11 NALSHNEELTNFLKSLSDQPR-DLPHLLLYGPNGTGKKTRCMALLES   56 (252)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTT-CCCCEEEECSTTSSHHHHHHTHHHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCCeEEEECCCCCCHHHHHHHHHHh
Confidence            458999888888877776543 2334669999999999999998763

>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=98.18  E-value=6.5e-07  Score=75.55  Aligned_cols=132  Identities=11%  Similarity=0.031  Sum_probs=75.3

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCc---eeeEEEEEcCCCCCHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY---FDCHAWVPGTYPYDADQMLDIVI  231 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~---F~~~~wv~vs~~~~~~~il~~il  231 (334)
                      -.+++|.++.++.|..|+....  .+.+-++|++|+||||+|+.+.+.  +...   +.....+..+.......+...+-
T Consensus        11 ~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtl~~~i~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTKE--LYGPDLMKSRILELNASDERGISIVREKVK   86 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHHH--HHHHHHHTTSEEEECSSSCCCHHHHTTHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChHHHHHHHHHH--HcCCcccccchhheeccccccchHHHHHHH
Confidence            3468999999999999997654  344779999999999999999873  2111   11223344455545444333322


Q ss_pred             HHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCC
Q 038944          232 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTE  299 (334)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~  299 (334)
                      ........   ....      ..+.....++.-++|+|++..  ...+..+...+.......++|+||..
T Consensus        87 ~~~~~~~~---~~~~------~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~  147 (237)
T d1sxjd2          87 NFARLTVS---KPSK------HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY  147 (237)
T ss_dssp             HHHHSCCC---CCCT------THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHhhhhhh---hhhH------HHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccc
Confidence            21111111   0000      112223344445789999854  35566655555444456677776554

>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=98.09  E-value=1.1e-06  Score=75.41  Aligned_cols=43  Identities=16%  Similarity=0.253  Sum_probs=36.0

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|||+++.++|.+.      ..+++.|+|++|+|||+|++.+.+.
T Consensus        10 ~~~~f~GR~~el~~l~~~------~~~~i~i~G~~G~GKTsLl~~~~~~   52 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGL------RAPITLVLGLRRTGKSSIIKIGINE   52 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHT------CSSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhc------cCCEEEEEcCCCCcHHHHHHHHHHH
Confidence            456799999999998763      2357899999999999999999873

>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=98.09  E-value=8.9e-07  Score=74.37  Aligned_cols=124  Identities=12%  Similarity=0.139  Sum_probs=70.3

Q ss_pred             CCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCc-eee-EEEEEcCCCCCHHHHHHHHHH
Q 038944          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY-FDC-HAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~-F~~-~~wv~vs~~~~~~~il~~il~  232 (334)
                      -.+++|.++.++.|.+|+..+.  .+-+-++|++|+||||+|+.+.+.  +... +.. ..-+..+...+...+...+..
T Consensus        14 ~~d~ig~~~~~~~L~~~~~~~~--~~~~ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~   89 (224)
T d1sxjb2          14 LSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVVRNQIKH   89 (224)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHHHTHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHcCC--CCeEEEECCCCCCchhhHHHHHHH--HhccccccccccccccccCCceehhhHHHH
Confidence            3568999999999999998765  334668999999999999988763  2111 111 222334444333333222221


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                      .......                  ...++.-++|+|++...  .....++..+......+++++||...
T Consensus        90 ~~~~~~~------------------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          90 FAQKKLH------------------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             HHHBCCC------------------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             HHHhhcc------------------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCch
Confidence            1111100                  01235568889998643  34444444444444456666665543

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.09  E-value=1.3e-05  Score=67.79  Aligned_cols=45  Identities=20%  Similarity=0.199  Sum_probs=37.2

Q ss_pred             CCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..++.|..++..+.. ...+-++|.+|+||||+|+.+.+
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~-~~~~Ll~Gp~G~GKtt~a~~~~~   56 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRI-HHAYLFSGTRGVGKTSIARLLAK   56 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCC-CSEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHccChHHHHHHHHHHHHcCCC-CeeEEEECCCCCcHHHHHHHHHH
Confidence            4689999999999999977542 34567999999999999998765

>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=98.06  E-value=2e-06  Score=72.42  Aligned_cols=46  Identities=17%  Similarity=0.245  Sum_probs=39.5

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-.+++|.++.++.|..|+..+.  .+.+-++|++|+||||+|+.+.+
T Consensus        22 ~~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCcHHHHHHHHHH
Confidence            34579999999999999998764  44577999999999999999977

>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=97.99  E-value=1e-05  Score=68.71  Aligned_cols=106  Identities=11%  Similarity=0.072  Sum_probs=63.1

Q ss_pred             CCCeeechhhHHHHHHHHhc---------------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC
Q 038944          155 SRDTVGLDDRMEELLDLLIE---------------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY  219 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---------------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  219 (334)
                      -.+++|.+..+++|.+||..               +....+.+-++|++|+||||+|+.+.+..  ..   ...++..+.
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~--~~---~~~~~~~~~   87 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL--GY---DILEQNASD   87 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT--TC---EEEEECTTS
T ss_pred             HHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH--Hh---hhhcccccc
Confidence            35689999999999999853               12345688999999999999999999832  21   234566665


Q ss_pred             CCCHHHHHHHHHHHhCCCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCC
Q 038944          220 PYDADQMLDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVW  272 (334)
Q Consensus       220 ~~~~~~il~~il~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw  272 (334)
                      ..+...+ ....+..............      ........++..++++|++.
T Consensus        88 ~~~~~~~-~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~vi~ide~~  133 (253)
T d1sxja2          88 VRSKTLL-NAGVKNALDNMSVVGYFKH------NEEAQNLNGKHFVIIMDEVD  133 (253)
T ss_dssp             CCCHHHH-HHTGGGGTTBCCSTTTTTC----------CCSSTTSEEEEECSGG
T ss_pred             chhhHHH-HHHHHHHhhcchhhhhhhh------hhhcccccccceEEEeeecc
Confidence            5554333 3333332222111000000      01112235677889999975

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.95  E-value=3e-05  Score=63.16  Aligned_cols=133  Identities=11%  Similarity=0.135  Sum_probs=77.9

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc---CCCC-CceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS---SYVK-HYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~---~~~~-~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      .++||++++++++..|.....  .-+.+||.+|+|||+++..+...   .++- ...+.++|.-     |...++.    
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~k--~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l-----d~~~LiA----   91 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRTK--NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL-----DMGALVA----   91 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS--CEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE-----CHHHHHT----
T ss_pred             CCcCcHHHHHHHHHHHhccCC--CCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEe-----eHHHHhc----
Confidence            478999999999999987553  24579999999999988766641   1222 2234555532     3222221    


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHc--CCCeEEEEEeCCCCh----------hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLNVIDDVWNI----------EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L--~~kr~LlVlDdvw~~----------~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                         +.... +.    +++....+.+.+  .....++++|++-.-          +.-+.+...|..  ..-++|.||..+
T Consensus        92 ---g~~~r-G~----~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~IgatT~e  161 (195)
T d1jbka_          92 ---GAKYR-GE----FEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLD  161 (195)
T ss_dssp             ---TTCSH-HH----HHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEECHH
T ss_pred             ---cCCcc-HH----HHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhC--CCceEEecCCHH
Confidence               11110 11    223333333333  345799999998532          122334444432  236789999888


Q ss_pred             HHHhhccccC
Q 038944          301 KMFTFLLETL  310 (334)
Q Consensus       301 ~va~~~~~~~  310 (334)
                      +.......+.
T Consensus       162 ey~~~~e~d~  171 (195)
T d1jbka_         162 EYRQYIEKDA  171 (195)
T ss_dssp             HHHHHTTTCH
T ss_pred             HHHHHHHcCH
Confidence            8877665543

>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=97.95  E-value=7e-05  Score=64.20  Aligned_cols=134  Identities=16%  Similarity=0.153  Sum_probs=80.1

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc---CCCCCc-eeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS---SYVKHY-FDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~---~~~~~~-F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      .++||+++.++++..|.....  .-+.+||.+|+|||+++..+...   ..+... ...++|..-....           
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~k--~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l-----------   85 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRRK--NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL-----------   85 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS--CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------------
T ss_pred             cccChHHHHHHHHHHHhcCcc--CCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH-----------
Confidence            479999999999999987653  24459999999999988776642   122222 2345554211110           


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHc-CCCeEEEEEeCCCCh----------hHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYL-MTKRYLNVIDDVWNI----------EVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L-~~kr~LlVlDdvw~~----------~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                       +.+.... +.    +++....+.+.+ +.+..++++|++-.-          .+...+..|.-. ...-++|.||..++
T Consensus        86 -iag~~~~-g~----~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~-rg~i~vIgatT~ee  158 (268)
T d1r6bx2          86 -LAGTKYR-GD----FEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS-SGKIRVIGSTTYQE  158 (268)
T ss_dssp             --CCCCCS-SC----HHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS-SCCCEEEEEECHHH
T ss_pred             -hccCccc-hh----HHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh-CCCCeEEEeCCHHH
Confidence             1111110 11    224444444444 556789999997532          133444433322 22468999999999


Q ss_pred             HHhhccccC
Q 038944          302 MFTFLLETL  310 (334)
Q Consensus       302 va~~~~~~~  310 (334)
                      .........
T Consensus       159 y~~~~e~d~  167 (268)
T d1r6bx2         159 FSNIFEKDR  167 (268)
T ss_dssp             HHCCCCCTT
T ss_pred             HHHHHhhcH
Confidence            888776554

>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=97.82  E-value=6.1e-06  Score=68.76  Aligned_cols=121  Identities=18%  Similarity=0.138  Sum_probs=67.6

Q ss_pred             eeechhhH--HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          158 TVGLDDRM--EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       158 ~vGr~~~~--~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      ++|-.+..  .-+.++..........+.|+|.+|+|||.|++.+++.  ........+++      +..++...+...+.
T Consensus        13 ~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~------~~~~~~~~~~~~~~   84 (213)
T d1l8qa2          13 IVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYS------SADDFAQAMVEHLK   84 (213)
T ss_dssp             CCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEE------EHHHHHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHH--hccCccceEEe------chHHHHHHHHHHHH
Confidence            45654333  2333444433334445789999999999999999984  22233344555      34455555555443


Q ss_pred             CCCCccccchhhHHHHHHHHHHHcCCCeEEEEEeCCCCh---hHHHHHHhhCCC--CCCCeEEEEecCCh
Q 038944          236 PSSRLSEIMDKNYEMKKIILHEYLMTKRYLNVIDDVWNI---EVCDIIREILPD--NQNRSRVLITLTEI  300 (334)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~~---~~w~~l~~~l~~--~~~gsrIivTTr~~  300 (334)
                      ....       .  ....    .+. .--+|+|||+...   ..|+.....+-+  ...|.+||+||+..
T Consensus        85 ~~~~-------~--~~~~----~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~  140 (213)
T d1l8qa2          85 KGTI-------N--EFRN----MYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRH  140 (213)
T ss_dssp             HTCH-------H--HHHH----HHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             ccch-------h--hHHH----HHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCc
Confidence            2211       0  2222    222 3458999999532   455543322211  23578899998853

>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=97.82  E-value=5.2e-05  Score=64.36  Aligned_cols=48  Identities=17%  Similarity=0.122  Sum_probs=35.1

Q ss_pred             CCCeeechhhHHHHHHHHh-------cC-CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          155 SRDTVGLDDRMEELLDLLI-------EG-PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~-------~~-~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+.++|..+.++.+++-+.       .. ..+.+-|-++|++|+|||++|+.+.+.
T Consensus         8 ~~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~   63 (246)
T d1d2na_           8 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE   63 (246)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhc
Confidence            3457887777776665543       22 234566789999999999999999983

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.71  E-value=5.2e-05  Score=64.78  Aligned_cols=46  Identities=15%  Similarity=0.250  Sum_probs=36.1

Q ss_pred             CCeeechhhHHHHHHHH----hc-------CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          156 RDTVGLDDRMEELLDLL----IE-------GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L----~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|.+..+++|.+.+    ..       +-...+-+-++|++|+|||+||+.+.+
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~   60 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN   60 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHH
Confidence            46889999998887764    22       112345678999999999999999998

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.48  E-value=0.00016  Score=65.21  Aligned_cols=131  Identities=11%  Similarity=0.137  Sum_probs=69.1

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHH----HHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHH
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAG----EAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIK  232 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~----~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~  232 (334)
                      .++||+++++++++.|.....+  -+-+||.+|+|||+++.    .+.+..--....+.++|.--..     .++..   
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k~--n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~-----~l~ag---   92 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTKN--NPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMG-----SLLAG---   92 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSCC--CCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--------------
T ss_pred             CCcCcHHHHHHHHHHHhcCCCC--CCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHh-----hhhcc---
Confidence            3789999999999999875432  23677999999999764    4444322223345566643211     11110   


