Psyllid ID: psy3261

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340--
Protein Sequence
TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCSFK
Secondary Structure (PSIPRED)
ccccccccccEEEEcHHHHHHHHHcccccHHHHHHHHHccccEEEEcHHHHHHHHHHHHcccccccccEEEEEcccccHHHHHHHHHHHHHHHccEEEEEccccccccccccccccccccccccccHHHHHHHHHHHHHHcHHHHccccccccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccEEEEEEcccccccccccccccccccccccccccHHHHHHHHHcccccccEEEEEEccccccccccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHcccHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccHccccEEEEccHHHHHHHcccccccHHHHHHHHHcccccEEEcHHHHHHHHHHHHHccccccccEEEEEccccccHHHHHHHHHHHHHHcccEEEEcccHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccEEEccEEccccccccccccHHHHHHHcccccHcHHHHHHHHHHHHHHHcccccccEEEEEcccHHHccccccccccccccccHHHHHHHHHHHHHHcccccccEEEEEEccccccccccHccccHHHHccccccccccccEEEcccccHHHHHHHHHHHHHcccccccccHHHHHHHccccHHHHHHHHccc
Coil and Loop (DISEMBL)
tkhskqdlykfytlpdeVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKsmtnfdrpsprfvlygehgvGKSMALVYALQYAHENNYLLVHIPWVlrwfaypkevshsltkegmVDLNIDAAMWLRHFQKQNtkwledprlttsqeyvwsprekseaniPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVcvdgynsffaektnckpedkskvlpsrvTLTRSVINLVQSDWNNGAIVLalspranlpdrreshlplymlkkagfesidpfvpihvpelndeEFHNLLNLYESkkwlqtsegREEIAFLTKRvpqkmyefcsfk
Flexible Loop (DISEMBL)
tkhskqdlykfytlpdevrSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKqntkwledprlTTSQEyvwsprekseaNIPLAALIEHGITRVKYASDVVDVLFTEIkklstegvcrTFVCVDGYNSFfaektnckpedkskvlpsrvTLTRSVINLVQSDWNNGAIVLALspranlpdRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKkwlqtsegREEIafltkrvpqkmyefcsfk
Low Complexity Region (SEG)
TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCSFK
Disordered region (IsUnstruct)
*******LYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCK*****KVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLP**RESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC***
Disordered Region (DISOPRED)
******DLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSM****RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQ*************IPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL*DR*ESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQT*EGREEIAFLTKRVPQKMYEFCSFK
Disordered Region (DISEMBL)
TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCSFK
Disordered Region (DISPRO)
******DLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCSFK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCSFK
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	342	2.2.26 [Sep-21-2011]
P82922	397	28S ribosomal protein S29	yes	N/A	0.982	0.846	0.349	6e-60
Q9ER88	391	28S ribosomal protein S29	yes	N/A	0.979	0.856	0.342	3e-59
P51398	398	28S ribosomal protein S29	yes	N/A	0.982	0.844	0.332	6e-56

>sp|P82922|RT29_BOVIN 28S ribosomal protein S29, mitochondrial OS=Bos taurus GN=DAP3 PE=1 SV=3

 Score =  231 bits (589), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 121/346 (34%), Positives = 203/346 (58%), Gaps = 10/346 (2%)

Query: 1   TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSM 60
            KH +Q + + Y +  +    +F  G   R F  Q + FNE+ +++R   LEL+ YLK+ 
Sbjct: 56  AKHGEQHVGQHYNISIQELKTVFPHGLPPR-FVMQVKTFNEACLMVRKPALELLHYLKN- 113

Query: 61  TNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTK 120
           TNF  P+ R+VLYGE G GK+++L + + +  + ++L++HIP    W    +++  S   
Sbjct: 114 TNFAHPAVRYVLYGEKGTGKTLSLCHIIHFCAKQDWLILHIPDAHLWVKNCRDLLQSTYN 173

Query: 121 EGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITR 180
           +   D  ++A++WL++F+  N ++L   ++    +YVW+ RE +E   PLA ++E GI R
Sbjct: 174 KQRFDQPLEASIWLKNFKTANERFLS--QIKVQDKYVWNKRESTEKGSPLAEVVEQGIMR 231

Query: 181 VKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTR 240
           V+ A+D V ++  E+K+ S+ GV R  V VDG N+ +  +T  K EDKS + P  + L  
Sbjct: 232 VRNATDAVGIVLKELKRQSSLGVFRLLVAVDGVNALWG-RTTLKREDKSPITPEELALIY 290

Query: 241 SVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDE 300
           ++  +V++DW  GAIVL +S   +L   R+++LP  +L K GF+++DPF+PI V   N +
Sbjct: 291 NLRKMVKNDWQGGAIVLTVSQTGSLFKPRKAYLPQELLGKEGFDTLDPFIPILVSNYNPK 350

Query: 301 EFHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
           EF   +  Y    WLQ     T EG++E+ FL+ R P  +   C++
Sbjct: 351 EFEGCIQYYLENNWLQHEKAHTEEGKKELLFLSNRNPGLLERLCAY 396

Involved in mediating interferon-gamma-induced cell death.
Bos taurus (taxid: 9913)

>sp|Q9ER88|RT29_MOUSE 28S ribosomal protein S29, mitochondrial OS=Mus musculus GN=Dap3 PE=2 SV=1

 Score =  229 bits (584), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 118/345 (34%), Positives = 204/345 (59%), Gaps = 10/345 (2%)

Query: 1   TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSM 60
            KH +Q   + Y++P +    +F  G   R +  Q + F E+ +++R   LEL+GYLK+ 
Sbjct: 50  AKHGEQHEGQHYSIPLQDLKTVFPHGLPPR-YMMQVKTFGEACLMVRKPALELLGYLKN- 107

Query: 61  TNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTK 120
           TNF  P+ R++LYGE G GK+++L +A+ +   +++L++HIP    W    +E+  S   
Sbjct: 108 TNFAHPAVRYLLYGEKGTGKTLSLCHAVHFCARHDWLILHIPDAHLWVKNCRELLQSTHN 167

Query: 121 EGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITR 180
           +   D  ++A+ WL++F+  N ++L   ++   ++YVW+ RE +E   PL  ++E G+TR
Sbjct: 168 KQRFDQPLEASTWLKNFKTTNERFLS--QIKVQEKYVWNKRESTEKGSPLGEVVEQGLTR 225

Query: 181 VKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTR 240
           V+ A+D V V+  E+K  S  G+    V VDG N+ +  +T  K ED++ + P  ++L  
Sbjct: 226 VRNATDAVGVVLKELKAQSALGLFHLLVAVDGVNALWG-RTTLKKEDRTLIAPEELSLVH 284

Query: 241 SVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDE 300
           ++  +V++DW+ GAIVL+LS   +L   R ++LP  +L K GF +++PF+PI +P  N +
Sbjct: 285 NLRKMVKNDWHGGAIVLSLSQTGSLFKSRTAYLPHELLGKEGFNALEPFLPILIPNYNPK 344

Query: 301 EFHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCS 340
           EF +    Y    WLQ     T EGR+E+ FL+   P+++   C+
Sbjct: 345 EFESSFQYYLENNWLQHEKASTEEGRKELRFLSNCNPEQLERLCA 389

Involved in mediating interferon-gamma-induced cell death.

Mus musculus (taxid: 10090)

>sp|P51398|RT29_HUMAN 28S ribosomal protein S29, mitochondrial OS=Homo sapiens GN=DAP3 PE=1 SV=1

 Score =  218 bits (554), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 115/346 (33%), Positives = 201/346 (58%), Gaps = 10/346 (2%)

Query: 1   TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSM 60
            KH  Q   + Y +  +    +F  G   R F  Q + F+E+ +++R   LEL+ YLK+ 
Sbjct: 57  AKHGDQHEGQHYNISPQDLETVFPHGLPPR-FVMQVKTFSEACLMVRKPALELLHYLKN- 114

Query: 61  TNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTK 120
           T+F  P+ R++LYGE G GK+++L + + +  + ++L++HIP    W    +++  S   
Sbjct: 115 TSFAYPAIRYLLYGEKGTGKTLSLCHVIHFCAKQDWLILHIPDAHLWVKNCRDLLQSSYN 174

Query: 121 EGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITR 180
           +   D  ++A+ WL++F+  N ++L   ++   ++YVW+ RE +E   PL  ++E GITR
Sbjct: 175 KQRFDQPLEASTWLKNFKTTNERFLN--QIKVQEKYVWNKRESTEKGSPLGEVVEQGITR 232

Query: 181 VKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTR 240
           V+ A+D V ++  E+K+ S+ G+    V VDG N+ +  +T  K EDKS + P  + L  
Sbjct: 233 VRNATDAVGIVLKELKRQSSLGMFHLLVAVDGINALWG-RTTLKREDKSPIAPEELALVH 291

Query: 241 SVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDE 300
           ++  ++++DW+ GAIV ALS   +L   R+++LP  +L K GF+++DPF+PI V   N +
Sbjct: 292 NLRKMMKNDWHGGAIVSALSQTGSLFKPRKAYLPQELLGKEGFDALDPFIPILVSNYNPK 351

Query: 301 EFHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
           EF + +  Y    WLQ     T EG++E+ FL+   P  +   C++
Sbjct: 352 EFESCIQYYLENNWLQHEKAPTEEGKKELLFLSNANPSLLERHCAY 397

Involved in mediating interferon-gamma-induced cell death.

Homo sapiens (taxid: 9606)

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	342
328697944	376	PREDICTED: 28S ribosomal protein S29, mi	0.985	0.896	0.463	1e-90
157116602	385	mitochondrial ribosomal protein, S29, pu	0.985	0.875	0.414	3e-82
195585700	392	GD25129 [Drosophila simulans] gi|1941946	0.985	0.859	0.417	3e-79
195346722	390	GM15640 [Drosophila sechellia] gi|194135	0.985	0.864	0.417	1e-78
17647691	392	mitochondrial ribosomal protein S29 [Dro	0.985	0.859	0.411	1e-78
170051615	383	mitochondrial 28S ribosomal protein S29	0.988	0.882	0.413	2e-78
27462217	390	DAP3 [Drosophila melanogaster]	0.985	0.864	0.411	2e-78
194754910	388	GF13020 [Drosophila ananassae] gi|190621	0.985	0.868	0.405	2e-78
195154459	392	GL16923 [Drosophila persimilis] gi|19411	0.982	0.857	0.411	3e-78
195488691	392	GE11679 [Drosophila yakuba] gi|194178522	0.985	0.859	0.411	3e-78

>gi|328697944|ref|XP_001951372.2| PREDICTED: 28S ribosomal protein S29, mitochondrial-like [Acyrthosiphon pisum]

 Score =  339 bits (870), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 157/339 (46%), Positives = 230/339 (67%), Gaps = 2/339 (0%)

Query: 3   HSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTN 62
           H  QD+ KFYT+  +  S IF+ GG+ + F EQT +F E++++IR   LE++  LKS T+
Sbjct: 37  HDSQDVSKFYTIDPKTVSNIFQTGGLPKPFTEQTNMFAETALMIRQPALEVINSLKS-TD 95

Query: 63  FDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYP-KEVSHSLTKE 121
           F +P+ R++LYG+ G GKS++L + L YA+ + ++L HIP+V  W  Y  KEV+ S +K 
Sbjct: 96  FQKPAVRYLLYGQTGSGKSLSLAHILHYAYSSKFILYHIPYVPIWLKYDRKEVNWSSSKN 155

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM D+ + AA WL+HF  QN   L +  LTTSQ+YVWS RE +     L  L+ HGI R 
Sbjct: 156 GMADIPLIAAQWLKHFVHQNGALLNELNLTTSQDYVWSQRETTPQGTTLNELVTHGINRA 215

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYA D +D+L  E+K   +   C+  V +DG+N+FF EKT+ K ED+ KV P ++T+ ++
Sbjct: 216 KYACDCMDILLNELKAHCSNNRCKMLVAIDGFNAFFNEKTDLKTEDRVKVTPQQITMVQT 275

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            ++ V SDWNNGAI++  SPRA L  +RESHLP+Y++ + GFE IDPF+P+ VPEL+  E
Sbjct: 276 GLSAVLSDWNNGAIIMVTSPRAALNTKRESHLPIYLIGRQGFEHIDPFIPVMVPELSTVE 335

Query: 302 FHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCS 340
           F+N+L+ YE K+WLQ   GR+E+ FLT ++P  +   C+
Sbjct: 336 FNNMLDYYEEKRWLQKPGGRKELEFLTSKLPADLMARCA 374

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157116602|ref|XP_001658571.1| mitochondrial ribosomal protein, S29, putative [Aedes aegypti] gi|108876397|gb|EAT40622.1| AAEL007668-PA [Aedes aegypti]

 Score =  311 bits (797), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 141/340 (41%), Positives = 221/340 (65%), Gaps = 3/340 (0%)

Query: 3   HSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTN 62
           HS+  L +FYT+P +VR  +F  GG  + F +Q + FNES +++R   +EL+ Y+ +  +
Sbjct: 45  HSRSHLSRFYTIPADVRKQVFSYGGFPKTFEKQIKTFNESCLMVREPAVELINYMNA-AD 103

Query: 63  FDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEG 122
           + +P+ RFVLYG+ GVGKS+ L + L Y +   ++LVH+PWV  W    KE ++S+T EG
Sbjct: 104 YSKPANRFVLYGKDGVGKSIVLAHLLHYGYNQEFVLVHVPWVPNWMKRAKETANSITHEG 163

Query: 123 MVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVK 182
            +DL +D A WL HF+ QN+K L    L  S++YVW+ RE + A  P+  LI+HGI R K
Sbjct: 164 CLDLPLDGAAWLIHFKNQNSKLLAKLDLKVSRDYVWTKRETTPAGAPMLELIDHGINRAK 223

Query: 183 YASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSV 242
           ++ D +  L  E+K+ ST+G  +T V +DG+N+FF  +T    E+K +V P +VTLT+  
Sbjct: 224 FSCDAIAALLGELKQQSTQGKLKTMVIIDGFNAFFHPQTRITTENKVRVTPDKVTLTKPF 283

Query: 243 INLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEF 302
           +++ + DW NG  +LA+   A   DR ES LP+Y L++ GFE +DPFVPI V   ++EE+
Sbjct: 284 LDITRPDWCNGVCILAVDRMALTEDRMESELPMYQLRREGFEHLDPFVPIRVDNYSEEEY 343

Query: 303 HNLLNLYESKKWLQTSEG--REEIAFLTKRVPQKMYEFCS 340
           ++ +  Y ++KW+QT+E    +E+ FL+ R P ++ E C+
Sbjct: 344 YSCVQYYLNRKWIQTTEQGFDKELEFLSGRNPFELMELCA 383

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195585700|ref|XP_002082618.1| GD25129 [Drosophila simulans] gi|194194627|gb|EDX08203.1| GD25129 [Drosophila simulans]

 Score =  301 bits (771), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 142/340 (41%), Positives = 212/340 (62%), Gaps = 3/340 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFYT+P E +  IF  GG+ + + +Q + F E+ +++RN  LEL+ Y+K   
Sbjct: 51  EHSAMQVAKFYTIPAEQKKQIFSGGGLPKQYEQQIKTFTEACLMVRNPALELLQYIKD-G 109

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R+VLYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct: 110 DLTKPVVRYVLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 169

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN   L+  +L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct: 170 GMIDLPFDAAAWLVHFKAQNGPLLQRLQLKTSKEYVWSKRESTPAGSSLIELVEHGIARI 229

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYAS+    L  E+K+LST G C+  V +DG+N+FF   T    ++K  V P RVTLT+ 
Sbjct: 230 KYASETTAALIAELKQLSTAGQCKVMVAIDGFNAFFHPVTRIFSDNKQLVTPDRVTLTQP 289

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++   DW NG  VL++   A      +S++P Y+L K GFE +DPFVPIHV    D+E
Sbjct: 290 FLDITNYDWTNGVCVLSVDKIAMTEGYMDSYMPRYLLGKEGFEHLDPFVPIHVENYTDKE 349

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FH+ +N Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 350 FHSYINYYLDRHWINKTPQGFEEQLKFMSNKNPYSLMQLV 389

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195346722|ref|XP_002039906.1| GM15640 [Drosophila sechellia] gi|194135255|gb|EDW56771.1| GM15640 [Drosophila sechellia]

 Score =  299 bits (766), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 142/340 (41%), Positives = 212/340 (62%), Gaps = 3/340 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFYT+P E +  IF  GG+ + + +Q + F E+ +++RN  LEL+ Y+K   
Sbjct: 49  EHSAMQVAKFYTIPAEQKKQIFGGGGLPKQYEQQIKTFTEACLMVRNPALELLQYIKD-G 107

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R+VLYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct: 108 DLTKPVVRYVLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 167

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN   L+  +L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct: 168 GMIDLPFDAAAWLVHFKAQNGPLLQRLQLKTSKEYVWSKRESTPAGSSLIELVEHGIARI 227