Q ss_pred             HhCCCCCccccchhhHHHHHHHHHHHc-CC-CeEEEEEeCCCCh----------hHHHHHHhhCCCCCCCeEEEEecCCh
Q 038944          233 FLMPSSRLSEIMDKNYEMKKIILHEYL-MT-KRYLNVIDDVWNI----------EVCDIIREILPDNQNRSRVLITLTEI  300 (334)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~l~~~l~~~L-~~-kr~LlVlDdvw~~----------~~w~~l~~~l~~~~~gsrIivTTr~~  300 (334)
                       ....    +.    ++.....+...+ .. ..++|++|++-..          +.-+-|.++|..+  .-++|-+|..+
T Consensus        93 -~~~~----g~----~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg--~~~~I~~tT~~  161 (387)
T d1qvra2          93 -AKYR----GE----FEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARG--ELRLIGATTLD  161 (387)
T ss_dssp             ----------C----HHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTT--CCCEEEEECHH
T ss_pred             -cCcc----hh----HHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCC--CcceeeecCHH
Confidence             0000    11    223333333333 33 4799999999543          1223334444232  35688888888


Q ss_pred             HHHhhcccc
Q 038944          301 KMFTFLLET  309 (334)
Q Consensus       301 ~va~~~~~~  309 (334)
                      +... +..+
T Consensus       162 ey~~-~e~d  169 (387)
T d1qvra2         162 EYRE-IEKD  169 (387)
T ss_dssp             HHHH-HTTC
T ss_pred             HHHH-hccc
Confidence            8765 4443

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.45  E-value=7.7e-05  Score=62.50  Aligned_cols=47  Identities=19%  Similarity=0.199  Sum_probs=37.7

Q ss_pred             CCeeechhhHHHHHHHHhcC---CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.+..++.|..|+...   ....+-+-++|++|+||||+|+.+.+.
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhc
Confidence            46899999999999888532   223445678999999999999999883

>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=97.40  E-value=0.00014  Score=60.86  Aligned_cols=47  Identities=17%  Similarity=0.224  Sum_probs=37.3

Q ss_pred             CCeeechhhHHHHHHHHhc---CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDLLIE---GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++||.+..+++|..++..   .....+-+-++|++|+||||+|+.+.+.
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~   58 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHE   58 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999988888763   2233455668999999999999999983

>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=97.38  E-value=8.3e-05  Score=58.40  Aligned_cols=22  Identities=14%  Similarity=0.208  Sum_probs=20.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999987

>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=97.32  E-value=0.00047  Score=56.56  Aligned_cols=127  Identities=11%  Similarity=0.057  Sum_probs=67.9

Q ss_pred             chhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC---CCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCC
Q 038944          161 LDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS---YVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPS  237 (334)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~---~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~  237 (334)
                      .+...+++.+.+..+. -...+-++|+.|+||||+|+.+.+.-   .....-.|      ....+.    ..+.......
T Consensus         7 ~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~------~~~~~~----~~i~~~~~~~   75 (207)
T d1a5ta2           7 LRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSC------GHCRGC----QLMQAGTHPD   75 (207)
T ss_dssp             GHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCC------SCSHHH----HHHHHTCCTT
T ss_pred             cHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccc------cccchh----hhhhhccccc
Confidence            3455677777776654 23458889999999999999776521   00000000      000011    1111111100


Q ss_pred             CCc------cccchhhHHHHHHHHHHHc-----CCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCChH
Q 038944          238 SRL------SEIMDKNYEMKKIILHEYL-----MTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEIK  301 (334)
Q Consensus       238 ~~~------~~~~~~~~~~l~~~l~~~L-----~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~~  301 (334)
                      ...      ......+  + ...+.+.+     .+++-++|+||+..  .+..+.++..+-.....+++|+||.+.+
T Consensus        76 ~~~~~~~~~~~~i~~~--~-ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~  149 (207)
T d1a5ta2          76 YYTLAPEKGKNTLGVD--A-VREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPE  149 (207)
T ss_dssp             EEEECCCTTCSSBCHH--H-HHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGG
T ss_pred             cchhhhhhcccccccc--h-hhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChh
Confidence            000      0011111  2 22233332     35677999999964  4678888887766667888888777654

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=97.27  E-value=0.00012  Score=62.32  Aligned_cols=47  Identities=26%  Similarity=0.282  Sum_probs=35.2

Q ss_pred             CCeeechhhHHHHHHH---HhcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDL---LIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~---L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.++.+++|.+.   +...       ....+-+-++|++|+|||+||+.+.+.
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~   68 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHH
Confidence            5789998888877554   3321       123456779999999999999999983

>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=0.0002  Score=57.03  Aligned_cols=25  Identities=32%  Similarity=0.379  Sum_probs=22.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +...+|-++|++|+||||+|+.+..
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999998876

>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=97.21  E-value=7.2e-05  Score=64.18  Aligned_cols=51  Identities=25%  Similarity=0.267  Sum_probs=37.0

Q ss_pred             CCeeechhhHHHHHHHHh----c-------CCCCceEEEEEccCCccHHHHHHHHHccCCCCCc
Q 038944          156 RDTVGLDDRMEELLDLLI----E-------GPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHY  208 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~----~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~  208 (334)
                      .+++|.++.+++|.+.+.    .       +-...+-|-++|++|+|||+||+.+.+  ...-+
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~--~~~~~   68 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQAN   68 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHH--HTTCE
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHH--HhCCc
Confidence            457888888777766652    1       123455677999999999999999998  44444

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.20  E-value=0.00035  Score=61.24  Aligned_cols=44  Identities=18%  Similarity=0.306  Sum_probs=35.3

Q ss_pred             eeechhhHHHHHHHHhc-------CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          158 TVGLDDRMEELLDLLIE-------GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.+..++.+.+.+..       ++.+..++..+|+.|+|||.||+.+.+
T Consensus        25 v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~   75 (315)
T d1qvra3          25 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA   75 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH
T ss_pred             EeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHH
Confidence            78999999888776642       223456889999999999999998876

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=97.18  E-value=0.00021  Score=60.46  Aligned_cols=47  Identities=21%  Similarity=0.322  Sum_probs=34.5

Q ss_pred             CCeeechhhHHHHHHH---HhcC-------CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          156 RDTVGLDDRMEELLDL---LIEG-------PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       156 ~~~vGr~~~~~~l~~~---L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++|.++.++.|.+.   +...       -...+-+-++|++|+|||+||+.+.+.
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~   65 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   65 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHH
Confidence            4688998887766543   3221       123456889999999999999999983

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.17  E-value=9e-05  Score=58.83  Aligned_cols=23  Identities=17%  Similarity=0.162  Sum_probs=21.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.|.|.|++|+||||||+.+.+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            68899999999999999999987

>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=97.17  E-value=8.9e-05  Score=58.20  Aligned_cols=23  Identities=9%  Similarity=0.135  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|+.|+|..|+|||||++.+.+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~   24 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46999999999999999999986

>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=97.16  E-value=7.4e-05  Score=58.02  Aligned_cols=22  Identities=9%  Similarity=0.279  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|.++|++|+||||+|+.+.+
T Consensus         3 k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4688889999999999999998

>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=97.01  E-value=0.00017  Score=55.60  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=19.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|+|++|+||||||+.+..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5788999999999999998876

>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=96.97  E-value=0.00043  Score=55.42  Aligned_cols=37  Identities=14%  Similarity=0.058  Sum_probs=27.3

Q ss_pred             HHHHHHHHhc-CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIE-GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++.|.+.... ...+.-+|+|.|.+|+||||||+.+.+
T Consensus         7 ~~~~~~~~~~~~~~~~~iIgI~G~~GSGKSTla~~L~~   44 (198)
T d1rz3a_           7 IDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ   44 (198)
T ss_dssp             HHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3444444333 334567999999999999999999986

>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=96.95  E-value=0.00019  Score=56.64  Aligned_cols=24  Identities=17%  Similarity=0.029  Sum_probs=21.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +-.+|.++|++|+||||+|+.+..
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~   28 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQV   28 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999999987

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.86  E-value=0.0002  Score=56.20  Aligned_cols=23  Identities=17%  Similarity=0.335  Sum_probs=20.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++.|.|.|++|+||||+|+.+.+
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            34577999999999999999987

>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=96.84  E-value=0.0053  Score=49.63  Aligned_cols=122  Identities=10%  Similarity=0.056  Sum_probs=68.0

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC--CCCCceeeEEEEEcC-CCCCHHHHHHHHHHHhCCCCCcc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS--YVKHYFDCHAWVPGT-YPYDADQMLDIVIKFLMPSSRLS  241 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~--~~~~~F~~~~wv~vs-~~~~~~~il~~il~~~~~~~~~~  241 (334)
                      ++-+.+++..+  ...-+-++|.+|+||||+|..+.+..  .-..|-| ..++.-. ....+..+ +++.+.+....   
T Consensus         3 ~~~l~~~i~~~--~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~I-R~i~~~~~~~~---   75 (198)
T d2gnoa2           3 LETLKRIIEKS--EGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSP---   75 (198)
T ss_dssp             HHHHHHHHHTC--SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCC---
T ss_pred             HHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHH-HHHHHHHhhCc---
Confidence            44455555544  47789999999999999999877631  1122322 2333211 12222222 22333332211   


Q ss_pred             ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhCCCCCCCeEEEEecCCh-HHHhhccccC
Q 038944          242 EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREILPDNQNRSRVLITLTEI-KMFTFLLETL  310 (334)
Q Consensus       242 ~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l~~~~~gsrIivTTr~~-~va~~~~~~~  310 (334)
                                       ..+++=++|+|++..  .+.++.++..+-.-..++.+|++|.+. .+-.+.-+.+
T Consensus        76 -----------------~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC  130 (198)
T d2gnoa2          76 -----------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRV  130 (198)
T ss_dssp             -----------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTS
T ss_pred             -----------------ccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcce
Confidence                             124555889999864  478888887775545567766666554 3444444433

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.82  E-value=0.00054  Score=57.91  Aligned_cols=41  Identities=17%  Similarity=0.383  Sum_probs=30.2

Q ss_pred             chhhHHHHHHHHhcC---CCCceEEEEEccCCccHHHHHHHHHc
Q 038944          161 LDDRMEELLDLLIEG---PPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       161 r~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+...+.++.|..+   ....+.|-++|++|+||||||+.+.+
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          11 FENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             HHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            344455555556543   24567788999999999999999998

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.81  E-value=0.00029  Score=55.41  Aligned_cols=23  Identities=9%  Similarity=0.027  Sum_probs=21.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|++|+|..|+|||||+..+..
T Consensus         1 Mkii~I~G~~gSGKTTli~~l~~   23 (165)
T d1xjca_           1 MNVWQVVGYKHSGKTTLMEKWVA   23 (165)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHH
Confidence            36999999999999999999876

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.79  E-value=0.00037  Score=56.22  Aligned_cols=26  Identities=19%  Similarity=0.252  Sum_probs=23.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+.+|.|+|++|+||||+|+.+.++
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999999873

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.79  E-value=0.0004  Score=56.12  Aligned_cols=27  Identities=26%  Similarity=0.400  Sum_probs=24.2

Q ss_pred             CCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          176 PPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       176 ~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++..+||.|.|++|+||||+|+.+.++
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            356899999999999999999999884

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00025  Score=55.98  Aligned_cols=23  Identities=17%  Similarity=0.219  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.|.|+|++|+|||||++.+...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            46899999999999999999853

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.72  E-value=0.00036  Score=55.26  Aligned_cols=22  Identities=23%  Similarity=0.264  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++|.|.|++|+||||+++.+.+
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999976

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.71  E-value=0.00017  Score=57.91  Aligned_cols=25  Identities=12%  Similarity=-0.044  Sum_probs=22.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..-.+|.++|++|+||||+|+.+..
T Consensus        17 ~~g~vI~L~G~pGSGKTTiAk~La~   41 (195)
T d1x6va3          17 FRGCTVWLTGLSGAGKTTVSMALEE   41 (195)
T ss_dssp             CCCEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3456899999999999999999976

>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=96.68  E-value=0.0016  Score=54.13  Aligned_cols=23  Identities=17%  Similarity=0.140  Sum_probs=20.6

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999973

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.68  E-value=0.0006  Score=53.48  Aligned_cols=23  Identities=17%  Similarity=0.200  Sum_probs=21.4

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -++|.|.|++|+||||+|+.+.+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999987

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.67  E-value=0.00047  Score=55.94  Aligned_cols=23  Identities=9%  Similarity=0.098  Sum_probs=21.2

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.+|.++|.+|+||||+|+.+.+
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.66  E-value=0.00052  Score=53.80  Aligned_cols=26  Identities=19%  Similarity=0.203  Sum_probs=22.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +....|.|.|++|+||||+|+.+.+.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            34567899999999999999999873

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.63  E-value=0.00061  Score=53.31  Aligned_cols=25  Identities=24%  Similarity=0.307  Sum_probs=22.7

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..+++.|.|++|+||||+|+.+..
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999999987

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.60  E-value=0.00055  Score=53.62  Aligned_cols=23  Identities=4%  Similarity=0.060  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.|.|.+|+||||+|+.+.+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999988

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.58  E-value=0.00039  Score=54.68  Aligned_cols=20  Identities=15%  Similarity=0.190  Sum_probs=17.6

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |.++||+|+||||+++.+.+
T Consensus         4 IvliG~~G~GKSTig~~La~   23 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAK   23 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34559999999999999998

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.54  E-value=0.00041  Score=54.38  Aligned_cols=21  Identities=19%  Similarity=0.333  Sum_probs=19.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++||+|+||||+++.+...
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678899999999999999883

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.0085  Score=47.67  Aligned_cols=24  Identities=21%  Similarity=0.213  Sum_probs=21.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.+|.|.|++|+||||+|+.+.++
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999999883

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=96.50  E-value=0.0022  Score=56.01  Aligned_cols=113  Identities=9%  Similarity=0.085  Sum_probs=64.1

Q ss_pred             CeeechhhHHHHHHHHh-------cCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHH
Q 038944          157 DTVGLDDRMEELLDLLI-------EGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDI  229 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~-------~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~  229 (334)
                      .++|.+..++.+...+.       +.+.+..++..+|+.|+|||.||+.+..-  +..   ..+-+..+.--+...    
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~--l~~---~~i~~d~s~~~~~~~----   93 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA--LGI---ELLRFDMSEYMERHT----   93 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH--HTC---EEEEEEGGGCSSSSC----
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhh--ccC---CeeEeccccccchhh----
Confidence            48999999999877763       12345668889999999999999999872  222   223333332110000    


Q ss_pred             HHHHhCCCCCcc-ccchhhHHHHHHHHHHHcCCCeEEEEEeCCCC--hhHHHHHHhhC
Q 038944          230 VIKFLMPSSRLS-EIMDKNYEMKKIILHEYLMTKRYLNVIDDVWN--IEVCDIIREIL  284 (334)
Q Consensus       230 il~~~~~~~~~~-~~~~~~~~~l~~~l~~~L~~kr~LlVlDdvw~--~~~w~~l~~~l  284 (334)
                       ...+-+..+.- +.....  .+...+.   +....+++||++..  .+.|+.+...+
T Consensus        94 -~~~l~g~~~gy~g~~~~~--~l~~~~~---~~~~~vvl~DeieKa~~~V~~~lLqil  145 (315)
T d1r6bx3          94 -VSRLIGAPPGYVGFDQGG--LLTDAVI---KHPHAVLLLDEIEKAHPDVFNILLQVM  145 (315)
T ss_dssp             -CSSSCCCCSCSHHHHHTT--HHHHHHH---HCSSEEEEEETGGGSCHHHHHHHHHHH
T ss_pred             -hhhhcccCCCccccccCC--hhhHHHH---hCccchhhhcccccccchHhhhhHHhh
Confidence             01111111100 111111  2333332   34567888999974  46777777655

>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=96.39  E-value=0.00087  Score=53.14  Aligned_cols=23  Identities=9%  Similarity=0.237  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +++|.|.|++|+||||+++.+..
T Consensus         1 mkiivi~G~~GsGKTT~~~~La~   23 (194)
T d1nksa_           1 MKIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999976

>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=96.39  E-value=0.0005  Score=54.27  Aligned_cols=21  Identities=10%  Similarity=0.154  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.++|++|+||||+|+.+.+
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            466889999999999999987

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.35  E-value=0.0008  Score=53.01  Aligned_cols=20  Identities=15%  Similarity=0.346  Sum_probs=18.9

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |+|+|++|+|||||++.+..
T Consensus         3 i~I~G~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHh
Confidence            79999999999999999986

>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=96.31  E-value=0.00077  Score=58.78  Aligned_cols=46  Identities=13%  Similarity=0.156  Sum_probs=34.7

Q ss_pred             CeeechhhHHHHHHHHhc------------CCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIE------------GPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~------------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|.++.++.+...+..            .+...+-+..+|++|+|||.||+.+.+.
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhc
Confidence            478999998888765521            0123456678999999999999999983

>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=96.24  E-value=0.0029  Score=51.75  Aligned_cols=25  Identities=16%  Similarity=0.236  Sum_probs=20.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ....||.++|+.|+||||.+-++..
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~   31 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLAR   31 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999995555543

>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=96.23  E-value=0.0062  Score=51.69  Aligned_cols=87  Identities=18%  Similarity=0.079  Sum_probs=57.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-++.-|+|.+|+||||||-.+........  ...+|+..-..++...     +++++......   .....+  +..+
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E--~~~~  128 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGE--QALE  128 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHH--HHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHH--HHHH
Confidence            5567999999999999999977765322222  3578999999998765     56666543321   111222  5555


Q ss_pred             HHHHHc-CCCeEEEEEeCCC
Q 038944          254 ILHEYL-MTKRYLNVIDDVW  272 (334)
Q Consensus       254 ~l~~~L-~~kr~LlVlDdvw  272 (334)
                      .+.... .++.-|||+|.+-
T Consensus       129 ~~~~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1         129 IADMLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             HHHHHHHTTCEEEEEEECST
T ss_pred             HHHHHHhcCCCCEEEEeccc
Confidence            444444 4567799999984

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.15  E-value=0.0063  Score=51.71  Aligned_cols=114  Identities=13%  Similarity=0.158  Sum_probs=66.4

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCC----CCcc
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPS----SRLS  241 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~----~~~~  241 (334)
                      +.++.|..=..+- -++|.|..|+|||+|+..+.++. .+.+=++++++-+.+.. .+.++.+++.+.--..    ....
T Consensus        57 raID~l~pigkGQ-r~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~t  134 (276)
T d2jdid3          57 KVVDLLAPYAKGG-KIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKV  134 (276)
T ss_dssp             HHHHHHSCEETTC-EEEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCE
T ss_pred             eeeeeeccccCCC-EEEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceE
Confidence            5667665422122 48999999999999998887642 22333467888888764 5667777777642111    0000


Q ss_pred             ----ccchhh------HHHHHHHHHHHc---CCCeEEEEEeCCCC-hhHHHHHHh
Q 038944          242 ----EIMDKN------YEMKKIILHEYL---MTKRYLNVIDDVWN-IEVCDIIRE  282 (334)
Q Consensus       242 ----~~~~~~------~~~l~~~l~~~L---~~kr~LlVlDdvw~-~~~w~~l~~  282 (334)
                          ...++.      .-...-.+-+++   +||..|+++||+-. .+.+.++..
T Consensus       135 vvv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~A~A~reis~  189 (276)
T d2jdid3         135 ALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSA  189 (276)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHHHHHHHHHG
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHHHHHHHHHHH
Confidence                000110      002233455565   48999999999943 345555443

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.15  E-value=0.0012  Score=53.81  Aligned_cols=42  Identities=12%  Similarity=0.169  Sum_probs=31.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKF  233 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~  233 (334)
                      .+||+|-|++|+||||+|+.+.++..    |..         .+...+++.+...
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~g----l~~---------iStGdLlR~~a~~   44 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQ----WHL---------LDSGAIYRVLALA   44 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHT----CEE---------EEHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC----CcE---------ECHHHHHHHHHHH
Confidence            36999999999999999999998322    111         2567888877653

>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=96.12  E-value=0.0025  Score=55.85  Aligned_cols=36  Identities=17%  Similarity=0.101  Sum_probs=28.8

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++++.+.....+..+|+|+|.+|+|||||...+..
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~   76 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGM   76 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHH
Confidence            455555655556789999999999999999988764

>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=96.08  E-value=0.0017  Score=51.89  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=21.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++.+|+|.|+.|+||||+|..+-+
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998754

>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=96.02  E-value=0.0018  Score=52.73  Aligned_cols=24  Identities=4%  Similarity=0.007  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +-||+|.|..|+||||+|+.+.+.
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998773

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=95.99  E-value=0.002  Score=51.45  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=20.0

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.++| |+|++|+||||+|+.+.+
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHH
Confidence            45666 789999999999999987

>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=95.98  E-value=0.0096  Score=48.40  Aligned_cols=24  Identities=17%  Similarity=0.188  Sum_probs=19.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.+||.++|+.|+||||.+-++..
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~   28 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGR   28 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999996555544

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.87  E-value=0.0041  Score=54.36  Aligned_cols=37  Identities=16%  Similarity=0.170  Sum_probs=29.4

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..++++.+.....+..+|+|.|++|+|||||...+..
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~   73 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGS   73 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHH
Confidence            4455666655566789999999999999999988764

>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=95.82  E-value=0.002  Score=51.51  Aligned_cols=23  Identities=13%  Similarity=-0.048  Sum_probs=20.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..|.|.|++|+||||+|+.+.+.
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35779999999999999999873

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.78  E-value=0.0022  Score=50.64  Aligned_cols=21  Identities=19%  Similarity=0.242  Sum_probs=19.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999999999773

>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=95.75  E-value=0.011  Score=50.95  Aligned_cols=25  Identities=16%  Similarity=0.106  Sum_probs=22.6

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ...-+|+|.|..|+||||+|+.+..
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~  102 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHH
Confidence            4567999999999999999999976

>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=95.75  E-value=0.0025  Score=51.10  Aligned_cols=24  Identities=8%  Similarity=0.185  Sum_probs=22.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .++|.|.|++|+||||+|+.+.+.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            579999999999999999999883

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=95.72  E-value=0.0026  Score=53.82  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=19.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.|+|+|-||+||||+|-.+..
T Consensus         1 mr~Iai~gKGGvGKTT~a~nLA~   23 (269)
T d1cp2a_           1 MRQVAIYGKGGIGKSTTTQNLTS   23 (269)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCcCCHHHHHHHHHH
Confidence            47899999999999999987654

>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=95.65  E-value=0.0025  Score=52.01  Aligned_cols=23  Identities=13%  Similarity=0.001  Sum_probs=20.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -+|+|-|++|+||||+|+.+..+
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~   26 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKD   26 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999999874

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=95.64  E-value=0.0026  Score=50.41  Aligned_cols=22  Identities=18%  Similarity=0.222  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .|.|.|++|+||||+|+.+.+.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999999999984

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.63  E-value=0.0027  Score=50.25  Aligned_cols=22  Identities=23%  Similarity=0.199  Sum_probs=19.5

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|.|++|+||||+|+.+.+.
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3678899999999999999874

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.62  E-value=0.0035  Score=49.70  Aligned_cols=23  Identities=17%  Similarity=0.156  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|.|+|++|+|||||++.+.+.
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            57889999999999999999873

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=95.61  E-value=0.0034  Score=50.32  Aligned_cols=25  Identities=16%  Similarity=0.213  Sum_probs=20.8

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...-|.|.|++|+||||+|+.+...
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHH
Confidence            3445668899999999999999883

>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=95.61  E-value=0.011  Score=50.14  Aligned_cols=95  Identities=16%  Similarity=0.083  Sum_probs=61.1

Q ss_pred             HHHHhc-CC-CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---cc
Q 038944          169 LDLLIE-GP-PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EI  243 (334)
Q Consensus       169 ~~~L~~-~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~  243 (334)
                      ++.++. +. +.-++.-|+|.+|+|||||+-.+.....-..  -.++|+..-..+++.     ++++++......   ..
T Consensus        45 lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~  117 (268)
T d1xp8a1          45 LDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQP  117 (268)
T ss_dssp             HHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECC
T ss_pred             HHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcC
Confidence            344443 32 4556999999999999999988776422111  347899998899874     667777654321   11


Q ss_pred             chhhHHHHHHHHHHHcC-CCeEEEEEeCCC
Q 038944          244 MDKNYEMKKIILHEYLM-TKRYLNVIDDVW  272 (334)
Q Consensus       244 ~~~~~~~l~~~l~~~L~-~kr~LlVlDdvw  272 (334)
                      .+.+  +..+.+...++ ++--|||+|-+-
T Consensus       118 ~~~E--~~~~~~~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         118 DNGE--QALEIMELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             SSHH--HHHHHHHHHHTTTCCSEEEEECTT
T ss_pred             CCHH--HHHHHHHHHHhcCCCcEEEEeccc
Confidence            1222  55555555554 345699999983

>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=95.58  E-value=0.0036  Score=51.07  Aligned_cols=25  Identities=12%  Similarity=-0.019  Sum_probs=22.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ++..||-+.|++|+||||||+.+..
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999999986

>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=95.54  E-value=0.0069  Score=51.22  Aligned_cols=86  Identities=13%  Similarity=-0.006  Sum_probs=54.2