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYAS+    L  E+K+LST G C+  V +DG+NSFF   T    ++K  V P RVTLT+ 
Sbjct: 228 KYASETTAALIAELKQLSTAGQCKVMVAIDGFNSFFHPVTRIFSDNKQLVTPDRVTLTQP 287

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++   DW NG  VL++   A      +S++P Y+L K GFE +DPFVPIHV    D+E
Sbjct: 288 FLDITNYDWTNGVCVLSVDKIAMTEGYMDSYMPRYLLGKEGFEHLDPFVPIHVENYTDKE 347

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FH+ ++ Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 348 FHSYISYYLDRHWINKTPQGFEEQLKFMSNKNPYSLMQLV 387

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17647691|ref|NP_523811.1| mitochondrial ribosomal protein S29 [Drosophila melanogaster] gi|7291419|gb|AAF46846.1| mitochondrial ribosomal protein S29 [Drosophila melanogaster] gi|17862624|gb|AAL39789.1| LD41023p [Drosophila melanogaster]

 Score =  299 bits (766), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 140/340 (41%), Positives = 212/340 (62%), Gaps = 3/340 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFYT+P E +  IF  GG+ + + +Q + F E+ +++RN  LEL+ Y+K   
Sbjct: 51  EHSAMQVAKFYTIPAEQKKQIFTGGGLPKQYEQQIKTFTEACLMVRNPALELLQYIKD-G 109

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R+VLYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct: 110 DLTKPVVRYVLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 169

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN   L+  +L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct: 170 GMIDLPFDAAAWLVHFKTQNGPLLQRLQLKTSKEYVWSKRESTPAGSSLIELVEHGIARI 229

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYAS+    L  E+K+LST G C+  V +DG+N+FF   T    ++K  V P RVTLT+ 
Sbjct: 230 KYASETTAALIAELKQLSTAGQCKVMVAIDGFNAFFHPVTRIFSDNKQLVTPDRVTLTQP 289

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++   DW NG  +L++   A      +S++P Y+L K GFE +DPFVPIHV    D+E
Sbjct: 290 FLDITNYDWTNGVCILSVDKIAMTEGHMDSYMPRYLLGKEGFEHLDPFVPIHVENYTDKE 349

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FH+ ++ Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 350 FHSYISYYLDRHWINKTPQGFEEQLKFMSNKNPYSLMQLV 389

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170051615|ref|XP_001861844.1| mitochondrial 28S ribosomal protein S29 [Culex quinquefasciatus] gi|167872800|gb|EDS36183.1| mitochondrial 28S ribosomal protein S29 [Culex quinquefasciatus]

 Score =  299 bits (765), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/341 (41%), Positives = 215/341 (63%), Gaps = 3/341 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +H++  L +FYT+P +VR  IF  GG  + + +Q + FNE+ +++R   +EL+G+L + T
Sbjct: 42  RHNQSHLSRFYTIPADVRKQIFAHGGFPKTYEKQIKTFNEACLMVRPAAVELIGHLNA-T 100

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +F RP+ RFVLYGE G GKSM L + L Y     ++LVH+PWV  W    KE + S T+E
Sbjct: 101 DFRRPANRFVLYGEDGAGKSMVLAHLLHYGFCQEFVLVHVPWVPNWMKRAKETAISGTRE 160

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           G +DL +D A WL HF+ QN   L    L  S++YVWS RE + A  P+  LI+HGI R 
Sbjct: 161 GCLDLPLDGAAWLVHFKNQNAPLLAKLDLKVSRDYVWSKRETTPAGAPMLELIDHGINRA 220

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           K++ D +  L  E+K+ ST G  +T V +DG+N+FF   T    E+K +V P ++TLTR 
Sbjct: 221 KFSCDAIAALLGELKEQSTAGRVKTMVVIDGFNAFFHPHTRILTENKVRVTPDKLTLTRP 280

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++  +DW NG  ++ +   A   DR ES LP+Y L++ GFE +DPFVP+ V   ++EE
Sbjct: 281 FLDITGADWCNGVCIVTVDRMALTEDRMESTLPMYQLRREGFEHLDPFVPVRVDNYSEEE 340

Query: 302 FHNLLNLYESKKWLQ-TSEG-REEIAFLTKRVPQKMYEFCS 340
           FH+ +  Y ++KW+Q T +G  +E+ FL+ + P K+ +  +
Sbjct: 341 FHSAVQYYLNRKWIQITKDGFDKELEFLSGKNPFKLMQLSA 381

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|27462217|gb|AAO15385.1|AF348494_1 DAP3 [Drosophila melanogaster]

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 140/340 (41%), Positives = 212/340 (62%), Gaps = 3/340 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFYT+P E +  IF  GG+ + + +Q + F E+ +++RN  LEL+ Y+K   
Sbjct: 49  EHSAMQVAKFYTIPAEQKKQIFTGGGLPKQYEQQIKTFTEACLMVRNPALELLQYIKD-G 107

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R+VLYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct: 108 DLTKPVVRYVLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 167

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN   L+  +L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct: 168 GMIDLPFDAAAWLVHFKTQNGPLLQRLQLKTSKEYVWSKRESTPAGSSLIELVEHGIARI 227

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYAS+    L  E+K+LST G C+  V +DG+N+FF   T    ++K  V P RVTLT+ 
Sbjct: 228 KYASETTAALIAELKQLSTAGKCKVMVAIDGFNAFFHPVTRIFSDNKQLVTPDRVTLTQP 287

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++   DW NG  +L++   A      +S++P Y+L K GFE +DPFVPIHV    D+E
Sbjct: 288 FLDITNYDWTNGVCILSVDKIAMTEGHMDSYMPRYLLGKEGFEHLDPFVPIHVENYTDKE 347

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FH+ ++ Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 348 FHSYISYYLDRHWINKTPQGFEEQLKFMSNKNPYSLMQLV 387

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194754910|ref|XP_001959735.1| GF13020 [Drosophila ananassae] gi|190621033|gb|EDV36557.1| GF13020 [Drosophila ananassae]

 Score =  298 bits (763), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 138/340 (40%), Positives = 214/340 (62%), Gaps = 3/340 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFYT+P E +  IF  GG+ + + +Q + F E+ +++RN  LE++ Y+K   
Sbjct: 47  EHSALQVAKFYTIPAEQKKQIFAGGGLPKQYEQQIKTFTEACLMVRNPALEVLEYIKK-A 105

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R++LYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct: 106 DLSKPVVRYLLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 165

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN+K L+   L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct: 166 GMIDLPFDAAAWLVHFKGQNSKLLQRLELKTSKEYVWSKRESTPAGSTLLELVEHGIARI 225

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYAS+    L +E+K LST G C+  V +DGYN+FF   T    ++K +V P ++TLT  
Sbjct: 226 KYASETTAALISELKLLSTAGKCKVMVAIDGYNAFFHPVTRIFSDNKQRVTPDKITLTHP 285

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +N+ + DW NG  +L++   A      +S++P Y+L   GFE +DPFVPIHV   +D+E
Sbjct: 286 FLNITRYDWTNGVCILSVDKIAMTEGHMDSYMPRYLLGTEGFEHLDPFVPIHVENYSDKE 345

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FH+ ++ Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 346 FHSYISYYLDRHWINKTPQGFEEQLKFMSNKNPYALMQLV 385

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195154459|ref|XP_002018139.1| GL16923 [Drosophila persimilis] gi|194113935|gb|EDW35978.1| GL16923 [Drosophila persimilis]

 Score =  298 bits (762), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 140/340 (41%), Positives = 217/340 (63%), Gaps = 4/340 (1%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFYT+P E +  IF  GG+ + + +Q + F E  +++R+  LEL+ Y+K+  
Sbjct: 52  EHSALHVAKFYTIPVEQKKQIFTGGGLPKQYEQQIKTFTEPCLMVRSPALELLHYIKN-A 110

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R+VLYG++GVGK++ + + L Y   N++LLVH+PW   W   PKE S++ ++E
Sbjct: 111 DLTKPVVRYVLYGDNGVGKTLTMAHVLHYGAINDFLLVHVPWAPNWMKRPKEASNA-SQE 169

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN K L+  +L T++EYVWS RE + A   L  L+EHGI R+
Sbjct: 170 GMLDLPFDAAAWLVHFKTQNAKLLQQLQLKTNKEYVWSKRESTPAGSSLIELVEHGIARI 229

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYA+D    L +E+K+LST G C+  V +DG+N+FF  +T    ++K +V P R+TLT+ 
Sbjct: 230 KYATDTTVALISELKQLSTAGQCKIMVAIDGFNAFFHPETRIFSDNKQRVTPDRITLTQP 289

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++   DW NG  +L++   A      +S++P Y+L   GFE IDPFVPIHV    D+E
Sbjct: 290 FLDITNYDWTNGVCILSVDKIAMTEGYMDSYMPRYLLGTEGFEHIDPFVPIHVENYTDKE 349

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FHN +N Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 350 FHNYINYYLDRHWINKTPQGFEEQLKFMSNKNPYTLMQLV 389

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195488691|ref|XP_002092421.1| GE11679 [Drosophila yakuba] gi|194178522|gb|EDW92133.1| GE11679 [Drosophila yakuba]

 Score =  298 bits (762), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 140/340 (41%), Positives = 212/340 (62%), Gaps = 3/340 (0%)

Query: 2   KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
           +HS   + KFY++P E +  IF  GG+ + + +Q + F E+ +++RN  LEL+ Y+K   
Sbjct: 51  EHSALQVAKFYSIPAEQKKLIFSGGGLPKQYEQQIKTFTEACLMVRNPALELLQYIKD-G 109

Query: 62  NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
           +  +P  R+VLYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct: 110 DLTKPVVRYVLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 169

Query: 122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
           GM+DL  DAA WL HF+ QN   L+  +L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct: 170 GMIDLPFDAAAWLVHFKNQNGPLLQRLQLKTSKEYVWSKRESTPAGSSLIELVEHGIARI 229

Query: 182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
           KYAS+    L  E+K+LST G C+  V +DG+N+FF   T    ++K  V P RVTLT+ 
Sbjct: 230 KYASETTAALIAELKQLSTAGQCKIMVAIDGFNAFFHPVTRIFSDNKQLVTPDRVTLTQP 289

Query: 242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
            +++   DW NG  +L++   A      ES++P Y+L K GFE +DPFVPIHV    D+E
Sbjct: 290 FLDITNYDWTNGVCILSVDKIAMTEGHMESYMPRYLLGKEGFEHLDPFVPIHVENYTDKE 349

Query: 302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYEFC 339
           FH+ ++ Y  + W+ +T +G EE + F++ + P  + +  
Sbjct: 350 FHSYISYYLDRHWINKTPQGFEEQLKFMSNKNPYSLMQLV 389

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	342
FB|FBgn0034727	392	mRpS29 "mitochondrial ribosoma	0.979	0.854	0.414	4.5e-75
UNIPROTKB|P82922	397	DAP3 "28S ribosomal protein S2	0.979	0.843	0.350	2.2e-57
UNIPROTKB|F1P6P0	393	DAP3 "Uncharacterized protein"	0.979	0.852	0.350	4.6e-57
MGI|MGI:1929538	391	Dap3 "death associated protein	0.976	0.854	0.343	1.2e-56
UNIPROTKB|H9L0M5	398	H9L0M5 "Uncharacterized protei	0.941	0.809	0.373	2e-56
UNIPROTKB|F1RLM4	424	LOC100625274 "Uncharacterized	0.979	0.790	0.347	2.5e-56
UNIPROTKB|I3LS10	398	LOC100625274 "Uncharacterized	0.979	0.841	0.347	2.5e-56
RGD|1305339	391	Dap3 "death associated protein	0.976	0.854	0.343	5.3e-56
UNIPROTKB|P51398	398	DAP3 "28S ribosomal protein S2	0.979	0.841	0.333	2.6e-54
ZFIN|ZDB-GENE-051129-2	402	dap3 "death associated protein	0.982	0.835	0.339	2.4e-51

FB|FBgn0034727 mRpS29 "mitochondrial ribosomal protein S29" [Drosophila melanogaster (taxid:7227)]

 Score = 757 (271.5 bits), Expect = 4.5e-75, P = 4.5e-75
 Identities = 140/338 (41%), Positives = 212/338 (62%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             +HS   + KFYT+P E +  IF  GG+ + + +Q + F E+ +++RN  LEL+ Y+K   
Sbjct:    51 EHSAMQVAKFYTIPAEQKKQIFTGGGLPKQYEQQIKTFTEACLMVRNPALELLQYIKD-G 109

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             +  +P  R+VLYGE+G GK++ + + L Y   N++LLVH+PW   W   PKE S++  +E
Sbjct:   110 DLTKPVVRYVLYGENGTGKTLTMAHVLHYGALNDFLLVHVPWAPNWMKRPKEASNAAGQE 169

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
             GM+DL  DAA WL HF+ QN   L+  +L TS+EYVWS RE + A   L  L+EHGI R+
Sbjct:   170 GMIDLPFDAAAWLVHFKTQNGPLLQRLQLKTSKEYVWSKRESTPAGSSLIELVEHGIARI 229

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             KYAS+    L  E+K+LST G C+  V +DG+N+FF   T    ++K  V P RVTLT+ 
Sbjct:   230 KYASETTAALIAELKQLSTAGQCKVMVAIDGFNAFFHPVTRIFSDNKQLVTPDRVTLTQP 289

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
              +++   DW NG  +L++   A      +S++P Y+L K GFE +DPFVPIHV    D+E
Sbjct:   290 FLDITNYDWTNGVCILSVDKIAMTEGHMDSYMPRYLLGKEGFEHLDPFVPIHVENYTDKE 349

Query:   302 FHNLLNLYESKKWL-QTSEGREE-IAFLTKRVPQKMYE 337
             FH+ ++ Y  + W+ +T +G EE + F++ + P  + +
Sbjct:   350 FHSYISYYLDRHWINKTPQGFEEQLKFMSNKNPYSLMQ 387

GO:0006412 "translation" evidence=ISS

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0005763 "mitochondrial small ribosomal subunit" evidence=ISS

GO:0006915 "apoptotic process" evidence=IEA

UNIPROTKB|P82922 DAP3 "28S ribosomal protein S29, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 590 (212.7 bits), Expect = 2.2e-57, P = 2.2e-57
 Identities = 121/345 (35%), Positives = 203/345 (58%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             KH +Q + + Y +  +    +F  G   R F  Q + FNE+ +++R   LEL+ YLK+ T
Sbjct:    57 KHGEQHVGQHYNISIQELKTVFPHGLPPR-FVMQVKTFNEACLMVRKPALELLHYLKN-T 114

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P+ R+VLYGE G GK+++L + + +  + ++L++HIP    W    +++  S   +
Sbjct:   115 NFAHPAVRYVLYGEKGTGKTLSLCHIIHFCAKQDWLILHIPDAHLWVKNCRDLLQSTYNK 174

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A++WL++F+  N ++L   ++    +YVW+ RE +E   PLA ++E GI RV
Sbjct:   175 QRFDQPLEASIWLKNFKTANERFLS--QIKVQDKYVWNKRESTEKGSPLAEVVEQGIMRV 232

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V ++  E+K+ S+ GV R  V VDG N+ +  +T  K EDKS + P  + L  +
Sbjct:   233 RNATDAVGIVLKELKRQSSLGVFRLLVAVDGVNALWG-RTTLKREDKSPITPEELALIYN 291

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V++DW  GAIVL +S   +L   R+++LP  +L K GF+++DPF+PI V   N +E
Sbjct:   292 LRKMVKNDWQGGAIVLTVSQTGSLFKPRKAYLPQELLGKEGFDTLDPFIPILVSNYNPKE 351

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
             F   +  Y    WLQ     T EG++E+ FL+ R P  +   C++
Sbjct:   352 FEGCIQYYLENNWLQHEKAHTEEGKKELLFLSNRNPGLLERLCAY 396

GO:0005739 "mitochondrion" evidence=ISS

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

UNIPROTKB|F1P6P0 DAP3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 587 (211.7 bits), Expect = 4.6e-57, P = 4.6e-57
 Identities = 121/345 (35%), Positives = 203/345 (58%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             +H +Q     Y +P +    +F  G   R F  Q + FNE+ +++R   LEL+ YLK+ T
Sbjct:    53 RHGEQHAALHYHIPLQDLKTVFPQGLPPR-FIMQVKTFNEACLMVRKPALELLHYLKN-T 110

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P+ R+VLYGE G GK+++L + + +  + ++L++HIP    W    + +  S   +
Sbjct:   111 NFAHPAVRYVLYGEKGTGKTLSLCHVVHFCAKQDWLILHIPDAHLWVKNCRGLLQSSYNK 170

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A++WL++F+  N ++L   ++   ++YVW+ RE +E   PL A++E G+TRV
Sbjct:   171 QRFDQPVEASIWLKNFKTANERFLS--QIKVQEKYVWNKRESTEKGSPLGAVVEQGLTRV 228

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V ++  E+K  S  G     V VDG N+ +  +T+ K EDKS + P  + L  S
Sbjct:   229 RNATDAVGIVLKELKNQSCLGAFHLLVAVDGVNALWG-RTSLKREDKSLIAPEELALVCS 287