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc---ccchhhHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS---EIMDKNYEMKKI  253 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~---~~~~~~~~~l~~  253 (334)
                      +.-++.-|+|.+|+|||||+-.+.....-.  =...+|+..-..++...     ++.++......   .....+  +..+
T Consensus        52 ~~g~itei~G~~gsGKTtl~l~~~~~~q~~--g~~~vyidtE~~~~~~~-----a~~~Gvd~d~v~~~~~~~~E--~~~~  122 (263)
T d1u94a1          52 PMGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGE--QALE  122 (263)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHH--HHHH
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcC--CCEEEEEccccccCHHH-----HHHhCCCHHHEEEecCCCHH--HHHH
Confidence            345699999999999999998887642222  23578999888888643     56666553321   111122  4444


Q ss_pred             HHHHHcC-CCeEEEEEeCC
Q 038944          254 ILHEYLM-TKRYLNVIDDV  271 (334)
Q Consensus       254 ~l~~~L~-~kr~LlVlDdv  271 (334)
                      .+....+ ++--|||+|-+
T Consensus       123 ~i~~l~~~~~~~liViDSi  141 (263)
T d1u94a1         123 ICDALARSGAVDVIVVDSV  141 (263)
T ss_dssp             HHHHHHHHTCCSEEEEECG
T ss_pred             HHHHHHhcCCCCEEEEECc
Confidence            4444443 33458899998

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.52  E-value=0.0039  Score=49.74  Aligned_cols=29  Identities=17%  Similarity=0.271  Sum_probs=22.4

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceee
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDC  211 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~  211 (334)
                      -|.|+|++|+|||||++.+.+.  ....|..
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~--~~~~~~~   31 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAE--YPDSFGF   31 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH--CTTTEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHh--CCcceeE
Confidence            3779999999999999999873  3334543

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.48  E-value=0.0036  Score=50.08  Aligned_cols=25  Identities=24%  Similarity=0.250  Sum_probs=22.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..+|+|-|..|+||||+++.+.+
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHH
Confidence            4566999999999999999998876

>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=95.31  E-value=0.0041  Score=51.26  Aligned_cols=22  Identities=27%  Similarity=0.416  Sum_probs=19.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ||.|+|+.|+|||||...+..+
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Confidence            8999999999999999988753

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.27  E-value=0.0042  Score=48.98  Aligned_cols=22  Identities=14%  Similarity=0.069  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .|.|.|++|+||||+|+.+.++
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3668999999999999999873

>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=95.27  E-value=0.0072  Score=47.15  Aligned_cols=34  Identities=15%  Similarity=0.010  Sum_probs=25.1

Q ss_pred             HHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          168 LLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       168 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++.+.-.....+ |.++|.+|+|||||...+...
T Consensus         3 ~~~~~~~~~k~~k-I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_           3 VLQFLGLYKKTGK-LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             HHHHHTCTTCCEE-EEEEEETTSSHHHHHHHHSCC
T ss_pred             hHHhccccCCCCE-EEEECCCCCCHHHHHHHHhCC
Confidence            4455555544444 669999999999999988654

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=95.20  E-value=0.0063  Score=48.57  Aligned_cols=26  Identities=15%  Similarity=0.245  Sum_probs=22.9

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+++.|+|+|.+|+|||||...+.+.
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            45678999999999999999999863

>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=95.18  E-value=0.017  Score=49.06  Aligned_cols=99  Identities=12%  Similarity=0.026  Sum_probs=55.1

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCC-CHHHHHHHHHHHhCCC--------CCcccc--chhhHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPY-DADQMLDIVIKFLMPS--------SRLSEI--MDKNYE  249 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~il~~il~~~~~~--------~~~~~~--~~~~~~  249 (334)
                      -++|+|..|+|||+|+......  ...+-..++++-+.... .+.++..++.+.-..+        .+.+..  .-..  
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~--  144 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAP--  144 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHH--
T ss_pred             eEeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHH--
Confidence            3788999999999999875542  23334566777777654 3334444433221000        000000  0001  


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCCC-hhHHHHHHhh
Q 038944          250 MKKIILHEYL--MTKRYLNVIDDVWN-IEVCDIIREI  283 (334)
Q Consensus       250 ~l~~~l~~~L--~~kr~LlVlDdvw~-~~~w~~l~~~  283 (334)
                      ...-.+-+++  ++|+.|+++||+-. ...|.++...
T Consensus       145 ~~a~tiAEyfrd~G~~Vlll~Dsltr~A~A~rEis~~  181 (276)
T d1fx0a3         145 YTGAALAEYFMYRERHTLIIYDDLSKQAQAYRQMSLL  181 (276)
T ss_dssp             HHHHHHHHHHHHTTCEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCceeEEeeccHHHHHHHHHHHHH
Confidence            2233334444  68999999999943 3667766643

>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=95.17  E-value=0.0064  Score=53.93  Aligned_cols=42  Identities=14%  Similarity=0.223  Sum_probs=30.4

Q ss_pred             echhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          160 GLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      |.+....+..+.+..+.+.-+.+.++|++|+|||++|..+.+
T Consensus       135 ~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         135 KMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             THHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHH
Confidence            444333343444444555667999999999999999999998

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.15  E-value=0.0048  Score=48.77  Aligned_cols=21  Identities=19%  Similarity=0.243  Sum_probs=18.2

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|.|++|+||||+|+.+.+.
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            447799999999999999873

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.13  E-value=0.0042  Score=49.78  Aligned_cols=20  Identities=20%  Similarity=0.370  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |.|+|++|+|||||++.+.+
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            66999999999999999987

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.09  E-value=0.0057  Score=48.52  Aligned_cols=22  Identities=14%  Similarity=0.311  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|.|+|+.|+|||||++.+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~   25 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLIT   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            5788999999999999999986

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=95.03  E-value=0.0059  Score=52.11  Aligned_cols=22  Identities=14%  Similarity=0.173  Sum_probs=19.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .+.|+|.|-||+||||+|-.+.
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA   23 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLV   23 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHH
Confidence            5788999999999999887764

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.98  E-value=0.0048  Score=50.00  Aligned_cols=23  Identities=17%  Similarity=0.135  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999986

>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=94.98  E-value=0.015  Score=47.33  Aligned_cols=24  Identities=25%  Similarity=0.271  Sum_probs=15.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ....||.+||+.|+||||.+-++.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA   33 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLA   33 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            467899999999999999544443

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.95  E-value=0.0064  Score=50.62  Aligned_cols=52  Identities=8%  Similarity=0.029  Sum_probs=32.6

Q ss_pred             HHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          254 ILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       254 ~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      .+-+.|..+.-+|++|.--..       .-|+.|....  ...|.-||++|.+.+.|..++
T Consensus       149 ~IAraL~~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~--~~~g~tvi~vTHd~~~~~~~~  207 (240)
T d1g2912         149 ALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQ--RQLGVTTIYVTHDQVEAMTMG  207 (240)
T ss_dssp             HHHHHHHTCCSEEEEECTTTTSCHHHHHHHHHHHHHHH--HHHTCEEEEEESCHHHHHHHC
T ss_pred             HHHHHHhcCCCEEEecCCCcccCHHHHHHHHHHHHHHH--hccCCEEEEEcCCHHHHHHhC
Confidence            344555566678999997543       2344443332  123777999999988877654

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=94.95  E-value=0.015  Score=51.57  Aligned_cols=45  Identities=13%  Similarity=0.125  Sum_probs=33.5

Q ss_pred             CeeechhhHHHHHHHHh----------------------------cCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          157 DTVGLDDRMEELLDLLI----------------------------EGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~----------------------------~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|.++.++.+...+.                            +.+.....+-.+|+.|+|||.||+.+..
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHh
Confidence            37898888777765441                            1233456688889999999999999876

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.88  E-value=0.0064  Score=50.29  Aligned_cols=51  Identities=10%  Similarity=0.225  Sum_probs=33.1

Q ss_pred             HHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecCChHHHhhc
Q 038944          254 ILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       254 ~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~  306 (334)
                      .+-+.|..+.-+|++|..=..       +.|+.+....  ...|.-||++|.+.++|..|
T Consensus       155 aIAraL~~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~--~~~g~tii~vTHd~~~a~~~  212 (230)
T d1l2ta_         155 AIARALANNPPIILADQPTGALDSKTGEKIMQLLKKLN--EEDGKTVVVVTHDINVARFG  212 (230)
T ss_dssp             HHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHH--HTTCCEEEEECSCHHHHTTS
T ss_pred             HHHhhhhcCCCEEEecCCccccCHHHHHHHHHHHHHHH--HhhCCEEEEECCCHHHHHhC
Confidence            344455566678999998543       3444444332  23477799999999998643

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=94.87  E-value=0.0064  Score=50.63  Aligned_cols=23  Identities=9%  Similarity=0.047  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||++.++.
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHcC
Confidence            35899999999999999999974

>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=94.86  E-value=0.021  Score=46.52  Aligned_cols=50  Identities=4%  Similarity=-0.016  Sum_probs=34.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQM  226 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~i  226 (334)
                      +.-+++-|.|.+|+|||||+-++........    .-...+|+.....++...+
T Consensus        32 ~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   85 (251)
T d1szpa2          32 ETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL   85 (251)
T ss_dssp             ESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGGG
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHHH
Confidence            4557999999999999999987765322211    1246788887777664333

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.80  E-value=0.0069  Score=50.90  Aligned_cols=23  Identities=17%  Similarity=0.147  Sum_probs=20.7

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999964

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.79  E-value=0.0071  Score=50.45  Aligned_cols=23  Identities=17%  Similarity=0.131  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -..++|+|..|.|||||++.+..
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35899999999999999999975

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.77  E-value=0.0079  Score=46.11  Aligned_cols=21  Identities=19%  Similarity=0.137  Sum_probs=19.1

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|+|.+|+|||||.+.+.++
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            779999999999999988775

>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=94.76  E-value=0.0078  Score=48.83  Aligned_cols=20  Identities=25%  Similarity=0.343  Sum_probs=18.4

Q ss_pred             EEEEEccCCccHHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +|+|+|+.|+||||+++.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998664

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.75  E-value=0.015  Score=48.60  Aligned_cols=46  Identities=20%  Similarity=0.131  Sum_probs=35.1

Q ss_pred             CeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          157 DTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++||....++++.+.+..-...-.-|.|.|..|+|||++|+.++..
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            3678888888888887653221223688999999999999999874

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=94.72  E-value=0.0079  Score=50.18  Aligned_cols=23  Identities=13%  Similarity=0.059  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -..++|+|..|.|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999963

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.70  E-value=0.0074  Score=50.86  Aligned_cols=23  Identities=26%  Similarity=0.218  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||++.+..
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            35899999999999999999975

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.69  E-value=0.0083  Score=49.87  Aligned_cols=53  Identities=4%  Similarity=0.036  Sum_probs=33.8

Q ss_pred             HHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          254 ILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       254 ~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      .|-..|..+.=+|+||..-..       ..|+.|.....  ..|.-||++|.+.+.|..++.
T Consensus       146 aiAraL~~~P~iLllDEPts~LD~~~~~~i~~ll~~l~~--~~g~tii~vTHd~~~a~~~~d  205 (239)
T d1v43a3         146 AVARAIVVEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQ--KLKVTTIYVTHDQVEAMTMGD  205 (239)
T ss_dssp             HHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHH--HHTCEEEEEESCHHHHHHHCS
T ss_pred             HHHhhhccCCCceeecCCcccCCHHHHHHHHHHHHHHHH--hcCCeEEEEeCCHHHHHHhCC
Confidence            445556667779999997543       34444443321  236669999999888876543

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.66  E-value=0.008  Score=50.45  Aligned_cols=23  Identities=22%  Similarity=0.179  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|+|||||++.+..
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            45899999999999999999975

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=94.65  E-value=0.0077  Score=45.83  Aligned_cols=21  Identities=5%  Similarity=-0.024  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|+|.+|+|||||...+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            569999999999999988764

>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=94.65  E-value=0.012  Score=45.78  Aligned_cols=29  Identities=14%  Similarity=0.154  Sum_probs=21.9

Q ss_pred             cCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          174 EGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       174 ~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .....---|.++|.+|+|||||...+...
T Consensus        11 ~~~~~~~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          11 SAPDQEVRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             SCCSSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHhcC
Confidence            33333345789999999999999988763

>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=94.64  E-value=0.016  Score=48.86  Aligned_cols=34  Identities=15%  Similarity=0.329  Sum_probs=25.6

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHH
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ...+.+.+..  +..+||.+.|-||+||||++-.+.
T Consensus         8 ~~~~~~~~~~--~~~~iii~sGKGGVGKTT~a~nLA   41 (279)
T d1ihua2           8 LSALVDDIAR--NEHGLIMLMGKGGVGKTTMAAAIA   41 (279)
T ss_dssp             HHHHHHHHHT--TSCEEEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHHHhhc--CCCEEEEEECCCCCCHHHHHHHHH
Confidence            4556666654  347899999999999999866664

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.60  E-value=0.0086  Score=51.13  Aligned_cols=24  Identities=17%  Similarity=0.106  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -.+++|+|+.|.|||||++.+..-
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            468999999999999999999863

>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=94.56  E-value=0.01  Score=46.73  Aligned_cols=34  Identities=21%  Similarity=0.207  Sum_probs=24.4

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+.+.|......++| .++|.+|+|||||...+..
T Consensus         6 ~~~~~l~~~~k~~KI-~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_           6 SMFDKLWGSNKELRI-LILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             HHHGGGTTCSSCEEE-EEEEETTSSHHHHHHHTCC
T ss_pred             HHHHHHhCCCceEEE-EEECCCCCCHHHHHHHHhc
Confidence            344444444555654 5999999999999998754

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.54  E-value=0.0095  Score=49.50  Aligned_cols=53  Identities=13%  Similarity=0.167  Sum_probs=32.8

Q ss_pred             HHHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          253 IILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       253 ~~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                      -.+-+.|-.+.-+|+||..-..       ..|+.|...-  ...|.-||++|.+.+.|..++
T Consensus       135 vaiAral~~~P~illlDEPts~LD~~~~~~i~~~i~~l~--~~~g~tvi~vtHd~~~~~~~a  194 (240)
T d2onka1         135 VALARALVIQPRLLLLDEPLSAVDLKTKGVLMEELRFVQ--REFDVPILHVTHDLIEAAMLA  194 (240)
T ss_dssp             HHHHHHHTTCCSSBEEESTTSSCCHHHHHHHHHHHHHHH--HHHTCCEEEEESCHHHHHHHC
T ss_pred             HHHHHHHhccCCceEecCccccCCHHHHHHHHHHHHHHH--HhcCCeEEEEeCCHHHHHHhC
Confidence            3455556677789999997542       3444444331  123566888888877666654

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.54  E-value=0.0063  Score=50.04  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=21.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+.|+|-|+-|+||||+++.+.+.
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999988873

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.54  E-value=0.027  Score=45.75  Aligned_cols=49  Identities=6%  Similarity=-0.014  Sum_probs=31.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCC-CCCHHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTY-PYDADQMLDIVIK  232 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~il~~il~  232 (334)
                      -+.|+|-|.-|+||||+++.+.+  ..+.++.   .+.... ......+++.++.
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~--~L~~~~~---~~~~p~~~~~~g~~ir~~l~   52 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYK--KLQPNCK---LLKFPERSTRIGGLINEYLT   52 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH--HTTTSEE---EEESSCTTSHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHH--HHHhCCE---EEEECCCCchHhHhHHHhhh
Confidence            36799999999999999999988  4444332   233332 2233455555553

>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=94.52  E-value=0.019  Score=48.95  Aligned_cols=27  Identities=19%  Similarity=0.158  Sum_probs=22.8

Q ss_pred             CCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          175 GPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       175 ~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +....-+|+|-|..|+|||||+..+..
T Consensus        23 ~~~~P~iIGi~G~qGSGKSTl~~~l~~   49 (286)
T d1odfa_          23 GNKCPLFIFFSGPQGSGKSFTSIQIYN   49 (286)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCCCEEEEeECCCCCCHHHHHHHHHH
Confidence            344567999999999999999988865

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.36  E-value=0.012  Score=48.42  Aligned_cols=25  Identities=16%  Similarity=0.151  Sum_probs=22.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++.|+|=|+-|+||||+++.+.++
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            3678999999999999999999874

>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=94.35  E-value=0.016  Score=46.88  Aligned_cols=23  Identities=9%  Similarity=0.245  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++|.|+|++|+|||||.+.+...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            57889999999999999999873

>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=94.33  E-value=0.064  Score=43.79  Aligned_cols=50  Identities=8%  Similarity=0.189  Sum_probs=35.1

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCC----CceeeEEEEEcCCCCCHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVK----HYFDCHAWVPGTYPYDADQM  226 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~i  226 (334)
                      +.-.++-|.|.+|+||||++.++..+....    ......+|+.....++...+
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            456799999999999999998776532211    12345788888777776544

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=94.29  E-value=0.0093  Score=49.24  Aligned_cols=23  Identities=26%  Similarity=0.202  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            35899999999999999999974

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.23  E-value=0.013  Score=47.86  Aligned_cols=23  Identities=9%  Similarity=0.114  Sum_probs=19.9

Q ss_pred             ceEEEEE-ccCCccHHHHHHHHHc
Q 038944          179 LSVVVIL-DSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~Iv-G~gGvGKTtLa~~v~~  201 (334)
                      .+||+|+ |-||+||||+|..+..
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~   24 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGV   24 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCChHHHHHHHHHH
Confidence            4799999 7799999999998765

>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=94.21  E-value=0.0095  Score=51.92  Aligned_cols=45  Identities=18%  Similarity=0.162  Sum_probs=31.8

Q ss_pred             CCCCeeechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHH
Q 038944          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +-.+++|.+..+..|.-.+....  ..-+-++|.+|+||||||+.+.
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~--~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhccC--CCeEEEECCCCccHHHHHHHHH
Confidence            34578999887775543333211  2247899999999999999874

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.21  E-value=0.015  Score=44.81  Aligned_cols=21  Identities=10%  Similarity=0.207  Sum_probs=18.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999877653

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.19  E-value=0.013  Score=45.18  Aligned_cols=22  Identities=5%  Similarity=0.185  Sum_probs=19.0

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.++
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3679999999999999888764

>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=94.16  E-value=0.014  Score=47.52  Aligned_cols=25  Identities=20%  Similarity=0.308  Sum_probs=19.8

Q ss_pred             CCCceEEEEEccCCccHHHHHHHHH
Q 038944          176 PPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       176 ~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      .....||.++|+.|+||||.+-++.
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLA   32 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLA   32 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHH
Confidence            3567899999999999999554444

>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=94.15  E-value=0.013  Score=49.76  Aligned_cols=23  Identities=9%  Similarity=0.065  Sum_probs=19.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ..++|.+.|-||+||||+|-.+.
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA   29 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATA   29 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHH
Confidence            36788999999999999776664

>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=94.14  E-value=0.015  Score=47.20  Aligned_cols=23  Identities=13%  Similarity=0.105  Sum_probs=18.7

Q ss_pred             CceEEEEEccCCccHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +.+||.++|+.|+||||.+-++.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA   31 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLA   31 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            45899999999999998655554

>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=94.14  E-value=0.0089  Score=51.04  Aligned_cols=35  Identities=17%  Similarity=0.017  Sum_probs=26.6

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++++.|..=.. -.-++|+|..|+|||+|+..+.++
T Consensus        32 r~ID~l~Pigr-GQr~~I~g~~g~GKT~l~~~i~~~   66 (289)
T d1xpua3          32 RVLDLASPIGR-GQRGLIVAPPKAGKTMLLQNIAQS   66 (289)
T ss_dssp             HHHHHHSCCBT-TCEEEEEECSSSSHHHHHHHHHHH
T ss_pred             eeeeecccccC-CCeeeEeCCCCCCHHHHHHHHHHH
Confidence            67887764221 135899999999999999988874

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=94.08  E-value=0.012  Score=48.87  Aligned_cols=23  Identities=13%  Similarity=0.156  Sum_probs=20.9

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999975

>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=94.05  E-value=0.013  Score=48.74  Aligned_cols=52  Identities=21%  Similarity=0.352  Sum_probs=33.7

Q ss_pred             HHHHHcCCCeEEEEEeCCCCh-------hHHHHHHhhCCCCCCCeEEEEecCChHHHhhccc
Q 038944          254 ILHEYLMTKRYLNVIDDVWNI-------EVCDIIREILPDNQNRSRVLITLTEIKMFTFLLE  308 (334)
Q Consensus       254 ~l~~~L~~kr~LlVlDdvw~~-------~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~  308 (334)
                      .+-..|..+.=+++||..-..       .-|+-|... .  ..|--||+||.+.+.+...+.
T Consensus       143 ~iA~al~~~p~illLDEPt~gLD~~~~~~i~~~i~~~-~--~~g~tii~~tH~l~~~~~~~d  201 (238)
T d1vpla_         143 LIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQA-S--QEGLTILVSSHNMLEVEFLCD  201 (238)
T ss_dssp             HHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHH-H--HTTCEEEEEECCHHHHTTTCS
T ss_pred             HHHHHHhcCCCEEEecCCCCCCCHHHHHHHHHHHHHH-H--hcCCEEEEEeCCHHHHHHhCC
Confidence            444556667778899998543       244444432 2  236679999999888876554

>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=94.03  E-value=0.035  Score=43.02  Aligned_cols=25  Identities=8%  Similarity=0.058  Sum_probs=20.5

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..++ |.++|.+|+|||||...+.++
T Consensus        11 k~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          11 KEMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CCEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             CeEE-EEEECCCCCCHHHHHHHHhcC
Confidence            3466 558999999999999998764

>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=94.00  E-value=0.014  Score=44.96  Aligned_cols=21  Identities=10%  Similarity=0.079  Sum_probs=18.6

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            669999999999999998764

>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=93.98  E-value=0.084  Score=42.97  Aligned_cols=49  Identities=4%  Similarity=0.009  Sum_probs=36.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccC----CCCCceeeEEEEEcCCCCCHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSS----YVKHYFDCHAWVPGTYPYDADQ  225 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~----~~~~~F~~~~wv~vs~~~~~~~  225 (334)
                      +.-.++-|+|.+|+|||++|.++..+.    .....+....|+.....++...
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDR   87 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHH
Confidence            556799999999999999998776432    1233456788888887776543

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=93.97  E-value=0.014  Score=47.08  Aligned_cols=22  Identities=23%  Similarity=0.234  Sum_probs=19.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+|+|.|..|+||||+|+.+-.
T Consensus         3 ~iIgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999997743

>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=93.95  E-value=0.034  Score=50.44  Aligned_cols=73  Identities=11%  Similarity=0.130  Sum_probs=46.4

Q ss_pred             eeechhhHHHHHHHHhc--------C----CCCceEEEEEccCCccHHHHHHHHHccCCCCCcee---eEEEEEcC-CCC
Q 038944          158 TVGLDDRMEELLDLLIE--------G----PPQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFD---CHAWVPGT-YPY  221 (334)
Q Consensus       158 ~vGr~~~~~~l~~~L~~--------~----~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~---~~~wv~vs-~~~  221 (334)
                      +||.++.+..+--.+..        .    +-..+-|-++|+.|+|||.||+.+..  .+.-+|-   +.-+.-+. -.-
T Consensus        16 VvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk--~l~VPFv~~daT~fTeaGYvG~   93 (443)
T d1g41a_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK--LANAPFIKVEATKFTEVGYVGK   93 (443)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH--HTTCCEEEEEGGGGC----CCC
T ss_pred             ccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHH--HhCCCEEEeecceeeecceeec
Confidence            88988888877665531        1    11234688999999999999999998  4444451   11121111 123


Q ss_pred             CHHHHHHHHHH
Q 038944          222 DADQMLDIVIK  232 (334)
Q Consensus       222 ~~~~il~~il~  232 (334)
                      |++.+.++++.
T Consensus        94 DVesii~~L~~  104 (443)
T d1g41a_          94 EVDSIIRDLTD  104 (443)
T ss_dssp             CTHHHHHHHHH
T ss_pred             chhHHHHHHHH
Confidence            77777777764

>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=93.95  E-value=0.017  Score=44.95  Aligned_cols=24  Identities=8%  Similarity=0.200  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +..|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            567999999999999999999863

>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=93.93  E-value=0.014  Score=47.32  Aligned_cols=22  Identities=9%  Similarity=0.075  Sum_probs=20.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..|+|-|+.|+||||+++.+.+
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~   25 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVE   25 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5788899999999999999987

>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=93.92  E-value=0.015  Score=45.29  Aligned_cols=22  Identities=14%  Similarity=0.253  Sum_probs=18.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||+..+.++
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3678999999999999987754

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.91  E-value=0.014  Score=49.01  Aligned_cols=22  Identities=18%  Similarity=0.261  Sum_probs=20.6

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|+.|.|||||++.+..
T Consensus        31 ei~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHHC
Confidence            5899999999999999999986

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.90  E-value=0.02  Score=44.33  Aligned_cols=21  Identities=14%  Similarity=0.241  Sum_probs=18.1

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999887654

>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=93.89  E-value=0.0087  Score=51.13  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=17.9

Q ss_pred             CceEEEEEccCCccHHHHHHHHHc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.+||+|.|.+|+||||+++.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHH
Confidence            346999999999999999997765

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.86  E-value=0.017  Score=44.87  Aligned_cols=22  Identities=14%  Similarity=0.235  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .|+|+|.+|+|||||...+...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999998753

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.78  E-value=0.021  Score=44.15  Aligned_cols=21  Identities=19%  Similarity=0.300  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.|+|.+|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999888764

>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=93.78  E-value=0.019  Score=47.14  Aligned_cols=90  Identities=11%  Similarity=-0.055  Sum_probs=51.4