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V++DW+ GAIVL LS   +L   R+++LP  +L K GF+++DPF+PI V   N +E
Sbjct:   288 LRKMVRNDWHGGAIVLTLSQTGSLFKPRKAYLPQELLGKEGFDALDPFIPILVSNYNPKE 347

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
             F + +  Y   KWLQ     T EG++E+ FL+   P ++   C++
Sbjct:   348 FESCIQYYLENKWLQHEKAHTEEGKKELLFLSDANPGQLERLCAY 392

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

MGI|MGI:1929538 Dap3 "death associated protein 3" [Mus musculus (taxid:10090)]

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 118/344 (34%), Positives = 204/344 (59%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             KH +Q   + Y++P +    +F  G   R +  Q + F E+ +++R   LEL+GYLK+ T
Sbjct:    51 KHGEQHEGQHYSIPLQDLKTVFPHGLPPR-YMMQVKTFGEACLMVRKPALELLGYLKN-T 108

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P+ R++LYGE G GK+++L +A+ +   +++L++HIP    W    +E+  S   +
Sbjct:   109 NFAHPAVRYLLYGEKGTGKTLSLCHAVHFCARHDWLILHIPDAHLWVKNCRELLQSTHNK 168

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A+ WL++F+  N ++L   ++   ++YVW+ RE +E   PL  ++E G+TRV
Sbjct:   169 QRFDQPLEASTWLKNFKTTNERFLS--QIKVQEKYVWNKRESTEKGSPLGEVVEQGLTRV 226

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V V+  E+K  S  G+    V VDG N+ +  +T  K ED++ + P  ++L  +
Sbjct:   227 RNATDAVGVVLKELKAQSALGLFHLLVAVDGVNALWG-RTTLKKEDRTLIAPEELSLVHN 285

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V++DW+ GAIVL+LS   +L   R ++LP  +L K GF +++PF+PI +P  N +E
Sbjct:   286 LRKMVKNDWHGGAIVLSLSQTGSLFKSRTAYLPHELLGKEGFNALEPFLPILIPNYNPKE 345

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCS 340
             F +    Y    WLQ     T EGR+E+ FL+   P+++   C+
Sbjct:   346 FESSFQYYLENNWLQHEKASTEEGRKELRFLSNCNPEQLERLCA 389

GO:0005739 "mitochondrion" evidence=ISO;IDA

GO:0005759 "mitochondrial matrix" evidence=IDA

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006915 "apoptotic process" evidence=RCA

GO:0008637 "apoptotic mitochondrial changes" evidence=IDA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0042981 "regulation of apoptotic process" evidence=RCA

UNIPROTKB|H9L0M5 H9L0M5 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 581 (209.6 bits), Expect = 2.0e-56, P = 2.0e-56
 Identities = 124/332 (37%), Positives = 192/332 (57%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             +HS+Q   + Y++P E   A+F   G+   F +Q + F E+ +++R   LEL  YLK+ +
Sbjct:    58 QHSEQHEGRHYSIPLEEVKAVFP-HGLPYRFQQQIKTFQEACVMVRKPALELFTYLKN-S 115

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P  R+V+YGE G GK+M L + + +     +L++HIP    W    KE+  S   +
Sbjct:   116 NFAHPVVRYVIYGERGTGKTMTLCHVVHFCARQGWLVLHIPDAHLWVKNCKELMQSSYNK 175

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
               +D  + A+ WLR+F+  N  +L++  + T Q+YVW  R+ +E   PL  ++E G+TRV
Sbjct:   176 ERLDQPLQASFWLRNFRTTNEHFLKE--IKTQQKYVWGKRDSTEQGRPLGEVVEQGLTRV 233

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             K ASD V V+  EIK+    G  R  V VDG N+ +  +T  K EDKS V P  +TL  +
Sbjct:   234 KNASDAVGVVLKEIKQQCCLGSFRVLVAVDGVNALWG-RTTLKKEDKSPVSPEELTLVYN 292

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V ++W+ GA+V  LS   +L     +HLP  +L K GF+++DPFVPI VP   + E
Sbjct:   293 LRKMVMNNWSGGAVVTTLSQTGSLFKPSSAHLPHELLGKEGFDALDPFVPILVPNYTERE 352

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLT 328
             F +  + Y   +WLQ     T +G+EE+ FL+
Sbjct:   353 FESCYHYYLHCRWLQHEKARTEDGKEELRFLS 384

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA

UNIPROTKB|F1RLM4 LOC100625274 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 580 (209.2 bits), Expect = 2.5e-56, P = 2.5e-56
 Identities = 120/345 (34%), Positives = 200/345 (57%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             KH +Q   + Y +  +    +F  G   R F  Q + FNE+ +++R   LEL+ YLK+ T
Sbjct:    84 KHREQHEGQHYNISLQELKTVFPHGLPPR-FAMQVKTFNEACLMVRKPALELLHYLKN-T 141

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P+ R+VLYGE G GK+++L + L +  + N+L++HIP    W    +++  S   +
Sbjct:   142 NFAHPAVRYVLYGEKGTGKTLSLCHILHFCAKQNWLILHIPDAHIWVKNCRDLLQSNYNK 201

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A+ WL++F+  N  +L   ++   ++YVW+ RE +E   PL  ++E GI RV
Sbjct:   202 QRFDQPLEASTWLKNFKTANEHFLS--QIKVQEKYVWNKRESTEKGRPLGEVVEQGIMRV 259

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V ++  E+K+ S+ G+    V VDG N+ +  +T  K EDKS + P  + L  +
Sbjct:   260 RNATDAVGIVLKELKRQSSLGIFHLLVAVDGVNALWG-RTTLKREDKSPIAPEELALIHN 318

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V++DW  GAIVL +S   +L   R ++LP  +L K GF+++DPF+PI V   N +E
Sbjct:   319 LRKMVKNDWQGGAIVLTVSQTGSLFKPRNAYLPQELLGKEGFDALDPFIPILVSNYNPKE 378

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
             F + +  Y    WLQ     T EG++E+ FL+ R P ++   C++
Sbjct:   379 FESCIQYYLENNWLQHEKAHTEEGKKELLFLSNRNPGQLERLCAY 423

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

UNIPROTKB|I3LS10 LOC100625274 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 580 (209.2 bits), Expect = 2.5e-56, P = 2.5e-56
 Identities = 120/345 (34%), Positives = 200/345 (57%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             KH +Q   + Y +  +    +F  G   R F  Q + FNE+ +++R   LEL+ YLK+ T
Sbjct:    58 KHREQHEGQHYNISLQELKTVFPHGLPPR-FAMQVKTFNEACLMVRKPALELLHYLKN-T 115

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P+ R+VLYGE G GK+++L + L +  + N+L++HIP    W    +++  S   +
Sbjct:   116 NFAHPAVRYVLYGEKGTGKTLSLCHILHFCAKQNWLILHIPDAHIWVKNCRDLLQSNYNK 175

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A+ WL++F+  N  +L   ++   ++YVW+ RE +E   PL  ++E GI RV
Sbjct:   176 QRFDQPLEASTWLKNFKTANEHFLS--QIKVQEKYVWNKRESTEKGRPLGEVVEQGIMRV 233

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V ++  E+K+ S+ G+    V VDG N+ +  +T  K EDKS + P  + L  +
Sbjct:   234 RNATDAVGIVLKELKRQSSLGIFHLLVAVDGVNALWG-RTTLKREDKSPIAPEELALIHN 292

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V++DW  GAIVL +S   +L   R ++LP  +L K GF+++DPF+PI V   N +E
Sbjct:   293 LRKMVKNDWQGGAIVLTVSQTGSLFKPRNAYLPQELLGKEGFDALDPFIPILVSNYNPKE 352

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
             F + +  Y    WLQ     T EG++E+ FL+ R P ++   C++
Sbjct:   353 FESCIQYYLENNWLQHEKAHTEEGKKELLFLSNRNPGQLERLCAY 397

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

RGD|1305339 Dap3 "death associated protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 118/344 (34%), Positives = 204/344 (59%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             KH +Q   + Y++P +    +F  G   R +  Q + F E+ +++R   LEL+GYLK+ T
Sbjct:    51 KHGEQHEGQHYSIPPQDLKTVFPHGLPPR-YAMQVKTFGEACLMVRKPALELLGYLKN-T 108

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             NF  P+ R++LYGE G GK+++L +A+ +  ++++L++HIP    W     E+  S   +
Sbjct:   109 NFAHPAVRYLLYGEKGTGKTLSLCHAVHFCAKSDWLILHIPDAHLWVKNCGELLQSTYNK 168

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A+ WL++F+  N ++L   ++   ++YVW+ RE +E   PL  ++E G+TRV
Sbjct:   169 QRFDQPLEASTWLKNFKTTNERFLG--QIKVQEKYVWNKRESTEKGSPLGEVVEQGLTRV 226

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V V+  E+K  S+ G+    V VDG N+ +  +T  K ED++ + P  + L R+
Sbjct:   227 RNATDAVGVVLKELKTQSSLGLFHLLVAVDGVNALWG-RTTLKREDRTLIAPEELALVRN 285

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  +V++DW+ GAIVL+LS   +L   R ++LP  +L K GF +++PF+PI +   N +E
Sbjct:   286 LRKMVKNDWHGGAIVLSLSQTGSLFKSRTAYLPHELLGKEGFNALEPFLPILISNYNPKE 345

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCS 340
             F +    Y    WLQ     T EGR+E+ FL+   P+++   C+
Sbjct:   346 FESSFQYYLENNWLQHEKASTEEGRKELKFLSNCNPEQLERLCA 389

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=ISO

GO:0005759 "mitochondrial matrix" evidence=ISO

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA;ISO

GO:0015935 "small ribosomal subunit" evidence=IEA

UNIPROTKB|P51398 DAP3 "28S ribosomal protein S29, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 561 (202.5 bits), Expect = 2.6e-54, P = 2.6e-54
 Identities = 115/345 (33%), Positives = 201/345 (58%)

Query:     2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMT 61
             KH  Q   + Y +  +    +F  G   R F  Q + F+E+ +++R   LEL+ YLK+ T
Sbjct:    58 KHGDQHEGQHYNISPQDLETVFPHGLPPR-FVMQVKTFSEACLMVRKPALELLHYLKN-T 115

Query:    62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKE 121
             +F  P+ R++LYGE G GK+++L + + +  + ++L++HIP    W    +++  S   +
Sbjct:   116 SFAYPAIRYLLYGEKGTGKTLSLCHVIHFCAKQDWLILHIPDAHLWVKNCRDLLQSSYNK 175

Query:   122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRV 181
                D  ++A+ WL++F+  N ++L   ++   ++YVW+ RE +E   PL  ++E GITRV
Sbjct:   176 QRFDQPLEASTWLKNFKTTNERFLN--QIKVQEKYVWNKRESTEKGSPLGEVVEQGITRV 233

Query:   182 KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS 241
             + A+D V ++  E+K+ S+ G+    V VDG N+ +  +T  K EDKS + P  + L  +
Sbjct:   234 RNATDAVGIVLKELKRQSSLGMFHLLVAVDGINALWG-RTTLKREDKSPIAPEELALVHN 292

Query:   242 VINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE 301
             +  ++++DW+ GAIV ALS   +L   R+++LP  +L K GF+++DPF+PI V   N +E
Sbjct:   293 LRKMMKNDWHGGAIVSALSQTGSLFKPRKAYLPQELLGKEGFDALDPFIPILVSNYNPKE 352

Query:   302 FHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
             F + +  Y    WLQ     T EG++E+ FL+   P  +   C++
Sbjct:   353 FESCIQYYLENNWLQHEKAPTEEGKKELLFLSNANPSLLERHCAY 397

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005739 "mitochondrion" evidence=IDA

GO:0097190 "apoptotic signaling pathway" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-051129-2 dap3 "death associated protein 3" [Danio rerio (taxid:7955)]

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 119/351 (33%), Positives = 194/351 (55%)

Query:     1 TKHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSM 60
             T HS+    ++YTLP      +F  G   R F  Q + FNE  +++R   LEL+ YLK  
Sbjct:    56 TCHSETHTGQYYTLPPTHIQKLFPHGLPPR-FQMQVKTFNEGCVMVRPAALELISYLKK- 113

Query:    61 TNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTK 120
              ++++P  R+VLYG+ G GKS++L + L Y +   +L++H+P    W    KE+  S   
Sbjct:   114 ADYNKPPLRYVLYGQTGSGKSISLCHTLHYCYTQGWLILHVPDAHLWVKNCKEMLPSTYN 173

Query:   121 EGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITR 180
                 D  + A  WL+ F+  N  +L   ++ T++ YVW+ RE +E    L  LI+ G+ R
Sbjct:   174 PLRFDQPVQATQWLKDFKITNEHFLS--KIKTTRRYVWTKRESTEEGRTLGELIDQGVNR 231

Query:   181 VKYASDVVDVLFTEIKK---LSTEG--VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSR 235
             +K +SDVV  +  E++     +TEG  V +  V VDG N+ +   T  K ED++   P  
Sbjct:   232 MKSSSDVVGAVLRELRLQAGATTEGEEVFKLAVAVDGVNALWGN-TTLKKEDRTMCEPEE 290

Query:   236 VTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVP 295
             +TL  ++  ++++DW  GAI+ ALS   +L   R ++LP  +L + GF+ ++PFVP+ V 
Sbjct:   291 LTLIHNLRKMMKTDWRGGAILTALSQTGSLFKPRSAYLPSELLGEEGFDEMEPFVPVCVS 350

Query:   296 ELNDEEFHNLLNLYESKKWLQ-----TSEGREEIAFLTKRVPQKMYEFCSF 341
               N++EF +    Y  + WLQ     + EG++E+ FL+ R P  +   C+F
Sbjct:   351 GYNEKEFESCYLYYLDRNWLQHPHSRSEEGKKELIFLSNRNPSILERLCAF 401

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0001666 "response to hypoxia" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P51398	RT29_HUMAN	No assigned EC number	0.3323	0.9824	0.8442	yes	N/A
P82922	RT29_BOVIN	No assigned EC number	0.3497	0.9824	0.8463	yes	N/A
Q9ER88	RT29_MOUSE	No assigned EC number	0.3420	0.9795	0.8567	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	342
pfam10236	274	pfam10236, DAP3, Mitochondrial ribosomal death-ass	2e-56

>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein 3

 Score =  183 bits (468), Expect = 2e-56
 Identities = 83/297 (27%), Positives = 129/297 (43%), Gaps = 33/297 (11%)

Query: 45  LIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV 104
           L+R   LEL   LK   +  +   RFVL GE G GKS+ L  A+ YA    ++++H+P  
Sbjct: 2   LVREETLELTKKLKE-ADASKKVVRFVLTGERGSGKSVLLAQAMAYAFTQGWIVLHVPEA 60

Query: 105 LRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKS 164
             W     + +      G+ D  + AA WL+   K N + L+  +L  S++Y W  RE +
Sbjct: 61  EDWVNGTTDYAPDPGNPGLYDQPMYAAAWLQKILKANEEVLK--KLKLSKDYKWLKREST 118

Query: 165 EANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCK 224
            A   L  L   GI   K A DV   ++ E+K  S        V VDG+N+ F   ++ +
Sbjct: 119 PAGSTLLDLASLGINDPKSAWDVFQAVWKELKAQS--KAPPVLVAVDGFNALF-GPSDYR 175

Query: 225 PEDKSKVLPSRVTLTRSVINLVQ--SDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG 282
             D   + P  +TL R  ++L+   +D+ NG +V AL+        R             
Sbjct: 176 TPDFKPIHPHDLTLVRLFLDLLSGKNDFPNGGVVTALAATGVSNTPR------------- 222

Query: 283 FESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ----TSEGREEIAFLTKRVPQKM 335
                   PI VP L+ EE  +L+  Y     L          E+++ L    P ++
Sbjct: 223 --------PIRVPGLSKEEARSLMEYYADSGILLKKVDEELVDEKLSLLGNGNPGEL 271