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCc-----------cccch
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRL-----------SEIMD  245 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~-----------~~~~~  245 (334)
                      +.-.++-|+|.+|+|||+|+..+..+  ...+....+|++...  +...+.+. +..++.....           .....
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEE--SRAQLLRN-AYSWGMDFEEMERQNLLKIVCAYPES   98 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSS--CHHHHHHH-HHTTSCCHHHHHHTTSEEECCCCGGG
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccC--CHHHHHHH-HHHcCCChHHHhhcCceEEEEeecch
Confidence            45679999999999999999888874  334455677877643  33343333 2333221100           00111


Q ss_pred             hhHHHHHHHHHHHc-CCCeEEEEEeCC
Q 038944          246 KNYEMKKIILHEYL-MTKRYLNVIDDV  271 (334)
Q Consensus       246 ~~~~~l~~~l~~~L-~~kr~LlVlDdv  271 (334)
                      .........+...+ ..+--++|+|.+
T Consensus        99 ~~~~~~~~~i~~~i~~~~~~~vviDs~  125 (242)
T d1tf7a2          99 AGLEDHLQIIKSEINDFKPARIAIDSL  125 (242)
T ss_dssp             SCHHHHHHHHHHHHHTTCCSEEEEECH
T ss_pred             hhHHHHHHHHHHHHHhcCCceeeeecc
Confidence            11225555555554 345568888885

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.74  E-value=0.021  Score=43.81  Aligned_cols=21  Identities=14%  Similarity=0.207  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||+..+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987754

>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=93.73  E-value=0.022  Score=43.97  Aligned_cols=22  Identities=14%  Similarity=0.326  Sum_probs=18.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||+..+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999887653

>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=93.72  E-value=0.017  Score=46.26  Aligned_cols=21  Identities=14%  Similarity=0.161  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|+|-|.-|+||||+++.+.+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~   22 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG   22 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999998876

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.72  E-value=0.011  Score=49.13  Aligned_cols=23  Identities=22%  Similarity=0.107  Sum_probs=20.8

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -.+++|+|..|.|||||.+.+..
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            35899999999999999999974

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.70  E-value=0.02  Score=44.69  Aligned_cols=24  Identities=13%  Similarity=0.180  Sum_probs=21.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999864

>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=93.66  E-value=0.023  Score=46.57  Aligned_cols=25  Identities=16%  Similarity=0.319  Sum_probs=22.5

Q ss_pred             CceEEEEEccCCccHHHHHHHHHcc
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +++|.-|.|+-|.|||||.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5789999999999999999999864

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.65  E-value=0.018  Score=44.60  Aligned_cols=22  Identities=14%  Similarity=0.240  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999987654

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.64  E-value=0.013  Score=46.03  Aligned_cols=20  Identities=10%  Similarity=0.069  Sum_probs=18.6

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |+|+|.+|+|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999875

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.64  E-value=0.29  Score=39.91  Aligned_cols=112  Identities=12%  Similarity=0.104  Sum_probs=57.3

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccC---CCC-----Cc--ee--eEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccch
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSS---YVK-----HY--FD--CHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMD  245 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~---~~~-----~~--F~--~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~  245 (334)
                      +-+++-|.|+...||||+.+.+.--.   +..     +.  |.  .+++..+...-++..           .... ...+
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~-----------~~S~-F~~E  107 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLAS-----------GRST-FMVE  107 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------------------CHHH
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCccccc-----------chhH-HHHH
Confidence            34788999999999999999885210   111     11  11  133333332211111           0000 1111


Q ss_pred             hhHHHHHHHHHHHcCCCeEEEEEeCCCCh----h----HHHHHHhhCCCCCCCeEEEEecCChHHHhhcc
Q 038944          246 KNYEMKKIILHEYLMTKRYLNVIDDVWNI----E----VCDIIREILPDNQNRSRVLITLTEIKMFTFLL  307 (334)
Q Consensus       246 ~~~~~l~~~l~~~L~~kr~LlVlDdvw~~----~----~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~  307 (334)
                        +.++...+..  .+++.|+++|.+-..    +    .|..+....  ...++.+|+||....++....
T Consensus       108 --~~~~~~il~~--~~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l~--~~~~~~~i~tTH~~~l~~~~~  171 (234)
T d1wb9a2         108 --MTETANILHN--ATEYSLVLMDEIGRGTSTYDGLSLAWACAENLA--NKIKALTLFATHYFELTQLPE  171 (234)
T ss_dssp             --HHHHHHHHHH--CCTTEEEEEESCCCCSSSSHHHHHHHHHHHHHH--HTTCCEEEEECSCGGGGGHHH
T ss_pred             --HHHHHHHHHh--cccccEEeecccccCCChhhhhHHHHHhhhhhh--ccccceEEEecchHHHhhhhh
Confidence              1133332221  457889999999753    1    333333221  234678999999888776544

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.63  E-value=0.023  Score=44.09  Aligned_cols=22  Identities=14%  Similarity=0.332  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||.+.+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.61  E-value=0.033  Score=43.74  Aligned_cols=22  Identities=18%  Similarity=0.274  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||+..+.++
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3679999999999999988764

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.55  E-value=0.019  Score=44.54  Aligned_cols=22  Identities=27%  Similarity=0.273  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||++.+.+.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCcCHHHHHHHHhCC
Confidence            3678999999999999988653

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=93.54  E-value=0.097  Score=42.28  Aligned_cols=59  Identities=7%  Similarity=-0.028  Sum_probs=37.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCC--------------ceeeEEEEEcCCCCCHHHHHHHHHHHhCC
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKH--------------YFDCHAWVPGTYPYDADQMLDIVIKFLMP  236 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~--------------~F~~~~wv~vs~~~~~~~il~~il~~~~~  236 (334)
                      +.-.++-|.|.+|+|||+++..+..+.....              ....+.|++....++.. ..+.+...+..
T Consensus        32 ~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~~~  104 (258)
T d2i1qa2          32 ESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHAGI  104 (258)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHHTC
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhcch
Confidence            3457999999999999999988865332211              12346778776665533 34455555543

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.48  E-value=0.025  Score=43.92  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999987653

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.47  E-value=0.021  Score=45.55  Aligned_cols=23  Identities=9%  Similarity=0.076  Sum_probs=20.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.|.|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999998764

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.46  E-value=0.021  Score=43.20  Aligned_cols=22  Identities=14%  Similarity=0.051  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999888764

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.43  E-value=0.024  Score=43.65  Aligned_cols=22  Identities=9%  Similarity=0.256  Sum_probs=19.1

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.++
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999988764

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.41  E-value=0.026  Score=43.48  Aligned_cols=23  Identities=13%  Similarity=0.154  Sum_probs=19.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|.+|+|||||...+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            35778999999999999887653

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.39  E-value=0.026  Score=43.66  Aligned_cols=22  Identities=14%  Similarity=0.191  Sum_probs=18.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||+..+.++
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4689999999999999887754

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.37  E-value=0.027  Score=43.42  Aligned_cols=21  Identities=19%  Similarity=0.343  Sum_probs=18.7

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999888764

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=93.36  E-value=0.016  Score=47.87  Aligned_cols=22  Identities=9%  Similarity=0.229  Sum_probs=20.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+++|+|..|.|||||.+.+..
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999875

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.35  E-value=0.011  Score=49.58  Aligned_cols=23  Identities=13%  Similarity=0.023  Sum_probs=20.5

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -..++|+|..|+|||||++.+..
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh
Confidence            35899999999999999999864

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.34  E-value=0.027  Score=43.74  Aligned_cols=22  Identities=9%  Similarity=0.238  Sum_probs=18.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||+..+..+
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999887643

>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=93.33  E-value=0.1  Score=41.03  Aligned_cols=53  Identities=6%  Similarity=0.048  Sum_probs=34.0

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHccCCCCC----ceeeEEEEEcCCCCCHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNSSYVKH----YFDCHAWVPGTYPYDADQMLDI  229 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~il~~  229 (334)
                      +.-.++-|.|.+|+|||||+..+..+.....    .+....++..........+...
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAV   77 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHH
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHHHHHHH
Confidence            3456999999999999999988765432222    1234556666666655444333

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.32  E-value=0.028  Score=43.57  Aligned_cols=22  Identities=23%  Similarity=0.289  Sum_probs=18.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3788999999999999877654

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.31  E-value=0.023  Score=46.64  Aligned_cols=23  Identities=9%  Similarity=0.037  Sum_probs=21.0

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++|+|.|..|+||||+|+.+.+
T Consensus         1 M~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           1 MKLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999876

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.30  E-value=0.028  Score=43.29  Aligned_cols=22  Identities=32%  Similarity=0.360  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|-+|+|||||...+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4788999999999999888764

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.29  E-value=0.023  Score=44.26  Aligned_cols=23  Identities=22%  Similarity=0.278  Sum_probs=19.3

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      --|.|+|.+|+|||||...+.++
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34679999999999999887654

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.27  E-value=0.029  Score=43.27  Aligned_cols=22  Identities=18%  Similarity=0.149  Sum_probs=18.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||...+.++
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3679999999999999987653

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.26  E-value=0.027  Score=44.72  Aligned_cols=22  Identities=9%  Similarity=0.234  Sum_probs=19.0

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||||...+.++
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            3789999999999999987754

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.25  E-value=0.029  Score=43.39  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=18.4

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||+|.....++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999888764

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.24  E-value=0.022  Score=44.48  Aligned_cols=22  Identities=5%  Similarity=0.098  Sum_probs=19.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999864

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.23  E-value=0.027  Score=43.85  Aligned_cols=22  Identities=18%  Similarity=0.314  Sum_probs=19.0

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|..|+|||||+..+.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987654

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=93.20  E-value=0.025  Score=43.81  Aligned_cols=23  Identities=13%  Similarity=0.007  Sum_probs=19.2

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .-|.|+|.+|+|||||...+..+
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34679999999999999887764

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.18  E-value=0.03  Score=43.17  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=18.3

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||+|...+..+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678999999999999887654

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.14  E-value=0.025  Score=46.05  Aligned_cols=22  Identities=14%  Similarity=0.200  Sum_probs=19.1

Q ss_pred             eEEEEE-ccCCccHHHHHHHHHc
Q 038944          180 SVVVIL-DSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~Iv-G~gGvGKTtLa~~v~~  201 (334)
                      +||+|+ +-||+||||+|..+..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~   25 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSV   25 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCcHHHHHHHHHH
Confidence            689999 5699999999988864

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.03  E-value=0.052  Score=46.04  Aligned_cols=113  Identities=10%  Similarity=-0.067  Sum_probs=57.2

Q ss_pred             HHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccCC-----CCCce-eeEEEEEcCCCC-CHHHHHHHHHHHhCCC--
Q 038944          167 ELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSSY-----VKHYF-DCHAWVPGTYPY-DADQMLDIVIKFLMPS--  237 (334)
Q Consensus       167 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~-----~~~~F-~~~~wv~vs~~~-~~~~il~~il~~~~~~--  237 (334)
                      +.++.|..=.. -.-++|.|.+|+|||+|+..+.....     ....- ..++++-+.... .+.++...+...-..+  
T Consensus        57 raID~l~pig~-GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~t  135 (285)
T d2jdia3          57 KAVDSLVPIGR-GQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYT  135 (285)
T ss_dssp             HHHHHHSCCBT-TCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGE
T ss_pred             eEEecccCccC-CCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccce
Confidence            45666654211 12478899999999999877664311     11111 134566666654 3345555544321111  


Q ss_pred             ------CCccccc--hhh--HHHHHHHHHHHcCCCeEEEEEeCCCC-hhHHHHHHh
Q 038944          238 ------SRLSEIM--DKN--YEMKKIILHEYLMTKRYLNVIDDVWN-IEVCDIIRE  282 (334)
Q Consensus       238 ------~~~~~~~--~~~--~~~l~~~l~~~L~~kr~LlVlDdvw~-~~~w~~l~~  282 (334)
                            ...+...  -..  .=..++.+++  +||..|+++||+-. .+.+.++..
T Consensus       136 vvv~~ts~~~~~~r~~~~~~a~tiAEyfrd--~G~~VLll~Dsltr~A~A~rEis~  189 (285)
T d2jdia3         136 IVVSATASDAAPLQYLAPYSGCSMGEYFRD--NGKHALIIYDDLSKQAVAYRQMSL  189 (285)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEETHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHH--cCCcEEEEEcChHHHHHHHHHHHH
Confidence                  0100000  000  0023333432  79999999999943 345555544

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=92.93  E-value=0.062  Score=44.77  Aligned_cols=40  Identities=15%  Similarity=0.220  Sum_probs=30.1

Q ss_pred             hhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          163 DRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ..+.++...+...+..---|.++|..|+|||||...++..
T Consensus        16 ~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          16 TKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            3445566666655544556889999999999999999975

>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=92.89  E-value=0.029  Score=44.89  Aligned_cols=23  Identities=9%  Similarity=0.031  Sum_probs=19.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHcc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +-|.|+|.+|+|||||...+.+.
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999888764

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=92.72  E-value=0.019  Score=45.16  Aligned_cols=21  Identities=10%  Similarity=0.036  Sum_probs=19.0

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -|+|+|.+++|||||...+.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999865

>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=92.67  E-value=0.031  Score=43.52  Aligned_cols=22  Identities=14%  Similarity=0.037  Sum_probs=18.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||+|...+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999887764

>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=92.66  E-value=0.039  Score=42.57  Aligned_cols=21  Identities=14%  Similarity=0.237  Sum_probs=17.9

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|..|+|||+|...+.++
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999877653

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=92.64  E-value=0.049  Score=42.01  Aligned_cols=24  Identities=25%  Similarity=0.313  Sum_probs=20.1

Q ss_pred             ceEEEEEccCCccHHHHHHHHHcc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      +.-|.++|.+|+|||||...+.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            456789999999999999887654

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.039  Score=43.37  Aligned_cols=22  Identities=14%  Similarity=0.105  Sum_probs=19.0

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||+|...+.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4789999999999999887654

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=92.51  E-value=0.034  Score=42.67  Aligned_cols=21  Identities=10%  Similarity=0.078  Sum_probs=17.9

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+..+
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568899999999999877654

>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=92.50  E-value=0.057  Score=44.12  Aligned_cols=35  Identities=17%  Similarity=0.234  Sum_probs=27.8

Q ss_pred             hHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHccC
Q 038944          164 RMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      .++.|.++|.+     +...++|.+|+|||||...+..+.
T Consensus        85 g~~~L~~~l~~-----kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          85 GIEELKEYLKG-----KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             THHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             hHhhHHHHhcC-----CeEEEECCCCCCHHHHHHhhcchh
Confidence            36777777743     467889999999999999998653

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.49  E-value=0.041  Score=42.78  Aligned_cols=21  Identities=14%  Similarity=0.309  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999987653

>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=92.47  E-value=0.043  Score=42.95  Aligned_cols=22  Identities=9%  Similarity=0.051  Sum_probs=18.9

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||+|...+.++
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999877654

>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=92.46  E-value=0.033  Score=44.77  Aligned_cols=22  Identities=18%  Similarity=0.114  Sum_probs=19.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +.|+|-|..|+||||+++.+.+
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~   24 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVE   24 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4688899999999999999886

>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=92.43  E-value=0.043  Score=42.34  Aligned_cols=22  Identities=14%  Similarity=0.238  Sum_probs=18.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999877553

>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=92.42  E-value=0.048  Score=42.63  Aligned_cols=21  Identities=10%  Similarity=0.058  Sum_probs=18.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|-+|+|||+|......+
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            678999999999999887554

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.42  E-value=0.044  Score=42.35  Aligned_cols=22  Identities=18%  Similarity=0.351  Sum_probs=18.6

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|..|+|||||...+.++
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3567899999999999987764

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.30  E-value=0.033  Score=43.99  Aligned_cols=19  Identities=16%  Similarity=0.256  Sum_probs=17.0

Q ss_pred             EEEEEccCCccHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEA  199 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v  199 (334)
                      -|.++|.+|+|||||....
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4679999999999999877

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.29  E-value=0.046  Score=42.76  Aligned_cols=21  Identities=29%  Similarity=0.488  Sum_probs=18.5

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999887754

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.25  E-value=0.036  Score=42.98  Aligned_cols=21  Identities=24%  Similarity=0.322  Sum_probs=18.3

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -|.++|.+|+|||||.+.+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            477999999999999988764

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.23  E-value=0.037  Score=43.29  Aligned_cols=22  Identities=18%  Similarity=0.234  Sum_probs=19.3

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|+|+|..|+|||||...+.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4799999999999999888763

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=92.17  E-value=0.038  Score=41.99  Aligned_cols=20  Identities=20%  Similarity=0.165  Sum_probs=18.1

Q ss_pred             EEEEccCCccHHHHHHHHHc
Q 038944          182 VVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~  201 (334)
                      |+++|.+|+|||||...+..
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999998874

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.15  E-value=0.046  Score=42.33  Aligned_cols=22  Identities=18%  Similarity=0.332  Sum_probs=18.4

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||...+.++
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999776543

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.12  E-value=0.05  Score=42.53  Aligned_cols=21  Identities=14%  Similarity=0.134  Sum_probs=18.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|..|+|||+|++.+.++
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999877664

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=91.98  E-value=0.031  Score=43.37  Aligned_cols=26  Identities=12%  Similarity=-0.061  Sum_probs=21.8

Q ss_pred             CCceEEEEEccCCccHHHHHHHHHcc
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      .+..-|+|+|.+++|||||...+...
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34567999999999999999988653

>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=91.90  E-value=0.12  Score=39.75  Aligned_cols=28  Identities=11%  Similarity=0.108  Sum_probs=23.6

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCC
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYV  205 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~  205 (334)
                      +-.+|.+.|.=|+||||+++.+.+.-.+
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhccc
Confidence            4569999999999999999999975433

>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=91.86  E-value=0.033  Score=43.16  Aligned_cols=21  Identities=19%  Similarity=0.354  Sum_probs=17.1

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999877654

>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=91.76  E-value=0.048  Score=47.13  Aligned_cols=22  Identities=9%  Similarity=0.077  Sum_probs=19.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .++-++|++|+|||.||+.+..
T Consensus       124 g~~l~~G~pG~GKT~la~ala~  145 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGE  145 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHH
Confidence            4566689999999999999998

>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=91.74  E-value=0.051  Score=43.39  Aligned_cols=22  Identities=5%  Similarity=-0.028  Sum_probs=18.8

Q ss_pred             eEEEEEccC-CccHHHHHHHHHc
Q 038944          180 SVVVILDSI-GLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~g-GvGKTtLa~~v~~  201 (334)
                      +.+.|.|-| |+||||++-.+..
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~   24 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQ   24 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHH
Confidence            568999998 9999998877765

>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=91.69  E-value=0.058  Score=42.48  Aligned_cols=21  Identities=10%  Similarity=0.080  Sum_probs=17.7

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||+|...+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999998776654

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=91.58  E-value=0.18  Score=41.85  Aligned_cols=54  Identities=9%  Similarity=0.054  Sum_probs=35.0

Q ss_pred             eEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCC
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMP  236 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~  236 (334)
                      .++.|.|.+|+||||++..+..+......+. ++++  |-+.+...+...++.....
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~-v~~~--s~E~~~~~~~~r~~~~~~~   89 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGKK-VGLA--MLEESVEETAEDLIGLHNR   89 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCCC-EEEE--ESSSCHHHHHHHHHHHHTT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhcccc-eeEe--eeccchhhHHhHHHHHhhc
Confidence            4778999999999999877754321222232 2333  4456677887777766554

>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=91.48  E-value=0.052  Score=42.37  Aligned_cols=22  Identities=9%  Similarity=0.072  Sum_probs=18.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -|.++|.+|+|||||.....++
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999877653

>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=91.34  E-value=0.096  Score=44.18  Aligned_cols=34  Identities=18%  Similarity=0.163  Sum_probs=28.5

Q ss_pred             HHHHhcCCCCceEEEEEccCCccHHHHHHHHHcc
Q 038944          169 LDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       169 ~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ++.|..-+.++.||+|+|.-+.||+||...++..
T Consensus        22 l~~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          22 LKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            4555555667999999999999999999999874

>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=90.99  E-value=0.055  Score=42.43  Aligned_cols=21  Identities=14%  Similarity=0.150  Sum_probs=18.0

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |.++|.+|+|||+|......+
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            678999999999999887553

>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=90.51  E-value=0.039  Score=42.79  Aligned_cols=21  Identities=10%  Similarity=0.159  Sum_probs=8.7

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -|.++|.+|+|||||...+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377899999999999976654

>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=90.50  E-value=0.025  Score=43.03  Aligned_cols=21  Identities=19%  Similarity=0.319  Sum_probs=18.9

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+++|.+|+|||||...+...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998753

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=90.31  E-value=0.072  Score=43.41  Aligned_cols=22  Identities=14%  Similarity=0.271  Sum_probs=19.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +||+|+|-.+.|||||+..+..
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHh
Confidence            5799999999999999988854

>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=90.04  E-value=0.074  Score=43.11  Aligned_cols=22  Identities=9%  Similarity=0.054  Sum_probs=18.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-|.++|.+|+|||||.+.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999987753

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=89.93  E-value=1.1  Score=36.09  Aligned_cols=107  Identities=18%  Similarity=0.162  Sum_probs=56.4

Q ss_pred             eEEEEEccCCccHHHHHHHHHccC---CCC-----C-----ceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCccccchh
Q 038944          180 SVVVILDSIGLDKAAFAGEAYNSS---YVK-----H-----YFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLSEIMDK  246 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~~~---~~~-----~-----~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~~~~~~  246 (334)
                      +++-|.|+...||||+.+.|.--.   +..     +     .|+ .++..+...-++.           ....   .-..
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d-~I~~~~~~~d~~~-----------~~~S---tF~~  100 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFD-GIYTRIGASDDLA-----------GGKS---TFMV  100 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCS-EEEEECCC-----------------CCS---HHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecc-eEEEEECCCcccc-----------CCcc---HHHH
Confidence            378899999999999999875210   111     1     122 3343333221111           1100   1111


Q ss_pred             hHHHHHHHHHHHcCCCeEEEEEeCCCCh-h-------HHHHHHhhCCCCCCCeEEEEecCChHHHhhc
Q 038944          247 NYEMKKIILHEYLMTKRYLNVIDDVWNI-E-------VCDIIREILPDNQNRSRVLITLTEIKMFTFL  306 (334)
Q Consensus       247 ~~~~l~~~l~~~L~~kr~LlVlDdvw~~-~-------~w~~l~~~l~~~~~gsrIivTTr~~~va~~~  306 (334)
                      ++.++...+..  .+++.|+++|.+-.. +       .|.-+. .|  ...++.+++||...+++...
T Consensus       101 el~~~~~il~~--~~~~sLvliDE~~~gT~~~eg~ala~aile-~L--~~~~~~~i~tTH~~eL~~l~  163 (224)
T d1ewqa2         101 EMEEVALILKE--ATENSLVLLDEVGRGTSSLDGVAIATAVAE-AL--HERRAYTLFATHYFELTALG  163 (224)
T ss_dssp             HHHHHHHHHHH--CCTTEEEEEESTTTTSCHHHHHHHHHHHHH-HH--HHHTCEEEEECCCHHHHTCC
T ss_pred             hHHHHHHHhcc--CCCCcEEeecccccCcchhhhcchHHHHHH-HH--hhcCcceEEeeechhhhhhh
Confidence            11133333321  467899999999753 1       333332 23  22478899999998887653

>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=89.70  E-value=0.091  Score=44.30  Aligned_cols=23  Identities=17%  Similarity=0.144  Sum_probs=20.4

Q ss_pred             CceEEEEEccCCccHHHHHHHHH
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +++-|+|+|.+|.|||||+..+.
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll   27 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERIL   27 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHH
Confidence            46789999999999999998774

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=89.08  E-value=0.11  Score=43.56  Aligned_cols=22  Identities=14%  Similarity=0.295  Sum_probs=19.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHH
Q 038944          179 LSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      ++-|+|+|..|.|||||+..+.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            4679999999999999998773

>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=88.74  E-value=0.11  Score=41.63  Aligned_cols=23  Identities=17%  Similarity=0.200  Sum_probs=19.3

Q ss_pred             CCceEEEEEccCCccHHHHHHHH
Q 038944          177 PQLSVVVILDSIGLDKAAFAGEA  199 (334)
Q Consensus       177 ~~~~vi~IvG~gGvGKTtLa~~v  199 (334)
                      +.-.++-|.|.+|+|||+||..+
T Consensus        24 ~~G~~~~I~G~~G~GKT~la~~~   46 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLFSIQF   46 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHH
Confidence            44568999999999999999654

>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=88.56  E-value=0.11  Score=43.04  Aligned_cols=22  Identities=18%  Similarity=0.151  Sum_probs=18.5

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .+..|+|.+|+|||||+-.+.-
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            4777999999999999977654

>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=88.32  E-value=0.12  Score=40.17  Aligned_cols=21  Identities=14%  Similarity=0.110  Sum_probs=19.2

Q ss_pred             EEEEEccCCccHHHHHHHHHc
Q 038944          181 VVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      -|+|+|..++|||||...+..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            589999999999999998875

>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=87.64  E-value=1.1  Score=32.45  Aligned_cols=52  Identities=13%  Similarity=0.017  Sum_probs=33.2

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhC
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLM  235 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~  235 (334)
                      ...+.-|+++.|.|||+++-..+...      ..++.+.+....-..+..+.+.+.+.
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            45788899999999999987666521      23466666554444444444444443

>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=87.26  E-value=0.15  Score=43.93  Aligned_cols=106  Identities=11%  Similarity=0.016  Sum_probs=57.7