This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29). Length = 274

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	342
KOG3928|consensus	461		100.0
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	100.0
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.27
PF14516	331	AAA_35: AAA-like domain	99.12
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.73
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.71
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.54
PF05729	166	NACHT: NACHT domain	98.41
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.31
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.24
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.22
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	98.11
PRK04841	903	transcriptional regulator MalT; Provisional	98.11
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.1
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.09
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.01
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.01
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.01
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.0
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.99
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.99
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.95
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.95
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.94
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.94
PRK12402	337	replication factor C small subunit 2; Reviewed	97.94
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.91
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.9
CHL00176	638	ftsH cell division protein; Validated	97.88
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.87
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.83
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.83
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.82
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.78
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.77
PRK13342	413	recombination factor protein RarA; Reviewed	97.75
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.75
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.73
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.72
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.72
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.7
CHL00195	489	ycf46 Ycf46; Provisional	97.64
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.64
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.59
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.57
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.54
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.52
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.52
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.51
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.48
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.47
PRK04195	482	replication factor C large subunit; Provisional	97.46
PLN03025	319	replication factor C subunit; Provisional	97.45
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.44
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.44
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.43
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.42
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.38
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.32
KOG2228|consensus	408		97.32
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.31
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.31
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.29
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.28
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.27
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.27
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.27
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.24
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.24
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.21
PRK08084	235	DNA replication initiation factor; Provisional	97.2
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.18
PRK06835	329	DNA replication protein DnaC; Validated	97.18
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.16
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.12
PF13245	76	AAA_19: Part of AAA domain	97.11
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.11
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.1
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.06
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	97.02
KOG0731|consensus	774		97.01
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.98
PRK12377	248	putative replication protein; Provisional	96.98
PRK08116	268	hypothetical protein; Validated	96.95
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.94
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.94
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.92
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.89
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	96.88
PF13173	128	AAA_14: AAA domain	96.88
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.88
PRK08181	269	transposase; Validated	96.86
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.85
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.81
PRK06921	266	hypothetical protein; Provisional	96.81
PLN03210	1153	Resistant to P. syringae 6; Provisional	96.81
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.8
PRK13341	725	recombination factor protein RarA/unknown domain f	96.78
PRK06851	367	hypothetical protein; Provisional	96.78
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.78
smart00382	148	AAA ATPases associated with a variety of cellular	96.76
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.75
PRK09183	259	transposase/IS protein; Provisional	96.73
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.69
KOG1970|consensus	634		96.69
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.68
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.67
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.67
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.66
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.66
PRK12608	380	transcription termination factor Rho; Provisional	96.66
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.65
CHL00206	2281	ycf2 Ycf2; Provisional	96.63
PRK06526	254	transposase; Provisional	96.63
PRK05642	234	DNA replication initiation factor; Validated	96.6
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	96.6
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.56
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.56
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.54
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.53
PRK08727	233	hypothetical protein; Validated	96.48
PRK06893	229	DNA replication initiation factor; Validated	96.47
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.46
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.45
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.44
KOG0734|consensus	752		96.44
KOG2543|consensus	438		96.42
PRK07952	244	DNA replication protein DnaC; Validated	96.42
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.41
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.41
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.39
cd01128	249	rho_factor Transcription termination factor rho is	96.39
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.38
COG3899	849	Predicted ATPase [General function prediction only	96.28
PTZ00202	550	tuzin; Provisional	96.27
CHL00095	821	clpC Clp protease ATP binding subunit	96.24
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.24
COG4619	223	ABC-type uncharacterized transport system, ATPase	96.2
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	96.15
PRK08939	306	primosomal protein DnaI; Reviewed	96.15
PF00004	132	AAA: ATPase family associated with various cellula	96.14
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.13
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.1
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.06
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.01
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.01
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.01
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.99
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.99
PRK08769	319	DNA polymerase III subunit delta'; Validated	95.98
KOG2859|consensus	293		95.94
PRK04296	190	thymidine kinase; Provisional	95.93
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.91
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.9
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.84
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.8
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.78
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	95.75
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.75
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.73
PRK12422	445	chromosomal replication initiation protein; Provis	95.71
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.7
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.69
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.63
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.56
PRK07667	193	uridine kinase; Provisional	95.56
PRK13695	174	putative NTPase; Provisional	95.54
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.53
PRK09087	226	hypothetical protein; Validated	95.53
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.53
CHL00181	287	cbbX CbbX; Provisional	95.53
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	95.51
PF13479	213	AAA_24: AAA domain	95.51
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.5
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.49
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.49
PRK04328	249	hypothetical protein; Provisional	95.47
PRK05973	237	replicative DNA helicase; Provisional	95.44
PF12846	304	AAA_10: AAA-like domain	95.44
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.41
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.4
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.37
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.37
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.37
PHA03133	368	thymidine kinase; Provisional	95.35
PRK06067	234	flagellar accessory protein FlaH; Validated	95.32
PRK14974	336	cell division protein FtsY; Provisional	95.31
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.3
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.3
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	95.29
PRK06696	223	uridine kinase; Validated	95.28
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	95.27
PF13555	62	AAA_29: P-loop containing region of AAA domain	95.25
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.22
KOG0780|consensus	483		95.22
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.19
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.18
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.16
PRK06851	367	hypothetical protein; Provisional	95.13
PRK06620	214	hypothetical protein; Validated	95.12
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	95.07
PRK13764	602	ATPase; Provisional	95.05
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.05
PHA03135	343	thymidine kinase; Provisional	95.03
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.03
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.02
KOG0743|consensus	457		95.01
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.98
cd03114	148	ArgK-like The function of this protein family is u	94.97
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.95
TIGR00235	207	udk uridine kinase. Model contains a number of lon	94.94
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.94
PRK00889	175	adenylylsulfate kinase; Provisional	94.92
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	94.91
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	94.91
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	94.9
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	94.89
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	94.88
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	94.88
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	94.87
PRK10263	1355	DNA translocase FtsK; Provisional	94.86
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.86
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	94.83
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	94.82
PRK06090	319	DNA polymerase III subunit delta'; Validated	94.81
PRK09354	349	recA recombinase A; Provisional	94.79
PRK09519	790	recA DNA recombination protein RecA; Reviewed	94.79
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.78
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	94.76
PRK01184	184	hypothetical protein; Provisional	94.76
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.75
PHA03138	340	thymidine kinase; Provisional	94.73
KOG0735|consensus	952		94.71
PRK11823	446	DNA repair protein RadA; Provisional	94.7
PRK14086	617	dnaA chromosomal replication initiation protein; P	94.68
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.65
KOG1514|consensus	767		94.64
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	94.63
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	94.62
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	94.6
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.6
PRK07261	171	topology modulation protein; Provisional	94.58
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.58
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	94.58
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	94.58
PHA00729	226	NTP-binding motif containing protein	94.57
PRK10416	318	signal recognition particle-docking protein FtsY;	94.54
PRK14532	188	adenylate kinase; Provisional	94.54
TIGR02533	486	type_II_gspE general secretory pathway protein E.	94.52
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	94.52
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	94.51
PHA03134	340	thymidine kinase; Provisional	94.49
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	94.49
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.46
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	94.44
PRK08118	167	topology modulation protein; Reviewed	94.42
KOG0736|consensus	953		94.39
PRK14738	206	gmk guanylate kinase; Provisional	94.32
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	94.32
PF00005	137	ABC_tran: ABC transporter This structure is on hol	94.3
KOG0727|consensus	408		94.28
PRK05480	209	uridine/cytidine kinase; Provisional	94.28
PRK10536	262	hypothetical protein; Provisional	94.27
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	94.25
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	94.23
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	94.21
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	94.2
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.2
KOG0741|consensus	744		94.2
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	94.19
PRK05541	176	adenylylsulfate kinase; Provisional	94.18
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	94.18
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	94.16
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.15
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.14
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	94.13
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	94.13
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	94.08
PRK00279	215	adk adenylate kinase; Reviewed	94.06
KOG0741|consensus	744		94.05
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	94.04
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	94.03
KOG2749|consensus	415		94.03
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	94.02
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.02
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	94.02
PRK10436	462	hypothetical protein; Provisional	94.01
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	94.0
PHA02544	316	44 clamp loader, small subunit; Provisional	94.0
PRK14530	215	adenylate kinase; Provisional	93.99
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.99
TIGR00665	434	DnaB replicative DNA helicase. This model describe	93.97
PRK00131	175	aroK shikimate kinase; Reviewed	93.97
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	93.96
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	93.95
PRK03846	198	adenylylsulfate kinase; Provisional	93.94
PHA02244	383	ATPase-like protein	93.93
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	93.93
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	93.9
PRK06547	172	hypothetical protein; Provisional	93.84
PF09820	284	AAA-ATPase_like: Predicted AAA-ATPase; InterPro: I	93.83
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	93.83
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	93.81
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	93.8
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	93.79
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.79
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	93.76
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	93.75
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	93.75
cd01673	193	dNK Deoxyribonucleoside kinase (dNK) catalyzes the	93.73
TIGR00376	637	DNA helicase, putative. The gene product may repre	93.71
smart00487	201	DEXDc DEAD-like helicases superfamily.	93.71
PRK06762	166	hypothetical protein; Provisional	93.68
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.66
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	93.66
PRK00698	205	tmk thymidylate kinase; Validated	93.65
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	93.63
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	93.6
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.6
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	93.59
PRK00300	205	gmk guanylate kinase; Provisional	93.57
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	93.56
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	93.55
PRK02496	184	adk adenylate kinase; Provisional	93.54
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	93.45
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	93.44
PRK09825	176	idnK D-gluconate kinase; Provisional	93.44
COG0593	408	DnaA ATPase involved in DNA replication initiation	93.44
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	93.43
COG3911	183	Predicted ATPase [General function prediction only	93.41
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	93.4
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	93.4
COG4778	235	PhnL ABC-type phosphonate transport system, ATPase	93.36
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	93.36
PRK14531	183	adenylate kinase; Provisional	93.34
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	93.33
PRK13700	732	conjugal transfer protein TraD; Provisional	93.32
PRK03839	180	putative kinase; Provisional	93.32
PRK05439	311	pantothenate kinase; Provisional	93.32
PRK13768	253	GTPase; Provisional	93.3
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	93.27
PHA03136	378	thymidine kinase; Provisional	93.27
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.27
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	93.27
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	93.27
PTZ00088	229	adenylate kinase 1; Provisional	93.25
PRK04301	317	radA DNA repair and recombination protein RadA; Va	93.24
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	93.24
PRK10867	433	signal recognition particle protein; Provisional	93.23
cd02034	116	CooC The accessory protein CooC, which contains a	93.23
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	93.22
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	93.19
PRK08233	182	hypothetical protein; Provisional	93.19
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	93.14
KOG0989|consensus	346		93.13
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	93.13
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	93.13
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	93.12
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	93.09
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.06
PRK08099	399	bifunctional DNA-binding transcriptional repressor	93.05
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	92.99
PRK04040	188	adenylate kinase; Provisional	92.97
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	92.94
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	92.9
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	92.89
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	92.88
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	92.88
PHA02774	613	E1; Provisional	92.87
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	92.84
KOG0781|consensus	587		92.73
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	92.72
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	92.68
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	92.67
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	92.66
cd01853	249	Toc34_like Toc34-like (Translocon at the Outer-env	92.66
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	92.64
cd03234	226	ABCG_White The White subfamily represents ABC tran	92.62
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	92.62
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	92.59
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	92.57
PRK06217	183	hypothetical protein; Validated	92.56
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	92.54
PLN02200	234	adenylate kinase family protein	92.52
PRK14528	186	adenylate kinase; Provisional	92.52
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	92.52
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	92.49
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	92.47
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	92.46
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	92.44
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	92.44
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	92.41
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	92.4
PF09439	181	SRPRB: Signal recognition particle receptor beta s	92.39
COG4136	213	ABC-type uncharacterized transport system, ATPase	92.39
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	92.39
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	92.36
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	92.36
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	92.34
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.33
cd03269	210	ABC_putative_ATPase This subfamily is involved in	92.33
PRK11608	326	pspF phage shock protein operon transcriptional ac	92.31
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	92.31
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	92.3
) 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	92.25
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	92.25
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	92.25
KOG0730|consensus	693		92.25
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	92.24
PRK14526	211	adenylate kinase; Provisional	92.23
PRK13833	323	conjugal transfer protein TrbB; Provisional	92.22
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	92.22
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	92.18
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	92.18
PRK09302	509	circadian clock protein KaiC; Reviewed	92.17
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	92.16
PRK06761	282	hypothetical protein; Provisional	92.15
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	92.14
TIGR00959	428	ffh signal recognition particle protein. This mode	92.14
PRK14527	191	adenylate kinase; Provisional	92.13
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	92.11
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	92.11
PTZ00132	215	GTP-binding nuclear protein Ran; Provisional	92.11
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	92.1
KOG0090|consensus	238		92.08
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	92.07
PRK08506	472	replicative DNA helicase; Provisional	92.06
PRK05416	288	glmZ(sRNA)-inactivating NTPase; Provisional	92.06
PRK13973	213	thymidylate kinase; Provisional	92.06
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	92.05
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	92.03
PHA02624	647	large T antigen; Provisional	92.0
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	92.0
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	91.98
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	91.97
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	91.96
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	91.96
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	91.92
cd03246	173	ABCC_Protease_Secretion This family represents the	91.91
PRK07429	327	phosphoribulokinase; Provisional	91.91
PRK14730	195	coaE dephospho-CoA kinase; Provisional	91.9
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	91.89
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	91.89
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	91.87
PTZ00133	182	ADP-ribosylation factor; Provisional	91.86
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	91.86
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	91.86
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	91.86
KOG0086|consensus	214		91.85
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	91.84
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	91.84
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	91.83
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	91.82
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	91.81
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	91.8
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	91.8
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	91.8
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	91.78
PHA02530	300	pseT polynucleotide kinase; Provisional	91.76
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	91.75
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	91.75
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	91.74
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	91.73
cd04129	187	Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that	91.73
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	91.73
TIGR00767	415	rho transcription termination factor Rho. Members	91.72
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	91.7
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	91.69
cd03116	159	MobB Molybdenum is an essential trace element in t	91.69
TIGR00991	313	3a0901s02IAP34 GTP-binding protein (Chloroplast En	91.69
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	91.68
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	91.68
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	91.66
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	91.65
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	91.64
cd03216	163	ABC_Carb_Monos_I This family represents the domain	91.64
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	91.63
PLN02674	244	adenylate kinase	91.63
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	91.61
PRK09302	509	circadian clock protein KaiC; Reviewed	91.6
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	91.57
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	91.57
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	91.56
KOG0733|consensus	802		91.56
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	91.55
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	91.55
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	91.55
PRK14731	208	coaE dephospho-CoA kinase; Provisional	91.55
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	91.54
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	91.53
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	91.52
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	91.52
PRK13949	169	shikimate kinase; Provisional	91.52
PRK05595	444	replicative DNA helicase; Provisional	91.51
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	91.51
PRK05748	448	replicative DNA helicase; Provisional	91.5
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	91.5
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	91.5
cd03215	182	ABC_Carb_Monos_II This family represents domain II	91.49

>KOG3928|consensus

Probab=100.00  E-value=5.7e-82  Score=602.17  Aligned_cols=337  Identities=33%  Similarity=0.575  Sum_probs=321.1

Q ss_pred             CCCccCcceEEEeCHHHHHHhhhcCCCChhhHHhhhhcCCceEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHH
Q psy3261           2 KHSKQDLYKFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKS   81 (342)
Q Consensus         2 ~h~~~~~g~~~~~~~~~~~~l~~~g~l~~~~~~~~~~~~~~~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS   81 (342)
                      .|+..++|++|+||++++++++++ |+|..+.|++++|.|+++|||++++|+.++++. .+...|..||||||+.|||||
T Consensus       116 ~~ssk~~gk~~~i~~~~lk~l~~~-G~p~~~~~q~~tf~ea~lLVRkpalel~~~~r~-~d~~~P~~r~vL~Ge~GtGKS  193 (461)
T KOG3928|consen  116 FHSSKTEGKVFKISEEQLKQLNPL-GLPFKKSQQFKTFTEAVLLVRKPALELLLYKRL-VDPMHPVKRFVLDGEPGTGKS  193 (461)
T ss_pred             ccccccccceeecCHHHHHhhccC-CCchHHHHHHHhhhcchheechHHHHHHHHhhh-ccccCcceEEEEeCCCCCchh
Confidence            489999999999999999999999 559999999999999999999999999999777 888889999999999999999


Q ss_pred             HHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCC
Q psy3261          82 MALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPR  161 (342)
Q Consensus        82 ~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~  161 (342)
                      ++|+|++|||..++|||||||+|..|++++++|.++....|+||||++|+.||++|+++|++.|++ +|+++++|+|+++
T Consensus       194 iaL~qa~h~a~~~~wlIlhip~a~~w~~~~~~~~y~~~~kg~~dqP~~a~~~L~~fkk~N~~~L~~-~lkt~~~yvwsk~  272 (461)
T KOG3928|consen  194 IALAQAVHYAADQKWLILHIPYAELWTNGRKDYSYDSDLKGLWDQPLYAKKILKNFKKTNEPALKK-QLKTSKDYVWSKR  272 (461)
T ss_pred             hHHHHHHHHHhcCCeEEEECCcHHHhhhccccccccccccccccChhHHHHHHHHHHhhccHHHHH-Hhccccceeeccc
Confidence            999999999999999999999999999999999999988999999999999999999999999984 5999999999999


Q ss_pred             CCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHH
Q psy3261         162 EKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRS  241 (342)
Q Consensus       162 e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~  241 (342)
                      |++++|++|.+|++.||.+...|++++++|++||+.++..+++|||||||+||+||+.+. |++.++++|+|.+|+++++
T Consensus       273 e~t~kG~pl~ei~e~gI~~i~~a~~~vg~llrelk~~s~~~~~kVLvaID~~n~l~~~T~-~k~~~~~~v~P~dl~li~~  351 (461)
T KOG3928|consen  273 ESTLKGKPLVEIVETGIASIKNAPDAVGILLRELKRLSVQSKVKVLVAIDNFNSLFTVTA-YKSEDNKPVTPLDLTLIHL  351 (461)
T ss_pred             CCccCCCcchhhHHhhhhhhccchHHHHHHHHHHHHhhhhcCccEEEEEcCcchheeeee-eeccccCcCCchhhhHHHH
Confidence            999999999999999999999999999999999999999999999999999999999766 9999999999999999999


Q ss_pred             HHHhhcCCCCCeEEEEEeC--CCCCCCCCc--cCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-
Q psy3261         242 VINLVQSDWNNGAIVLALS--PRANLPDRR--ESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-  316 (342)
Q Consensus       242 ~~~~~~~~~~~G~vv~AtS--~~~~~~~~~--~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-  316 (342)
                      ++++++|+|.+|+||+|+|  ...+.....  ..+.|++++|+.|||.+|||+||+|++|+++|++++++||.+++|+. 
T Consensus       352 ~~~~i~ndwt~g~vi~a~s~~~~~~a~~h~gv~~y~pr~llg~egfe~lqpf~pi~v~nYt~~E~~~~i~YYl~~nwl~k  431 (461)
T KOG3928|consen  352 LRDIISNDWTFGSVIMAISGVTTPSAFGHLGVAPYVPRKLLGEEGFEALQPFVPIEVENYTLDEFEALIDYYLQSNWLLK  431 (461)
T ss_pred             HHHHHhcccccceEEEEecccccchhccccccccCCchHhcCccchhhccCcCccccCCCCHHHHHHHHHHHHHhhHHHh
Confidence            9999999999999999999  554444444  58899999999999999999999999999999999999999999998 


Q ss_pred             ---CcchHHHHHHhhCCCHHHHhhhccCC
Q psy3261         317 ---TSEGREEIAFLTKRVPQKMYEFCSFK  342 (342)
Q Consensus       317 ---~e~~~~el~~lSgGNP~~l~~lc~~~  342 (342)
                         +|++..|++|||||||..++++|+++
T Consensus       432 kv~~Ee~~kql~fLSngNP~l~~~lca~~  460 (461)
T KOG3928|consen  432 KVPGEENIKQLYFLSNGNPSLMERLCAFL  460 (461)
T ss_pred             hcCcccchhhhhhhcCCCHHHHHHHHHhc
Confidence               57789999999999999999999974

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=6.3e-76  Score=561.86  Aligned_cols=289  Identities=34%  Similarity=0.583  Sum_probs=267.8

Q ss_pred             EEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCc
Q psy3261          44 ILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGM  123 (342)
Q Consensus        44 ~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~  123 (342)
                      +|||++|+||+++|++ ++.+++..|++|||++|||||++|+|+++||+++||||+|||++++|++++++|.+++.++|+
T Consensus         1 ~lvR~~t~el~~~l~~-~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~~wiVl~vp~a~~~~~~~~~~~~~~~~~~~   79 (309)
T PF10236_consen    1 SLVRKPTLELINKLKE-ADKSSKNNRYVLTGERGSGKSVLLAQAVHYARENGWIVLYVPSAQDWVNGTTDYAPSPYNPGL   79 (309)
T ss_pred             CccchHHHHHHHHHHH-hcccCCceEEEEECCCCCCHHHHHHHHHHHHHhCCEEEEEcCCHHHHhhCCeeEeeCCCCCCe
Confidence            5899999999999999 788899999999999999999999999999999999999999999999999999999888999


Q ss_pred             cccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCC
Q psy3261         124 VDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGV  203 (342)
Q Consensus       124 ~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~  203 (342)
                      ||||++|++||++|+++|+++|+  +|+++++|+|++++.+++|+||+||+++|++++++|++||++||+||++|+  .+
T Consensus        80 ~~qP~~a~~~L~~~~~~N~~~L~--~i~~s~~~~~~~~~~~~~g~tL~dLv~~g~~~~~~a~~~~~~l~~EL~~~~--~~  155 (309)
T PF10236_consen   80 YDQPMYAAKWLKKFLKANEELLK--KIKLSKDYKWSKRESTPKGSTLLDLVEQGINDPKYAWDVFQALIRELKAQS--KR  155 (309)
T ss_pred             eecHHHHHHHHHHHHHHhHHHHH--hccccccccccccccCCCCCCHHHHHHhhcccchhHHHHHHHHHHHHHhcc--cC
Confidence            99999999999999999999999  999999999999889999999999999999999999999999999999997  24


Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC--CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS--DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~--~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      +||||||||||+||++|. |+++++++|||++|+|+++|++++++  +|+||++|+|.+.+.....++...+|..+.++.
T Consensus       156 ~PVL~avD~~n~l~~~S~-Y~~~~~~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t~~~~~~~~~~l~~~L~~~~  234 (309)
T PF10236_consen  156 PPVLVAVDGFNALFGPSA-YRDPDFKPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAATSVSNAPKSPTLPVALGGKE  234 (309)
T ss_pred             CceEEEehhhHHhhCCcc-ccCCCCccccHHHhhHHHHHHHHhcCccccCCCeEEEEEeccccccccCCccchhhhcccc
Confidence            999999999999999966 99999999999999999999999765  699999975555544334555567999999999


Q ss_pred             CCCCCCCcc--------------eeecCCCCHHHHHHHHHHHHhCCCcc---Ccc-hHHHHHHhhCCCHHHHhhh
Q psy3261         282 GFESIDPFV--------------PIHVPELNDEEFHNLLNLYESKKWLQ---TSE-GREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       282 g~~~~dP~~--------------~i~v~~~s~~E~~~ll~yy~~~~~l~---~e~-~~~el~~lSgGNP~~l~~l  338 (342)
                      +++.+|||+              ||+|++||++|++++|+||.++||++   +++ +.+++.++|||||++|+|+
T Consensus       235 ~~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el~k~  309 (309)
T PF10236_consen  235 GFPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPRELEKL  309 (309)
T ss_pred             CCCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHhccC
Confidence            999999999              99999999999999999999999997   233 5566777889999999985

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>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=99.27  E-value=1.2e-10  Score=105.10  Aligned_cols=211  Identities=20%  Similarity=0.236  Sum_probs=108.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKW  144 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~  144 (342)
                      .+...++|+|++|+|||++|.+++....+.+..++|+-.........         ...+.+   ....-+.+...=...
T Consensus        18 ~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~---------~~~~~~---~~~~~~~l~~~~~~~   85 (234)
T PF01637_consen   18 GPSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESS---------LRSFIE---ETSLADELSEALGIS   85 (234)
T ss_dssp             --SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHH---------HHHHHH---HHHHHCHCHHHHHHH
T ss_pred             hcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhH---------HHHHHH---HHHHHHHHHHHHhhh
Confidence            45789999999999999999999999877787666663322211110         000000   000000110000111


Q ss_pred             cCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccc-cCCCcC
Q psy3261         145 LEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFF-AEKTNC  223 (342)
Q Consensus       145 L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~-~~s~~y  223 (342)
                      +.  +..+..               +.+      .....+...+..+++.|....    .+++|.+||++.+. ...   
T Consensus        86 ~~--~~~~~~---------------~~~------~~~~~~~~~l~~~~~~l~~~~----~~~iiviDe~~~~~~~~~---  135 (234)
T PF01637_consen   86 IP--SITLEK---------------ISK------DLSEDSFSALERLLEKLKKKG----KKVIIVIDEFQYLAIASE---  135 (234)
T ss_dssp             CC--TSTTEE---------------EEC------TS-GG-G--HHHHHHHHHHCH----CCEEEEEETGGGGGBCTT---
T ss_pred             cc--cccchh---------------hhh------cchhhHHHHHHHHHHHHHhcC----CcEEEEEecHHHHhhccc---
Confidence            11  111000               000      112345666777888888753    34999999999888 222   


Q ss_pred             CCCCCCcccCCccchHHHHHHhhcC--CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHH
Q psy3261         224 KPEDKSKVLPSRVTLTRSVINLVQS--DWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEE  301 (342)
Q Consensus       224 ~~~~~~~I~~~~l~l~~~~~~~~~~--~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E  301 (342)
                                ..-.+.+.|++++..  .-.+..+|.+.|...         +...+.+..+ +...-+..+.++.|+++|
T Consensus       136 ----------~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~~~---------~~~~~~~~~~-~~~~~~~~~~l~~l~~~e  195 (234)
T PF01637_consen  136 ----------EDKDFLKSLRSLLDSLLSQQNVSIVITGSSDS---------LMEEFLDDKS-PLFGRFSHIELKPLSKEE  195 (234)
T ss_dssp             ----------TTHHHHHHHHHHHHH----TTEEEEEEESSHH---------HHHHTT-TTS-TTTT---EEEE----HHH
T ss_pred             ----------chHHHHHHHHHHHhhccccCCceEEEECCchH---------HHHHhhcccC-ccccccceEEEeeCCHHH
Confidence                      114677777777765  234555666555421         1111111110 111222359999999999


Q ss_pred             HHHHHHHHHhCCCcc---CcchHHHHHHhhCCCHHHHhhh
Q psy3261         302 FHNLLNLYESKKWLQ---TSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       302 ~~~ll~yy~~~~~l~---~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      +..++...-... ..   +++...+++-+|||||+.|..+
T Consensus       196 ~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~gG~P~~l~~~  234 (234)
T PF01637_consen  196 AREFLKELFKEL-IKLPFSDEDIEEIYSLTGGNPRYLQEL  234 (234)
T ss_dssp             HHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHHHHHHHHh-hcccCCHHHHHHHHHHhCCCHHHHhcC
Confidence            999998865554 31   4666778999999999998653

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

>PF14516 AAA_35: AAA-like domain

Probab=99.12  E-value=1.6e-08  Score=97.95  Aligned_cols=224  Identities=20%  Similarity=0.229  Sum_probs=132.2

Q ss_pred             CceEEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCC
Q psy3261          41 ESSILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLT  119 (342)
Q Consensus        41 ~~~~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~  119 (342)
                      .|..+-|. .-.++.+.|.+      ++.-+.|.|+|.+|||++|.+++..+.++|..+++|.--. .  +...      
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~------~G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~-~--~~~~------   74 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQ------PGSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQ-L--GSAI------   74 (331)
T ss_pred             CCcccCchHHHHHHHHHHhc------CCCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeec-C--CCcc------
Confidence            46677788 55566667755      4678899999999999999999999999999999984221 1  1100      


Q ss_pred             CCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHH-Hhcc
Q psy3261         120 KEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTE-IKKL  198 (342)
Q Consensus       120 ~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~E-L~~~  198 (342)
                          +.   .--+|++.|..   .+-+  ++.+..              .+.+..+..+.    +..-+...++| |..+
T Consensus        75 ----~~---~~~~f~~~~~~---~i~~--~L~l~~--------------~l~~~w~~~~~----~~~~~~~~~~~~ll~~  124 (331)
T PF14516_consen   75 ----FS---DLEQFLRWFCE---EISR--QLKLDE--------------KLDEYWDEEIG----SKISCTEYFEEYLLKQ  124 (331)
T ss_pred             ----cC---CHHHHHHHHHH---HHHH--HcCCCh--------------hHHHHHHHhcC----ChhhHHHHHHHHHHhc
Confidence                11   11223444411   1122  233221              22233332222    12222344444 3332


Q ss_pred             ccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCc-cchHHHHHHhhc--CCCCCeEEEEEeCCCCCCCCCccCcchh
Q psy3261         199 STEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSR-VTLTRSVINLVQ--SDWNNGAIVLALSPRANLPDRRESHLPL  275 (342)
Q Consensus       199 ~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~-l~l~~~~~~~~~--~~~~~G~vv~AtS~~~~~~~~~~~~~p~  275 (342)
                         .+.|+++++|++.+++.... ..         .+ +.+.|....--.  ..|++-.+|++-|....        ++.
T Consensus       125 ---~~~~lVL~iDEiD~l~~~~~-~~---------~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~--------~~~  183 (331)
T PF14516_consen  125 ---IDKPLVLFIDEIDRLFEYPQ-IA---------DDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDY--------IIL  183 (331)
T ss_pred             ---CCCCEEEEEechhhhccCcc-hH---------HHHHHHHHHHHHhcccCcccceEEEEEecCcccc--------ccc
Confidence               26899999999999987543 00         01 133333332111  24777777777653221        110


Q ss_pred             HHhhhcCCCCCCCc---ceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         276 YMLKKAGFESIDPF---VPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       276 ~llg~~g~~~~dP~---~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      .   .    ...||   .++++++||.+|+..|++-|... |  ++....+++-++||.|+...++|.
T Consensus       184 ~---~----~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~-~--~~~~~~~l~~~tgGhP~Lv~~~~~  241 (331)
T PF14516_consen  184 D---I----NQSPFNIGQPIELPDFTPEEVQELAQRYGLE-F--SQEQLEQLMDWTGGHPYLVQKACY  241 (331)
T ss_pred             C---C----CCCCcccccceeCCCCCHHHHHHHHHhhhcc-C--CHHHHHHHHHHHCCCHHHHHHHHH
Confidence            0   0    12333   36999999999999999887433 2  344467799999999999999985

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

Probab=98.73  E-value=6.5e-07  Score=83.42  Aligned_cols=50  Identities=14%  Similarity=0.232  Sum_probs=38.4

Q ss_pred             eeecCCCCHHHHHHHHHHHHh-CCCc---c-CcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         291 PIHVPELNDEEFHNLLNLYES-KKWL---Q-TSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~-~~~l---~-~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      ++++++|+.+|++.++..... .|+-   . +++....+.-.|+|+|+.+..+|.
T Consensus       186 ~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~  240 (269)
T TIGR03015       186 SCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCD  240 (269)
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHH
Confidence            478999999999999876543 3331   1 555666788899999999998884

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.71  E-value=1.9e-06  Score=84.91  Aligned_cols=216  Identities=14%  Similarity=0.127  Sum_probs=116.7

Q ss_pred             eEEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCccccccCCcceeccCC
Q psy3261          43 SILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLRWFAYPKEVSHSLT  119 (342)
Q Consensus        43 ~~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~~~~~~~~~~~s~~  119 (342)
                      .+.-|+ +..+|...|+. .-.+.....++|+|++|+|||+++..+...+.+.  ++.++||.....             
T Consensus        31 ~l~~Re~e~~~l~~~l~~-~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~-------------   96 (394)
T PRK00411         31 NLPHREEQIEELAFALRP-ALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQID-------------   96 (394)
T ss_pred             CCCCHHHHHHHHHHHHHH-HhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcC-------------
Confidence            445577 55667777766 3223445668999999999999999999988765  477777743211             


Q ss_pred             CCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccc
Q psy3261         120 KEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLS  199 (342)
Q Consensus       120 ~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~  199 (342)
                       ..       ...++..+       ++  ++.-.        +....+.+.              ...+..+++.+..  
T Consensus        97 -~~-------~~~~~~~i-------~~--~l~~~--------~~~~~~~~~--------------~~~~~~~~~~l~~--  135 (394)
T PRK00411         97 -RT-------RYAIFSEI-------AR--QLFGH--------PPPSSGLSF--------------DELFDKIAEYLDE--  135 (394)
T ss_pred             -CC-------HHHHHHHH-------HH--HhcCC--------CCCCCCCCH--------------HHHHHHHHHHHHh--
Confidence             00       11334444       22  22100        000112121              2344455555554  


Q ss_pred             cCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCC-CeEEEEEeCCCCCCCCCccCcchhHHh
Q psy3261         200 TEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWN-NGAIVLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       200 ~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~-~G~vv~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                        .+.+++|.+|++..+.....              -.+...|.++...--. +-.+|++++... ....    +...+.
T Consensus       136 --~~~~~viviDE~d~l~~~~~--------------~~~l~~l~~~~~~~~~~~v~vI~i~~~~~-~~~~----l~~~~~  194 (394)
T PRK00411        136 --RDRVLIVALDDINYLFEKEG--------------NDVLYSLLRAHEEYPGARIGVIGISSDLT-FLYI----LDPRVK  194 (394)
T ss_pred             --cCCEEEEEECCHhHhhccCC--------------chHHHHHHHhhhccCCCeEEEEEEECCcc-hhhh----cCHHHH
Confidence              26789999999987762211              1234444444322111 333455544332 1110    111111


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc---CcchHHHHHHhh---CCCHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ---TSEGREEIAFLT---KRVPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~---~e~~~~el~~lS---gGNP~~l~~lc~  340 (342)
                      ...+     | ..+.+++|+.+|...+++.....++-.   .++....+.-.+   .|+++...++|.
T Consensus       195 s~~~-----~-~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~  256 (394)
T PRK00411        195 SVFR-----P-EEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLR  256 (394)
T ss_pred             hcCC-----c-ceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            1111     1 237899999999999998877654321   333333344455   788887777763

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.54  E-value=1e-05  Score=78.85  Aligned_cols=216  Identities=13%  Similarity=0.171  Sum_probs=112.9