Q ss_pred             EEEEEccCCccHHHHHHHHHccCCCCCceeeEEEEEcCCCCCHHHHHHHHHHHhCCCCCcc--ccchhhHHHHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSSYVKHYFDCHAWVPGTYPYDADQMLDIVIKFLMPSSRLS--EIMDKNYEMKKIILHEY  258 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~il~~il~~~~~~~~~~--~~~~~~~~~l~~~l~~~  258 (334)
                      -|.|.|..|+||||+.+.+...  +...- ..+-+.-+.++..           .......  ......  ...+.++..
T Consensus       168 nili~G~tgSGKTT~l~al~~~--i~~~~-rivtiEd~~El~l-----------~~~~~~~~~~~~~~~--~~~~ll~~~  231 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEF--IPKEE-RIISIEDTEEIVF-----------KHHKNYTQLFFGGNI--TSADCLKSC  231 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGG--SCTTC-CEEEEESSCCCCC-----------SSCSSEEEEECBTTB--CHHHHHHHH
T ss_pred             CEEEEeeccccchHHHHHHhhh--ccccc-ceeeccchhhhhc-----------ccccccceeccccch--hHHHHHHHH
Confidence            3788999999999999999873  21111 1111211222110           0000000  001112  344556667


Q ss_pred             cCCCeEEEEEeCCCChhHHHHHHhhCCCCCCCeEEEEecCChHHHhh
Q 038944          259 LMTKRYLNVIDDVWNIEVCDIIREILPDNQNRSRVLITLTEIKMFTF  305 (334)
Q Consensus       259 L~~kr~LlVlDdvw~~~~w~~l~~~l~~~~~gsrIivTTr~~~va~~  305 (334)
                      |+...=.||+..+.+.+.|.-+. +...+..|  ++.|..-.+....
T Consensus       232 lR~~pd~iivgEiR~~ea~~~l~-a~~tGh~g--~~tT~Ha~s~~~a  275 (323)
T d1g6oa_         232 LRMRPDRIILGELRSSEAYDFYN-VLCSGHKG--TLTTLHAGSSEEA  275 (323)
T ss_dssp             TTSCCSEEEESCCCSTHHHHHHH-HHHTTCSC--EEEEECCSSHHHH
T ss_pred             hccCCCcccCCccCchhHHHHHH-HHHhcCCc--EEEEECCCCHHHH
Confidence            76666679999999999887554 44344444  5566555554443

>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=87.13  E-value=0.33  Score=40.47  Aligned_cols=36  Identities=8%  Similarity=0.038  Sum_probs=28.7

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      ..+..+|....+.-..+.++|.|+.|||+++..+..
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~  126 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHH
Confidence            345556655556678899999999999999998887

>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=87.10  E-value=0.27  Score=39.10  Aligned_cols=36  Identities=17%  Similarity=0.220  Sum_probs=28.5

Q ss_pred             HHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          165 MEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..+..+|.. .++-..+.++|+++.|||++|..+.+
T Consensus        40 l~~l~~~l~~-~PKkn~i~~~GP~~TGKS~f~~sl~~   75 (205)
T d1tuea_          40 LGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIH   75 (205)
T ss_dssp             HHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCCceEEEEECCCCccHHHHHHHHHH
Confidence            4556666644 45668999999999999999988876

>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=86.81  E-value=0.28  Score=42.32  Aligned_cols=25  Identities=8%  Similarity=0.122  Sum_probs=21.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHccC
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      +-.|.|=|.-|+||||+++.+.+..
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHh
Confidence            4567788999999999999999853

>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=86.54  E-value=0.18  Score=39.28  Aligned_cols=22  Identities=27%  Similarity=0.182  Sum_probs=19.1

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +-+.|.|.+|+||||||-.+..
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            4578899999999999988776

>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=86.38  E-value=0.2  Score=39.10  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=18.8

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-+.|.|.+|+||||||-.+..
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            3577889999999999988775

>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=86.26  E-value=0.18  Score=44.16  Aligned_cols=34  Identities=15%  Similarity=0.034  Sum_probs=23.2

Q ss_pred             hhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHH
Q 038944          162 DDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       162 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +..+..+...+.     -++..|.|.+|.||||++..+.
T Consensus       151 ~~Q~~A~~~al~-----~~~~vI~G~pGTGKTt~i~~~l  184 (359)
T d1w36d1         151 NWQKVAAAVALT-----RRISVISGGPGTGKTTTVAKLL  184 (359)
T ss_dssp             CHHHHHHHHHHT-----BSEEEEECCTTSTHHHHHHHHH
T ss_pred             cHHHHHHHHHHc-----CCeEEEEcCCCCCceehHHHHH
Confidence            344444554442     2588899999999999875543

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=86.20  E-value=0.088  Score=43.10  Aligned_cols=22  Identities=14%  Similarity=0.205  Sum_probs=18.7

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      ...++|.+|+|||||...+..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            4568899999999999999874

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=85.81  E-value=0.18  Score=43.57  Aligned_cols=23  Identities=22%  Similarity=0.095  Sum_probs=20.3

Q ss_pred             ceEEEEEccCCccHHHHHHHHHc
Q 038944          179 LSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       179 ~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      +..|+|=|.-|+||||+++.+.+
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~   26 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVA   26 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC
T ss_pred             ceEEEEECCcCCCHHHHHHHHHH
Confidence            45688999999999999999976

>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=85.64  E-value=0.079  Score=41.25  Aligned_cols=20  Identities=15%  Similarity=0.109  Sum_probs=17.1

Q ss_pred             EEEEEccCCccHHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +..|+|+.|+||||+...++
T Consensus        26 ~tvi~G~NGsGKStil~Ai~   45 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFV   45 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            44578999999999999886

>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=85.33  E-value=0.23  Score=38.44  Aligned_cols=22  Identities=27%  Similarity=0.222  Sum_probs=18.9

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .-+.|.|.+|+||||||-.+..
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~   37 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIK   37 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            4578899999999999987776

>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=85.22  E-value=0.22  Score=39.70  Aligned_cols=20  Identities=10%  Similarity=0.099  Sum_probs=17.7

Q ss_pred             EEEEEccCCccHHHHHHHHH
Q 038944          181 VVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~  200 (334)
                      -|+|+|-.+.|||||+..+.
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHH
Confidence            38999999999999998874

>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=84.75  E-value=0.27  Score=42.63  Aligned_cols=34  Identities=6%  Similarity=0.185  Sum_probs=25.9

Q ss_pred             HHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHH
Q 038944          166 EELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAY  200 (334)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  200 (334)
                      +.+.+++. ...+++-|+|+|..|.|||||+-.+.
T Consensus         5 ~~~~~lm~-~~~~IRNI~iiGhvd~GKTTL~d~Ll   38 (341)
T d1n0ua2           5 DQMRSLMD-KVTNVRNMSVIAHVDHGKSTLTDSLV   38 (341)
T ss_dssp             HHHHHHHH-CGGGEEEEEEECCGGGTHHHHHHHHH
T ss_pred             HHHHHHhc-CcccCcEEEEEeCCCCcHHHHHHHHH
Confidence            34444444 34568889999999999999998775

>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=83.88  E-value=0.29  Score=40.92  Aligned_cols=22  Identities=9%  Similarity=0.037  Sum_probs=19.8

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -++|||++.+|||||-..+-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            5899999999999999988864

>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=83.34  E-value=0.33  Score=43.00  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=19.7

Q ss_pred             eEEEEEccCCccHHHHHHHHHc
Q 038944          180 SVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       180 ~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      --|+|+|.+|+|||||...+..
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            4589999999999999999974

>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=82.51  E-value=0.42  Score=41.11  Aligned_cols=23  Identities=17%  Similarity=0.176  Sum_probs=19.9

Q ss_pred             EEEEEccCCccHHHHHHHHHccC
Q 038944          181 VVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      .|+|=|.-|+||||+++.+.+..
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l   29 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHF   29 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47777999999999999998843

>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=82.45  E-value=0.41  Score=39.87  Aligned_cols=26  Identities=8%  Similarity=0.111  Sum_probs=22.1

Q ss_pred             CceEEEEEccCCccHHHHHHHHHccC
Q 038944          178 QLSVVVILDSIGLDKAAFAGEAYNSS  203 (334)
Q Consensus       178 ~~~vi~IvG~gGvGKTtLa~~v~~~~  203 (334)
                      ..--++|+|++.+||+||+..+....
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~~~  136 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAKKN  136 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEEecCccchhhhhhhhhccc
Confidence            34568999999999999999998753

>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=81.40  E-value=0.27  Score=41.03  Aligned_cols=67  Identities=7%  Similarity=0.133  Sum_probs=36.4

Q ss_pred             EEEEEeCCCCh--hHHHHHHhhCCCCCCCeEEEEecCChHHHhhccccC-----------cccccccC---CCChhHHHH
Q 038944          264 YLNVIDDVWNI--EVCDIIREILPDNQNRSRVLITLTEIKMFTFLLETL-----------FSLLICVS---RTPRDIQQA  327 (334)
Q Consensus       264 ~LlVlDdvw~~--~~w~~l~~~l~~~~~gsrIivTTr~~~va~~~~~~~-----------~~~l~~l~---~~~~~l~~i  327 (334)
                      -.|++|+.-+.  .+|.-+...+.  +.++-+++---++.+-...+...           ......|+   ++++++.++
T Consensus       208 ~~i~vDE~QD~~~~~~~~l~~~~~--~~~~~~~~GD~~Q~Iy~f~ga~~~~~~~~~~~~~~~~~~~L~~nyRs~~~I~~~  285 (306)
T d1uaaa1         208 RYLLVDEYQDTNTSQYELVKLLVG--SRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALKVIKLEQNYRSSGRILKA  285 (306)
T ss_dssp             SEEEESCGGGCBHHHHHHHHHHHT--TTCCEEEECCGGGCCCGGGTBCTTHHHHHHHHSTTCEEECCCCBSSSCHHHHHH
T ss_pred             hHHHHHHHHHhhHHHHhhhhhccc--CCCcceEeecCccceeccccCChHHHHHHHHhCCCCeEEECCCCCCCCHHHHHH
Confidence            37889999764  46666655442  22444554443333322222211           11222344   589999999


Q ss_pred             HHHhc
Q 038944          328 VISVV  332 (334)
Q Consensus       328 ~~~Iv  332 (334)
                      +..|.
T Consensus       286 an~l~  290 (306)
T d1uaaa1         286 ANILI  290 (306)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88774

>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=81.21  E-value=0.39  Score=40.76  Aligned_cols=21  Identities=14%  Similarity=0.178  Sum_probs=18.9

Q ss_pred             EEEEccCCccHHHHHHHHHcc
Q 038944          182 VVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       182 i~IvG~gGvGKTtLa~~v~~~  202 (334)
                      |+|+|.+.+|||||-..+-+.
T Consensus         3 v~lvG~pn~GKStlfn~lt~~   23 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATLV   23 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC-
T ss_pred             EeEECCCCCCHHHHHHHHHCC
Confidence            899999999999999999764

>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=81.11  E-value=0.4  Score=40.43  Aligned_cols=22  Identities=18%  Similarity=0.125  Sum_probs=20.1

Q ss_pred             EEEEEccCCccHHHHHHHHHcc
Q 038944          181 VVVILDSIGLDKAAFAGEAYNS  202 (334)
Q Consensus       181 vi~IvG~gGvGKTtLa~~v~~~  202 (334)
                      -++|+|.+.+|||||-..+.+.
T Consensus        12 kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          12 KTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4999999999999999999865

>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=80.37  E-value=0.35  Score=40.78  Aligned_cols=15  Identities=20%  Similarity=0.366  Sum_probs=12.7

Q ss_pred             EEEEccCCccHHHHH
Q 038944          182 VVILDSIGLDKAAFA  196 (334)
Q Consensus       182 i~IvG~gGvGKTtLa  196 (334)
                      +-|.|.+|+||||.+
T Consensus        27 ~lV~g~aGSGKTt~l   41 (318)
T d1pjra1          27 LLIMAGAGSGKTRVL   41 (318)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEEecCCccHHHHH
Confidence            668899999999854

>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=80.25  E-value=0.91  Score=39.93  Aligned_cols=41  Identities=15%  Similarity=0.296  Sum_probs=28.3

Q ss_pred             eechhhHHHHHHHHhcCCCCceEEEEEccCCccHHHHHHHHHc
Q 038944          159 VGLDDRMEELLDLLIEGPPQLSVVVILDSIGLDKAAFAGEAYN  201 (334)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  201 (334)
                      .|.....-..++.+....  -..|-|.|+.|+||||....+.+
T Consensus       140 LG~~~~~~~~l~~l~~~~--~GliLvtGpTGSGKSTTl~~~l~  180 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKRP--HGIILVTGPTGSGKSTTLYAGLQ  180 (401)
T ss_dssp             SCCCHHHHHHHHHHHTSS--SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHhhh--hceEEEEcCCCCCccHHHHHHhh
Confidence            455544444444444432  57999999999999998888776