Q ss_pred             EEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh--CC----eEEEEeCCccccccCCcceec
Q psy3261          44 ILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE--NN----YLLVHIPWVLRWFAYPKEVSH  116 (342)
Q Consensus        44 ~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~--~g----wiVl~vP~~~~~~~~~~~~~~  116 (342)
                      +.-|+ +..+|...|+. ...+.....++|+|++|||||+++..+.....+  .+    |.++||......  .      
T Consensus        17 l~gRe~e~~~l~~~l~~-~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~--~------   87 (365)
T TIGR02928        17 IVHRDEQIEELAKALRP-ILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILD--T------   87 (365)
T ss_pred             CCCcHHHHHHHHHHHHH-HHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCC--C------
Confidence            44577 44566677776 322345567999999999999999888876542  22    677776533110  0      


Q ss_pred             cCCCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHh
Q psy3261         117 SLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIK  196 (342)
Q Consensus       117 s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~  196 (342)
                            .+   ....++++.+..      .  +.+.           -..+.+              ....+..+++.|.
T Consensus        88 ------~~---~~~~~i~~~l~~------~--~~~~-----------~~~~~~--------------~~~~~~~l~~~l~  125 (365)
T TIGR02928        88 ------LY---QVLVELANQLRG------S--GEEV-----------PTTGLS--------------TSEVFRRLYKELN  125 (365)
T ss_pred             ------HH---HHHHHHHHHHhh------c--CCCC-----------CCCCCC--------------HHHHHHHHHHHHH
Confidence                  00   122233333311      1  1110           001111              2234556666665


Q ss_pred             ccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc-CCCC--CeEEEEEeCCCCCCCCCccCcc
Q psy3261         197 KLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ-SDWN--NGAIVLALSPRANLPDRRESHL  273 (342)
Q Consensus       197 ~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~-~~~~--~G~vv~AtS~~~~~~~~~~~~~  273 (342)
                      ..    ..|++|.||++..+.+...               .+...|.++.. ....  +-.+|++++... ...    .+
T Consensus       126 ~~----~~~~vlvIDE~d~L~~~~~---------------~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~-~~~----~l  181 (365)
T TIGR02928       126 ER----GDSLIIVLDEIDYLVGDDD---------------DLLYQLSRARSNGDLDNAKVGVIGISNDLK-FRE----NL  181 (365)
T ss_pred             hc----CCeEEEEECchhhhccCCc---------------HHHHhHhccccccCCCCCeEEEEEEECCcc-hHh----hc
Confidence            42    5789999999988863221               12333444421 2222  233444443321 100    01


Q ss_pred             hhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc---CcchHHH---HHHhhCCCHHHHhhhcc
Q psy3261         274 PLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ---TSEGREE---IAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       274 p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~---~e~~~~e---l~~lSgGNP~~l~~lc~  340 (342)
                      ...+.  ..|   .| ..+.++.|+.+|...++....+.++-.   .++....   +-..++|++|...++|.
T Consensus       182 ~~~~~--s~~---~~-~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~  248 (365)
T TIGR02928       182 DPRVK--SSL---CE-EEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLR  248 (365)
T ss_pred             CHHHh--ccC---Cc-ceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            11111  111   11 247899999999999998877633211   2322222   22356899999888773

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=98.41  E-value=9e-06  Score=69.28  Aligned_cols=83  Identities=16%  Similarity=0.304  Sum_probs=48.8

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..+++|.+|++..+......          ...-.+...|..++... ..+.-+++++....         .+ .+ .+ 
T Consensus        80 ~~~~llilDglDE~~~~~~~----------~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~---------~~-~~-~~-  137 (166)
T PF05729_consen   80 NKRVLLILDGLDELEEQDQS----------QERQRLLDLLSQLLPQALPPGVKLIITSRPRA---------FP-DL-RR-  137 (166)
T ss_pred             CCceEEEEechHhcccchhh----------hHHHHHHHHHHHHhhhccCCCCeEEEEEcCCh---------HH-HH-HH-
Confidence            67999999999888775430          11234555666666653 33444444443322         11 11 11 


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHH
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYE  310 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~  310 (342)
                      .+   .....++|.+|+.+|.+.+++-|-
T Consensus       138 ~~---~~~~~~~l~~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen  138 RL---KQAQILELEPFSEEDIKQYLRKYF  163 (166)
T ss_pred             hc---CCCcEEEECCCCHHHHHHHHHHHh
Confidence            11   111358999999999999996553

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.31  E-value=9.5e-06  Score=73.56  Aligned_cols=49  Identities=20%  Similarity=0.182  Sum_probs=36.8

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .++++.++.+|...++..+....-+. +++..+.|..-++||+++|+++.
T Consensus       153 ~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~l  202 (226)
T TIGR03420       153 VFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALL  202 (226)
T ss_pred             eEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            48999999999999998876543333 45444455568999999998763

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.

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

Probab=98.24  E-value=0.00011  Score=72.26  Aligned_cols=209  Identities=16%  Similarity=0.256  Sum_probs=122.3

Q ss_pred             EEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCccccccCCcceeccCCC
Q psy3261          44 ILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLRWFAYPKEVSHSLTK  120 (342)
Q Consensus        44 ~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~~~~~~~~~~~s~~~  120 (342)
                      +-.|+ +-.++...|..+...+.|.+ ++|||++|||||++...++....+.  +--++||-.- .              
T Consensus        19 l~~Re~ei~~l~~~l~~~~~~~~p~n-~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~-~--------------   82 (366)
T COG1474          19 LPHREEEINQLASFLAPALRGERPSN-IIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCL-E--------------   82 (366)
T ss_pred             ccccHHHHHHHHHHHHHHhcCCCCcc-EEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeee-e--------------
Confidence            44555 55566667766444444554 9999999999999999999887754  2224554211 1              


Q ss_pred             CCccccHHHH-HHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccc
Q psy3261         121 EGMVDLNIDA-AMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLS  199 (342)
Q Consensus       121 ~~~~~qP~~a-~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~  199 (342)
                         +.+|... .+++++|.       +   ++.             -          |.    .+.+++..+++.+..+ 
T Consensus        83 ---~~t~~~i~~~i~~~~~-------~---~p~-------------~----------g~----~~~~~~~~l~~~~~~~-  121 (366)
T COG1474          83 ---LRTPYQVLSKILNKLG-------K---VPL-------------T----------GD----SSLEILKRLYDNLSKK-  121 (366)
T ss_pred             ---CCCHHHHHHHHHHHcC-------C---CCC-------------C----------CC----chHHHHHHHHHHHHhc-
Confidence               2222222 22223331       1   110             0          22    4567777888888774 


Q ss_pred             cCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC--CCCCeEEEEEeCCCCCCCCCccCcchhHH
Q psy3261         200 TEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS--DWNNGAIVLALSPRANLPDRRESHLPLYM  277 (342)
Q Consensus       200 ~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~--~~~~G~vv~AtS~~~~~~~~~~~~~p~~l  277 (342)
                         +..++|+.|+++.+.....                  ..+..++.-  .....+.|.+.+....        + .+.
T Consensus       122 ---~~~~IvvLDEid~L~~~~~------------------~~LY~L~r~~~~~~~~v~vi~i~n~~~--------~-~~~  171 (366)
T COG1474         122 ---GKTVIVILDEVDALVDKDG------------------EVLYSLLRAPGENKVKVSIIAVSNDDK--------F-LDY  171 (366)
T ss_pred             ---CCeEEEEEcchhhhccccc------------------hHHHHHHhhccccceeEEEEEEeccHH--------H-HHH
Confidence               7899999999999987642                  233333331  1244455666554431        0 111


Q ss_pred             hhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc--CcchHHH----HHHhhCCCHHHHhhhcc
Q psy3261         278 LKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ--TSEGREE----IAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       278 lg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~--~e~~~~e----l~~lSgGNP~~l~~lc~  340 (342)
                      +...=.....|.. |.++.|+.+|+..++..-.+.++-.  .+++..+    +-...+|..|...++|.
T Consensus       172 ld~rv~s~l~~~~-I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr  239 (366)
T COG1474         172 LDPRVKSSLGPSE-IVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILR  239 (366)
T ss_pred             hhhhhhhccCcce-eeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHH
Confidence            1110000112222 7899999999999999888877544  2333333    23377889998888875

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.22  E-value=9.4e-05  Score=79.00  Aligned_cols=213  Identities=15%  Similarity=0.241  Sum_probs=115.8

Q ss_pred             eEEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH----hC---CeEEEEeCCccccccCCcce
Q psy3261          43 SILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH----EN---NYLLVHIPWVLRWFAYPKEV  114 (342)
Q Consensus        43 ~~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~----~~---gwiVl~vP~~~~~~~~~~~~  114 (342)
                      .+.-|+ +..+|...|..+.....++..++|+|++|||||++...++....    +.   ++.++||-.-          
T Consensus       756 ~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm----------  825 (1164)
T PTZ00112        756 YLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM----------  825 (1164)
T ss_pred             cCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC----------
Confidence            556788 77777788887344344555567999999999999999876543    22   2455555211          


Q ss_pred             eccCCCCCccccHHHHHHHH-HHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHH
Q psy3261         115 SHSLTKEGMVDLNIDAAMWL-RHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFT  193 (342)
Q Consensus       115 ~~s~~~~~~~~qP~~a~~~L-~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~  193 (342)
                              .+..|..+...| +++       ..  ..+             +.|.              .+..++..+++
T Consensus       826 --------~Lstp~sIYqvI~qqL-------~g--~~P-------------~~Gl--------------sS~evLerLF~  861 (1164)
T PTZ00112        826 --------NVVHPNAAYQVLYKQL-------FN--KKP-------------PNAL--------------NSFKILDRLFN  861 (1164)
T ss_pred             --------ccCCHHHHHHHHHHHH-------cC--CCC-------------Cccc--------------cHHHHHHHHHh
Confidence                    122222222222 222       12  110             1111              23356677777


Q ss_pred             HHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcc
Q psy3261         194 EIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHL  273 (342)
Q Consensus       194 EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~  273 (342)
                      ++...   .+..++|++||+..|.....              -.| ..|.++.. .-...++|.+++.....+.+   .+
T Consensus       862 ~L~k~---~r~v~IIILDEID~L~kK~Q--------------DVL-YnLFR~~~-~s~SKLiLIGISNdlDLper---Ld  919 (1164)
T PTZ00112        862 QNKKD---NRNVSILIIDEIDYLITKTQ--------------KVL-FTLFDWPT-KINSKLVLIAISNTMDLPER---LI  919 (1164)
T ss_pred             hhhcc---cccceEEEeehHhhhCccHH--------------HHH-HHHHHHhh-ccCCeEEEEEecCchhcchh---hh
Confidence            77442   25567999999987754321              112 22222221 12234556565543211211   11


Q ss_pred             hhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC--CCccCcchHHHHHH----hhCCCHHHHhhhcc
Q psy3261         274 PLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK--KWLQTSEGREEIAF----LTKRVPQKMYEFCS  340 (342)
Q Consensus       274 p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~--~~l~~e~~~~el~~----lSgGNP~~l~~lc~  340 (342)
                      | .+..+.+++.      +.++.|+.+|...++..-.+.  +.+  +++..++-.    ..+|+-|...++|.
T Consensus       920 P-RLRSRLg~ee------IvF~PYTaEQL~dILk~RAe~A~gVL--dDdAIELIArkVAq~SGDARKALDILR  983 (1164)
T PTZ00112        920 P-RCRSRLAFGR------LVFSPYKGDEIEKIIKERLENCKEII--DHTAIQLCARKVANVSGDIRKALQICR  983 (1164)
T ss_pred             h-hhhhcccccc------ccCCCCCHHHHHHHHHHHHHhCCCCC--CHHHHHHHHHhhhhcCCHHHHHHHHHH
Confidence            2 1222223322      566899999999999887664  344  333333222    55799999998884

>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=98.11  E-value=7.4e-05  Score=71.50  Aligned_cols=53  Identities=26%  Similarity=0.376  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC---CeEEEEe-CCc
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN---NYLLVHI-PWV  104 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~---gwiVl~v-P~~  104 (342)
                      +..|.+.|.+ . ......-+-|+|+.|||||+.|.++...-.++   +++++++ |+.
T Consensus         5 a~~la~~I~~-~-~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~~~~~~~~i~fn~w~   61 (325)
T PF07693_consen    5 AKALAEIIKN-P-DSDDPFVIGLYGEWGSGKSSFLNMLKEELKEDNKEKYIFIYFNAWE   61 (325)
T ss_pred             HHHHHHHHhc-c-CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccceeeEEEcccc
Confidence            3455666655 1 12567889999999999999999999998877   8999998 444

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 [].

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.11  E-value=0.00018  Score=78.19  Aligned_cols=117  Identities=13%  Similarity=0.200  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      ..+..++.+|...    ..|++|+|||+..+ ...                ++...+..++.....+..+|+ +|+.. +
T Consensus       107 ~~~~~~~~~l~~~----~~~~~lvlDD~h~~-~~~----------------~~~~~l~~l~~~~~~~~~lv~-~sR~~-~  163 (903)
T PRK04841        107 SLFAQLFIELADW----HQPLYLVIDDYHLI-TNP----------------EIHEAMRFFLRHQPENLTLVV-LSRNL-P  163 (903)
T ss_pred             HHHHHHHHHHhcC----CCCEEEEEeCcCcC-CCh----------------HHHHHHHHHHHhCCCCeEEEE-EeCCC-C
Confidence            4566777888652    57999999999444 321                234455555555555666666 45542 1


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecC--CCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVP--ELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~--~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      +      ++...+...|     -...+...  .||.+|+..++.-..... + +++...+++-.|+|||.-+.-+
T Consensus       164 ~------~~~~~l~~~~-----~~~~l~~~~l~f~~~e~~~ll~~~~~~~-~-~~~~~~~l~~~t~Gwp~~l~l~  225 (903)
T PRK04841        164 P------LGIANLRVRD-----QLLEIGSQQLAFDHQEAQQFFDQRLSSP-I-EAAESSRLCDDVEGWATALQLI  225 (903)
T ss_pred             C------CchHhHHhcC-----cceecCHHhCCCCHHHHHHHHHhccCCC-C-CHHHHHHHHHHhCChHHHHHHH
Confidence            1      1111111111     11123334  899999999886433322 3 4555678999999999887644

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

Probab=98.10  E-value=6e-06  Score=71.97  Aligned_cols=42  Identities=24%  Similarity=0.270  Sum_probs=27.7

Q ss_pred             CCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        62 ~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      ..+....-++|+|++|||||++|.+++..+...+++++++..
T Consensus        19 ~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~   60 (185)
T PF13191_consen   19 AQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINC   60 (185)
T ss_dssp             TSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEE
T ss_pred             HHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEE
Confidence            344556889999999999999999999999888766777643

>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=98.09  E-value=9.6e-05  Score=69.29  Aligned_cols=50  Identities=18%  Similarity=0.135  Sum_probs=34.4

Q ss_pred             ceeecCCCCHHHHHHHHHHHHhCCCc-c---CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         290 VPIHVPELNDEEFHNLLNLYESKKWL-Q---TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       290 ~~i~v~~~s~~E~~~ll~yy~~~~~l-~---~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+++|..|+.+|+..++..+....-. .   .++-..++--.++|+|..+.-++
T Consensus       150 ~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a  203 (287)
T PF00931_consen  150 KVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIA  203 (287)
T ss_dssp             EEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            35899999999999999888655441 1   33344577889999999886654

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.01  E-value=0.00013  Score=69.39  Aligned_cols=49  Identities=14%  Similarity=0.135  Sum_probs=37.6

Q ss_pred             eecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         292 IHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      +++..++.+|...+++......-+. +++....+--.|+|+||.+.++|.
T Consensus       154 ~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~  203 (305)
T TIGR00635       154 LRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLR  203 (305)
T ss_pred             EEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHH
Confidence            6888999999999998876643233 455555677799999999887773

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.

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

Probab=98.01  E-value=0.00091  Score=61.98  Aligned_cols=169  Identities=18%  Similarity=0.258  Sum_probs=100.6

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCcc
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTK  143 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~  143 (342)
                      ..+++.++|+|.+|||||.++..+......+|-=+|.|+...                                      
T Consensus        49 G~pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~--------------------------------------   90 (249)
T PF05673_consen   49 GLPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKED--------------------------------------   90 (249)
T ss_pred             CCCCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHH--------------------------------------
Confidence            368999999999999999999998887777774344332210                                      


Q ss_pred             ccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcC
Q psy3261         144 WLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNC  223 (342)
Q Consensus       144 ~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y  223 (342)
                       |.                      .|.+|+                  ++|+..    ..+.+|.+||+ + |...+  
T Consensus        91 -L~----------------------~l~~l~------------------~~l~~~----~~kFIlf~DDL-s-Fe~~d--  121 (249)
T PF05673_consen   91 -LG----------------------DLPELL------------------DLLRDR----PYKFILFCDDL-S-FEEGD--  121 (249)
T ss_pred             -hc----------------------cHHHHH------------------HHHhcC----CCCEEEEecCC-C-CCCCc--
Confidence             11                      122333                  355543    57999999998 3 33322  


Q ss_pred             CCCCCCcccCCccchHHHHHHhhcCC---CCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC--CCCCCC----------
Q psy3261         224 KPEDKSKVLPSRVTLTRSVINLVQSD---WNNGAIVLALSPRANLPDRRESHLPLYMLKKAG--FESIDP----------  288 (342)
Q Consensus       224 ~~~~~~~I~~~~l~l~~~~~~~~~~~---~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g--~~~~dP----------  288 (342)
                                  -+ -+.|+.++.|.   ++.-++|.|||...++-....       -...+  -+.+.|          
T Consensus       122 ------------~~-yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~-------~d~~~~~~~eih~~d~~eEklSL  181 (249)
T PF05673_consen  122 ------------TE-YKALKSVLEGGLEARPDNVLIYATSNRRHLVPESF-------SDREDIQDDEIHPSDTIEEKLSL  181 (249)
T ss_pred             ------------HH-HHHHHHHhcCccccCCCcEEEEEecchhhccchhh-------hhccCCCccccCcchHHHHHHhH
Confidence                        11 27788888874   455577888886553322111       11111  001111          


Q ss_pred             ---c-ceeecCCCCHHHHHHHHHHHHhC-CCccCcc---hHHHHHHhhC--CCHHHHhhhc
Q psy3261         289 ---F-VPIHVPELNDEEFHNLLNLYESK-KWLQTSE---GREEIAFLTK--RVPQKMYEFC  339 (342)
Q Consensus       289 ---~-~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~---~~~el~~lSg--GNP~~l~~lc  339 (342)
                         | ..+....++.++.-.++++|... |+-..++   .++.-|-+..  .+||..+..|
T Consensus       182 sDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSGRtA~QF~  242 (249)
T PF05673_consen  182 SDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQEALQWALRRGGRSGRTARQFI  242 (249)
T ss_pred             HHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence               2 14778899999999999999864 4442222   2223343333  3677666554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.01  E-value=0.00028  Score=73.28  Aligned_cols=118  Identities=15%  Similarity=0.202  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++++...+..++.+| +.||++..+ ..                 +-...|++++.....+.++|++|+.... 
T Consensus       102 d~IReIi~~~~~~P~~~~~KV-IIIDEad~L-t~-----------------~A~NaLLKtLEEPp~~tvfIL~Tt~~~K-  161 (605)
T PRK05896        102 DEIRNIIDNINYLPTTFKYKV-YIIDEAHML-ST-----------------SAWNALLKTLEEPPKHVVFIFATTEFQK-  161 (605)
T ss_pred             HHHHHHHHHHHhchhhCCcEE-EEEechHhC-CH-----------------HHHHHHHHHHHhCCCcEEEEEECCChHh-
Confidence            344555555554332345666 889998544 21                 2346788888766667777777754321 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                             ++..+..+ +       ..+++..++.+|+...+...... |.--.++....+.-+|+|+++.+..+
T Consensus       162 -------Ll~TI~SR-c-------q~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~GdlR~Alnl  220 (605)
T PRK05896        162 -------IPLTIISR-C-------QRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSI  220 (605)
T ss_pred             -------hhHHHHhh-h-------hhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHH
Confidence                   22222222 1       12788999999999888765443 43114444455666999999966544

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.00  E-value=0.00026  Score=68.48  Aligned_cols=75  Identities=15%  Similarity=0.095  Sum_probs=49.5

Q ss_pred             CCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhC
Q psy3261         251 NNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTK  329 (342)
Q Consensus       251 ~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSg  329 (342)
                      +..++|+||+....        ++..+..+-|+       .++++.++.+|...+++......-+. +++...++--.|+
T Consensus       149 ~~~~li~at~~~~~--------l~~~L~sRf~~-------~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~  213 (328)
T PRK00080        149 PPFTLIGATTRAGL--------LTSPLRDRFGI-------VQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSR  213 (328)
T ss_pred             CCceEEeecCCccc--------CCHHHHHhcCe-------eeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcC
Confidence            34567777765432        22233333222       36888999999999998776554333 5555666777999


Q ss_pred             CCHHHHhhhcc
Q psy3261         330 RVPQKMYEFCS  340 (342)
Q Consensus       330 GNP~~l~~lc~  340 (342)
                      |+|+.+..+|.
T Consensus       214 G~pR~a~~~l~  224 (328)
T PRK00080        214 GTPRIANRLLR  224 (328)
T ss_pred             CCchHHHHHHH
Confidence            99998877763

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.99  E-value=0.00036  Score=71.31  Aligned_cols=122  Identities=15%  Similarity=0.122  Sum_probs=67.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.|||+.+++.... ..   ....+...-..+..|+..+.+- -+++++|.++|...   +    .+...+++.-
T Consensus       146 ~~p~Il~iDEid~l~~~r~-~~---~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~---~----~ld~al~r~g  214 (495)
T TIGR01241       146 NAPCIIFIDEIDAVGRQRG-AG---LGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRP---D----VLDPALLRPG  214 (495)
T ss_pred             cCCCEEEEechhhhhhccc-cC---cCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCCh---h----hcCHHHhcCC
Confidence            3577899999988875422 10   1111111124445555555442 24456555555332   1    1223444332


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhC-CCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTK-RVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSg-GNP~~l~~lc~  340 (342)
                      .|+.     .+.|+..+.++-..+++.+....-+..+....++-..+. -+|.++..+|.
T Consensus       215 Rfd~-----~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~  269 (495)
T TIGR01241       215 RFDR-----QVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLN  269 (495)
T ss_pred             cceE-----EEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHH
Confidence            3432     378888889999999988876543422222334544554 48999998884

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.

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.99  E-value=0.00022  Score=73.03  Aligned_cols=118  Identities=11%  Similarity=0.165  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +-+..++++.......++++| |.||++..+ ..                 .-...|++.+........+|++|++... 
T Consensus       111 d~Ir~iie~a~~~P~~~~~KV-vIIDEa~~L-s~-----------------~a~naLLk~LEepp~~~vfI~aTte~~k-  170 (507)
T PRK06645        111 DDIRRIIESAEYKPLQGKHKI-FIIDEVHML-SK-----------------GAFNALLKTLEEPPPHIIFIFATTEVQK-  170 (507)
T ss_pred             HHHHHHHHHHHhccccCCcEE-EEEEChhhc-CH-----------------HHHHHHHHHHhhcCCCEEEEEEeCChHH-
Confidence            344455555443322245554 669998433 21                 2245677777765566777888764321 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                             ++..+..+ .       ..+++..++.+|....+++.... |.-.+++....+-..|+|++|.+..+
T Consensus       171 -------I~~tI~SR-c-------~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~  229 (507)
T PRK06645        171 -------IPATIISR-C-------QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSI  229 (507)
T ss_pred             -------hhHHHHhc-c-------eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                   22222222 1       13788999999999999776654 44324444455666999999987654

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.95  E-value=0.00039  Score=66.16  Aligned_cols=47  Identities=15%  Similarity=0.210  Sum_probs=35.7

Q ss_pred             eecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhh
Q psy3261         292 IHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      ++++.++.+|....++.+....-+. +++....+...++||++.+...
T Consensus       156 ~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~  203 (319)
T PRK00440        156 FRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINA  203 (319)
T ss_pred             eeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            7888999999999998776543332 5656666777999999986554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.95  E-value=0.00052  Score=68.13  Aligned_cols=119  Identities=19%  Similarity=0.290  Sum_probs=66.6

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhh---cC-CCCCeEEEEEeCCCCCCCCCccCcchhHHh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLV---QS-DWNNGAIVLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~---~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                      ..|.+|.+|++.+++....  .+...     .+-.+.+.+..++   .+ +..++++|.+++...   +    .++..++
T Consensus       223 ~~p~IlfiDEiD~l~~~r~--~~~~~-----~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~---~----~ld~all  288 (389)
T PRK03992        223 KAPSIIFIDEIDAIAAKRT--DSGTS-----GDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRI---D----ILDPAIL  288 (389)
T ss_pred             cCCeEEEEechhhhhcccc--cCCCC-----ccHHHHHHHHHHHHhccccCCCCCEEEEEecCCh---h----hCCHHHc
Confidence            4588899999988876422  11100     1122334444444   22 233445444444332   1    1334454


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      +...|+.     .|+|+..+.+|-..++..+....-+..+....++-. ..|-+|.++..+|.
T Consensus       289 RpgRfd~-----~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~  346 (389)
T PRK03992        289 RPGRFDR-----IIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICT  346 (389)
T ss_pred             CCccCce-----EEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            3333432     389999999999999998866544421122334433 56779999999885

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.94  E-value=0.00038  Score=68.34  Aligned_cols=119  Identities=20%  Similarity=0.278  Sum_probs=66.7

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc---C-CCCCeEEEEEeCCCCCCCCCccCcchhHHh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ---S-DWNNGAIVLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~---~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                      ..|.+|.+|++.+++....  .+...     .+-.+.+.+..++.   + +..++++|.+++....       .++..++
T Consensus       214 ~~p~il~iDEiD~l~~~~~--~~~~~-----~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~-------~ld~al~  279 (364)
T TIGR01242       214 KAPSIIFIDEIDAIAAKRT--DSGTS-----GDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD-------ILDPALL  279 (364)
T ss_pred             cCCcEEEhhhhhhhccccc--cCCCC-----ccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChh-------hCChhhc
Confidence            4688999999988865421  11111     11122333444332   2 3344555555443321       1333444


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhh-CCCHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLT-KRVPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lS-gGNP~~l~~lc~  340 (342)
                      +...|+.     .+.|+.++.+|-..+++.+....-+..+....++-..| |-+++++..+|.
T Consensus       280 r~grfd~-----~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~  337 (364)
T TIGR01242       280 RPGRFDR-----IIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICT  337 (364)
T ss_pred             CcccCce-----EEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHH
Confidence            3333432     37899999999999999887654442122344555544 668889988885

Many proteins may score above the trusted cutoff because an internal

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.94  E-value=0.00019  Score=74.93  Aligned_cols=103  Identities=11%  Similarity=0.154  Sum_probs=66.4

Q ss_pred             CCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         202 GVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       202 ~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ++++| +.||++..+ ..                 .-...|++.+.....+..+|++++....        +|.-++.+-
T Consensus       117 gk~KV-~IIDEVh~L-S~-----------------~A~NALLKtLEEPP~~v~FILaTtd~~k--------Ip~TIlSRC  169 (702)
T PRK14960        117 GRFKV-YLIDEVHML-ST-----------------HSFNALLKTLEEPPEHVKFLFATTDPQK--------LPITVISRC  169 (702)
T ss_pred             CCcEE-EEEechHhc-CH-----------------HHHHHHHHHHhcCCCCcEEEEEECChHh--------hhHHHHHhh
Confidence            45555 559999543 22                 2356788888776667778888754321        222232221


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                              ..+++..++.+|+...+...... |+-..++....+-..|+|++|.+..+|
T Consensus       170 --------q~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~GdLRdALnLL  220 (702)
T PRK14960        170 --------LQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDALSLT  220 (702)
T ss_pred             --------heeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                    13789999999999998776554 443245445556679999999987764

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.94  E-value=0.00047  Score=66.21  Aligned_cols=49  Identities=18%  Similarity=0.173  Sum_probs=35.5

Q ss_pred             eeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+++..++.+|+..++.....+ |+--+++..+.+-..++||++++...+
T Consensus       178 ~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l  227 (337)
T PRK12402        178 PLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTL  227 (337)
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            3788899999999999775543 432155555667778999999986543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.91  E-value=0.00031  Score=74.33  Aligned_cols=102  Identities=7%  Similarity=0.145  Sum_probs=66.4

Q ss_pred             CCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         202 GVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       202 ~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ++++|+| ||++..+ ..                 .-...|++.+.....+..+|++|+....+        +.-++.+ 
T Consensus       118 gr~KVII-IDEah~L-T~-----------------~A~NALLKtLEEPP~~v~FILaTtd~~KI--------p~TIrSR-  169 (830)
T PRK07003        118 ARFKVYM-IDEVHML-TN-----------------HAFNAMLKTLEEPPPHVKFILATTDPQKI--------PVTVLSR-  169 (830)
T ss_pred             CCceEEE-EeChhhC-CH-----------------HHHHHHHHHHHhcCCCeEEEEEECChhhc--------cchhhhh-
Confidence            4667655 9999544 21                 23567788887666777788888764422        2222222 


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                             ...+++..++.+|+...|+.... .|+-..++....|-..++|+.|....+
T Consensus       170 -------Cq~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmRdALsL  220 (830)
T PRK07003        170 -------CLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALSL  220 (830)
T ss_pred             -------eEEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                   12378899999999999977544 454324444555667999999987765

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.90  E-value=0.00048  Score=70.59  Aligned_cols=118  Identities=13%  Similarity=0.113  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+.+++......++++ +|.||+...+    +              -.....|++.+.....+..+|++++.... 
T Consensus        99 d~iR~l~~~~~~~p~~~~~k-VVIIDEad~l----s--------------~~a~naLLk~LEep~~~t~~Il~t~~~~k-  158 (504)
T PRK14963         99 EDVRDLREKVLLAPLRGGRK-VYILDEAHMM----S--------------KSAFNALLKTLEEPPEHVIFILATTEPEK-  158 (504)
T ss_pred             HHHHHHHHHHhhccccCCCe-EEEEECcccc----C--------------HHHHHHHHHHHHhCCCCEEEEEEcCChhh-
Confidence            34444544554332223445 5559998422    1              12345667777665566677777643221 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                             ++..+..+        ...+++..++.+|+...+.+.... |+-.+++....+-..|+|+++.+...
T Consensus       159 -------l~~~I~SR--------c~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~  217 (504)
T PRK14963        159 -------MPPTILSR--------TQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESL  217 (504)
T ss_pred             -------CChHHhcc--------eEEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                   11112111        113889999999999999886654 54325555666778999999988644

>CHL00176 ftsH cell division protein; Validated

Probab=97.88  E-value=0.00063  Score=71.54  Aligned_cols=122  Identities=18%  Similarity=0.139  Sum_probs=66.3

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.|||+.++...-..-..    .-+...-.....|+..+.+- -+.+++|.+++...   +    .+...+++.-
T Consensus       274 ~~P~ILfIDEID~l~~~r~~~~~----~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~---~----~LD~ALlRpG  342 (638)
T CHL00176        274 NSPCIVFIDEIDAVGRQRGAGIG----GGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRV---D----ILDAALLRPG  342 (638)
T ss_pred             CCCcEEEEecchhhhhcccCCCC----CCcHHHHHHHHHHHhhhccccCCCCeeEEEecCch---H----hhhhhhhccc
Confidence            56899999999888643210000    01111123344455545442 24456555555332   1    1223444332


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHh-hCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFL-TKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~l-SgGNP~~l~~lc~  340 (342)
                      .|+.     .+.++..+.++-..++..+....-+..+.....+-.. .|.++++|..+|.
T Consensus       343 RFd~-----~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvn  397 (638)
T CHL00176        343 RFDR-----QITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLN  397 (638)
T ss_pred             cCce-----EEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHH
Confidence            3432     3778888899999999888776443222222333334 4559999998873

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=0.00055  Score=73.66  Aligned_cols=101  Identities=12%  Similarity=0.155  Sum_probs=67.3

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      ..++.||++..+ .                 -.....|++.+..-..+..+|++|+....        ++.-++-+-   
T Consensus       120 ~KViIIDEAh~L-T-----------------~eAqNALLKtLEEPP~~vrFILaTTe~~k--------Ll~TIlSRC---  170 (944)
T PRK14949        120 FKVYLIDEVHML-S-----------------RSSFNALLKTLEEPPEHVKFLLATTDPQK--------LPVTVLSRC---  170 (944)
T ss_pred             cEEEEEechHhc-C-----------------HHHHHHHHHHHhccCCCeEEEEECCCchh--------chHHHHHhh---
Confidence            456889999555 2                 23456788888765666677777665432        222222221   


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ..+++.+++.+|++..+.+.... ++...++....+..+|+|++|....+|
T Consensus       171 -----q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd~R~ALnLL  221 (944)
T PRK14949        171 -----LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALSLT  221 (944)
T ss_pred             -----eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                 23789999999999999876554 544244445556779999999988876

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.83  E-value=0.00064  Score=66.57  Aligned_cols=119  Identities=18%  Similarity=0.222  Sum_probs=71.2

Q ss_pred             hhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCC
Q psy3261         184 ASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRA  263 (342)
Q Consensus       184 a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~  263 (342)
                      ..+.+-.+.+.+...+..++.+ +|.||+...+-                  -.-...+++.+.....+..+|+.++...
T Consensus       122 ~vd~iR~l~~~l~~~~~~g~~r-VviIDeAd~l~------------------~~aanaLLk~LEEpp~~~~fiLit~~~~  182 (351)
T PRK09112        122 TVDEIRRVGHFLSQTSGDGNWR-IVIIDPADDMN------------------RNAANAILKTLEEPPARALFILISHSSG  182 (351)
T ss_pred             CHHHHHHHHHHhhhccccCCce-EEEEEchhhcC------------------HHHHHHHHHHHhcCCCCceEEEEECChh
Confidence            3444555555555433234555 68899996552                  2234668888876666777666654432


Q ss_pred             CCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         264 NLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       264 ~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+       +|. +..+        ...++++.++.+|+..+++.... .+ + +++....+..+|+|+|+....+.
T Consensus       183 ~l-------lpt-IrSR--------c~~i~l~pl~~~~~~~~L~~~~~~~~-~-~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        183 RL-------LPT-IRSR--------CQPISLKPLDDDELKKALSHLGSSQG-S-DGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             hc-------cHH-HHhh--------ccEEEecCCCHHHHHHHHHHhhcccC-C-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            11       121 1111        11489999999999999987321 11 2 23334456679999999887765

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.83  E-value=0.00063  Score=69.79  Aligned_cols=116  Identities=11%  Similarity=0.163  Sum_probs=70.3

Q ss_pred             HHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCC
Q psy3261         189 DVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDR  268 (342)
Q Consensus       189 ~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~  268 (342)
                      ..+++.+......++++|+| ||++..+ ..                 .-...|++.+.....+..+|++|+....    
T Consensus       105 R~l~~~~~~~p~~~~~kV~i-IDE~~~l-s~-----------------~a~naLLk~LEepp~~~~fIlattd~~k----  161 (509)
T PRK14958        105 RELLDNIPYAPTKGRFKVYL-IDEVHML-SG-----------------HSFNALLKTLEEPPSHVKFILATTDHHK----  161 (509)
T ss_pred             HHHHHHHhhccccCCcEEEE-EEChHhc-CH-----------------HHHHHHHHHHhccCCCeEEEEEECChHh----
Confidence            33444433323345777755 9999544 22                 2346788888776677778888754321    


Q ss_pred             ccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         269 RESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       269 ~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                          +|.-+..+ ..       .+++..++.+|+...+...... |.-..++....+-..++|++|.+..++
T Consensus       162 ----l~~tI~SR-c~-------~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lL  221 (509)
T PRK14958        162 ----LPVTVLSR-CL-------QFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLL  221 (509)
T ss_pred             ----chHHHHHH-hh-------hhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence                22222222 11       2688899999999888766554 433134334456669999999987765

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.82  E-value=0.00097  Score=67.61  Aligned_cols=101  Identities=11%  Similarity=0.070  Sum_probs=66.1

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      ...++.||++..+ ..                 .....|++.+.....+..+|+||+....        ++..+..+-  
T Consensus       121 ~~KV~IIDEah~L-s~-----------------~A~NALLKtLEEPp~~viFILaTte~~k--------I~~TI~SRC--  172 (484)
T PRK14956        121 KYKVYIIDEVHML-TD-----------------QSFNALLKTLEEPPAHIVFILATTEFHK--------IPETILSRC--  172 (484)
T ss_pred             CCEEEEEechhhc-CH-----------------HHHHHHHHHhhcCCCceEEEeecCChhh--------ccHHHHhhh--
Confidence            3456889999655 21                 2356677777665667777888876432        333333321  


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                            ..+.+.+++.+++...+++... .|+-..++....+-..|+|++|....+
T Consensus       173 ------q~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd~RdAL~l  222 (484)
T PRK14956        173 ------QDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSF  222 (484)
T ss_pred             ------heeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCChHHHHHHH
Confidence                  1268889999999999987755 344324444455667999999987654

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

Probab=97.78  E-value=0.0012  Score=65.82  Aligned_cols=119  Identities=15%  Similarity=0.216  Sum_probs=65.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHh---hcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINL---VQSD-WNNGAIVLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~---~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                      ..|.+|.+|++.+++...  +.....     .+-.+.+.+..+   +.+- -..+++|.++|...   +    .++..++
T Consensus       237 ~~P~ILfIDEID~i~~~r--~~~~~~-----~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~---d----~LDpAll  302 (398)
T PTZ00454        237 NAPSIIFIDEVDSIATKR--FDAQTG-----ADREVQRILLELLNQMDGFDQTTNVKVIMATNRA---D----TLDPALL  302 (398)
T ss_pred             cCCeEEEEECHhhhcccc--ccccCC-----ccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCc---h----hCCHHHc
Confidence            468899999998887542  111111     112223333333   3332 23345444444321   1    1333454


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHH-HhhCCCHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIA-FLTKRVPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~-~lSgGNP~~l~~lc~  340 (342)
                      +...|+.     .|+++..+.++-+.+++.+....-+..+....++- ...|-+|.++..+|.
T Consensus       303 R~GRfd~-----~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~  360 (398)
T PTZ00454        303 RPGRLDR-----KIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQ  360 (398)
T ss_pred             CCCcccE-----EEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            3323432     37888899999999998887654342122233333 356889999999985

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.77  E-value=0.00068  Score=69.39  Aligned_cols=94  Identities=16%  Similarity=0.220  Sum_probs=55.9

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC-CCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW-NNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~-~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|++|.+|++.+++..-. - . ....   .+-+++..|+..+.|-. .++++|.++|...   +    .+...+++.-
T Consensus       288 g~p~IIfIDEiD~L~~~R~-~-~-~s~d---~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~---d----~LDpALlRpG  354 (512)
T TIGR03689       288 GRPVIVFFDEMDSIFRTRG-S-G-VSSD---VETTVVPQLLSELDGVESLDNVIVIGASNRE---D----MIDPAILRPG  354 (512)
T ss_pred             CCCceEEEehhhhhhcccC-C-C-ccch---HHHHHHHHHHHHhcccccCCceEEEeccCCh---h----hCCHhhcCcc
Confidence            5799999999999986421 0 0 0000   11246667777776643 2345444444321   1    1334454432


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCC
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKW  314 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~  314 (342)
                      .|+.     .|+++..+.++.+.++..|.....
T Consensus       355 RfD~-----~I~~~~Pd~e~r~~Il~~~l~~~l  382 (512)
T TIGR03689       355 RLDV-----KIRIERPDAEAAADIFSKYLTDSL  382 (512)
T ss_pred             ccce-----EEEeCCCCHHHHHHHHHHHhhccC
Confidence            3432     489999999999999988876543

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.75  E-value=0.00073  Score=67.52  Aligned_cols=49  Identities=14%  Similarity=0.234  Sum_probs=36.5

Q ss_pred             eeecCCCCHHHHHHHHHHHHhC---CCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESK---KWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~---~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+.+..++.+|+..+++.....   +.+. +++....+..+|+||++.+..++
T Consensus       145 ~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        145 VFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLL  197 (413)
T ss_pred             eeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            4789999999999999876543   4312 45555567779999999987654

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.75  E-value=0.00082  Score=70.76  Aligned_cols=85  Identities=7%  Similarity=0.104  Sum_probs=55.6

Q ss_pred             HHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccC
Q psy3261         239 TRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQT  317 (342)
Q Consensus       239 ~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~  317 (342)
                      ...|++.+.....+..+|++++....        ++.-++++-        ..+.+..++.+|+...+...... |+-..
T Consensus       136 ~NALLKtLEEPp~~v~fILaTtd~~k--------L~~TIrSRC--------~~f~f~~Ls~eeI~~~L~~Il~kEgi~id  199 (709)
T PRK08691        136 FNAMLKTLEEPPEHVKFILATTDPHK--------VPVTVLSRC--------LQFVLRNMTAQQVADHLAHVLDSEKIAYE  199 (709)
T ss_pred             HHHHHHHHHhCCCCcEEEEEeCCccc--------cchHHHHHH--------hhhhcCCCCHHHHHHHHHHHHHHcCCCcC
Confidence            45678888765566677777754321        222233321        12678899999999988766554 44324


Q ss_pred             cchHHHHHHhhCCCHHHHhhhc
Q psy3261         318 SEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       318 e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      ++....|...++|++|.+..++
T Consensus       200 ~eAL~~Ia~~A~GslRdAlnLL  221 (709)
T PRK08691        200 PPALQLLGRAAAGSMRDALSLL  221 (709)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHH
Confidence            4455667789999999988765

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

Probab=97.73  E-value=0.00033  Score=57.58  Aligned_cols=27  Identities=19%  Similarity=0.249  Sum_probs=20.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ..-++|+|++|||||+++.++......
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~   30 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNA   30 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHH
Confidence            567899999999999999999987653

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.72  E-value=0.00084  Score=59.42  Aligned_cols=109  Identities=16%  Similarity=0.173  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++++...+..+.++ +|.||++..+-.                  .....|++++.....+..+|+.++.... 
T Consensus        79 ~~i~~i~~~~~~~~~~~~~k-viiide~~~l~~------------------~~~~~Ll~~le~~~~~~~~il~~~~~~~-  138 (188)
T TIGR00678        79 DQVRELVEFLSRTPQESGRR-VVIIEDAERMNE------------------AAANALLKTLEEPPPNTLFILITPSPEK-  138 (188)
T ss_pred             HHHHHHHHHHccCcccCCeE-EEEEechhhhCH------------------HHHHHHHHHhcCCCCCeEEEEEECChHh-
Confidence            55556666665543223444 566999844422                  1345688888776667777777653211 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHH
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQK  334 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~  334 (342)
                             +...+..+ +       ..+++..++.+|....+...   | + +++....+.-.+||+|+.
T Consensus       139 -------l~~~i~sr-~-------~~~~~~~~~~~~~~~~l~~~---g-i-~~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       139 -------LLPTIRSR-C-------QVLPFPPLSEEALLQWLIRQ---G-I-SEEAAELLLALAGGSPGA  187 (188)
T ss_pred             -------ChHHHHhh-c-------EEeeCCCCCHHHHHHHHHHc---C-C-CHHHHHHHHHHcCCCccc
Confidence                   22222211 1       13889999999998888776   5 4 465566677799999974

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.72  E-value=0.0012  Score=69.40  Aligned_cols=117  Identities=11%  Similarity=0.174  Sum_probs=72.8

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++++......++++ ++.||++..+ ..                 .-...|++.+.....+..+|++|+....   
T Consensus       104 iR~li~~~~~~p~~g~~K-V~IIDEah~L-s~-----------------~a~NALLKtLEEPp~~v~FIL~Tt~~~k---  161 (647)
T PRK07994        104 TRELLDNVQYAPARGRFK-VYLIDEVHML-SR-----------------HSFNALLKTLEEPPEHVKFLLATTDPQK---  161 (647)
T ss_pred             HHHHHHHHHhhhhcCCCE-EEEEechHhC-CH-----------------HHHHHHHHHHHcCCCCeEEEEecCCccc---
Confidence            344444443322224444 5789999544 22                 3457788888776677778888765432   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ++.-+.-+        -..+.+..++.+|+...+.+.. ..|+-..++....+-.+|+|++|....+|
T Consensus       162 -----Ll~TI~SR--------C~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~Gs~R~Al~ll  221 (647)
T PRK07994        162 -----LPVTILSR--------CLQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAADGSMRDALSLT  221 (647)
T ss_pred             -----cchHHHhh--------heEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                 22222222        1137899999999999987754 34554233334456679999999888876

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.0015  Score=66.67  Aligned_cols=118  Identities=9%  Similarity=0.114  Sum_probs=71.0

Q ss_pred             HHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCC
Q psy3261         187 VVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLP  266 (342)
Q Consensus       187 ~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~  266 (342)
                      -+..++++.......++++ ++.||++..+ ..                 .-...|++.+........+|++|++...  
T Consensus       100 dIR~Iie~~~~~P~~~~~K-VvIIDEah~L-s~-----------------~A~NaLLK~LEePp~~v~fIlatte~~K--  158 (491)
T PRK14964        100 DIKVILENSCYLPISSKFK-VYIIDEVHML-SN-----------------SAFNALLKTLEEPAPHVKFILATTEVKK--  158 (491)
T ss_pred             HHHHHHHHHHhccccCCce-EEEEeChHhC-CH-----------------HHHHHHHHHHhCCCCCeEEEEEeCChHH--
Confidence            3444444443322123444 5789998333 21                 2346788888877677778888764321  


Q ss_pred             CCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         267 DRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       267 ~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            ++..+..+ .       ..+++..++.+|....+.....+ |.-.+++....+...++|+++.+..++
T Consensus       159 ------l~~tI~SR-c-------~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslL  218 (491)
T PRK14964        159 ------IPVTIISR-C-------QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLL  218 (491)
T ss_pred             ------HHHHHHHh-h-------eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  33323222 1       13788899999999888776554 443245445556679999999766543

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.0015  Score=64.14  Aligned_cols=119  Identities=10%  Similarity=0.112  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++.+.... .....-++.||++..+-.                  .-...|++.+.....+..+|++++.... 
T Consensus       102 ~~ir~i~~~~~~~p-~~~~~kviIIDEa~~l~~------------------~a~naLLk~lEe~~~~~~fIl~t~~~~~-  161 (363)
T PRK14961        102 EEMREILDNIYYSP-SKSRFKVYLIDEVHMLSR------------------HSFNALLKTLEEPPQHIKFILATTDVEK-  161 (363)
T ss_pred             HHHHHHHHHHhcCc-ccCCceEEEEEChhhcCH------------------HHHHHHHHHHhcCCCCeEEEEEcCChHh-
Confidence            33445555543321 112345788999754311                  1234577777655556566777654221 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                             ++..+..+-        ..++++.++.+|+...+...... |.-.+++....+-..|+|+||.+..+|
T Consensus       162 -------l~~tI~SRc--------~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l  221 (363)
T PRK14961        162 -------IPKTILSRC--------LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLL  221 (363)
T ss_pred             -------hhHHHHhhc--------eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                   222333221        24899999999999988775544 542245444556669999999877665

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.64  E-value=0.0017  Score=66.31  Aligned_cols=119  Identities=13%  Similarity=0.152  Sum_probs=70.9

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..|.+|.||++-.+|.....-.+.      ...-.+...|+..+... +++++|.||+...       ..+|.++++...
T Consensus       317 ~~P~IL~IDEID~~~~~~~~~~d~------~~~~rvl~~lL~~l~~~-~~~V~vIaTTN~~-------~~Ld~allR~GR  382 (489)
T CHL00195        317 LSPCILWIDEIDKAFSNSESKGDS------GTTNRVLATFITWLSEK-KSPVFVVATANNI-------DLLPLEILRKGR  382 (489)
T ss_pred             cCCcEEEehhhhhhhccccCCCCc------hHHHHHHHHHHHHHhcC-CCceEEEEecCCh-------hhCCHHHhCCCc
Confidence            469999999999888653211111      11124555666666543 4556666666532       125556665444


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc--CcchHHHHH-HhhCCCHHHHhhhcc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ--TSEGREEIA-FLTKRVPQKMYEFCS  340 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~--~e~~~~el~-~lSgGNP~~l~~lc~  340 (342)
                      |+.     .+.|+.-+.+|-..+++.|..+.-..  .+.....|- ...|-++.++..+|.
T Consensus       383 FD~-----~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~  438 (489)
T CHL00195        383 FDE-----IFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSII  438 (489)
T ss_pred             CCe-----EEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHH
Confidence            643     36777778899999998887664321  122222333 355888999988874

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.64  E-value=0.0013  Score=68.80  Aligned_cols=117  Identities=9%  Similarity=0.128  Sum_probs=71.2

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++.+......++++ ++.||++..+-.                  .-...|++.+.....+..+|++|++...   
T Consensus       109 IReLie~~~~~P~~gr~K-ViIIDEah~Ls~------------------~AaNALLKTLEEPP~~v~FILaTtep~k---  166 (700)
T PRK12323        109 MAQLLDKAVYAPTAGRFK-VYMIDEVHMLTN------------------HAFNAMLKTLEEPPEHVKFILATTDPQK---  166 (700)
T ss_pred             HHHHHHHHHhchhcCCce-EEEEEChHhcCH------------------HHHHHHHHhhccCCCCceEEEEeCChHh---
Confidence            334444443322234555 577999965522                  2346788888766677788888875432   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ++.-+..+-        ..+.+..++.+++...+.+... .|+-..++....+-..++|++|....++
T Consensus       167 -----LlpTIrSRC--------q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~Gs~RdALsLL  226 (700)
T PRK12323        167 -----IPVTVLSRC--------LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSLT  226 (700)
T ss_pred             -----hhhHHHHHH--------HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                 222222221        1268888999999988876644 3544233334456679999999987765

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

Probab=97.59  E-value=0.00053  Score=69.98  Aligned_cols=118  Identities=14%  Similarity=0.220  Sum_probs=79.9

Q ss_pred             hHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCC
Q psy3261         185 SDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRAN  264 (342)
Q Consensus       185 ~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~  264 (342)
                      .+=+..++++..-....++++|.+ ||++ ++++.                 .--.+|++-+...+.+-.+|+||++-..
T Consensus       101 VddiR~i~e~v~y~P~~~ryKVyi-IDEv-HMLS~-----------------~afNALLKTLEEPP~hV~FIlATTe~~K  161 (515)
T COG2812         101 VDDIREIIEKVNYAPSEGRYKVYI-IDEV-HMLSK-----------------QAFNALLKTLEEPPSHVKFILATTEPQK  161 (515)
T ss_pred             hHHHHHHHHHhccCCccccceEEE-EecH-HhhhH-----------------HHHHHHhcccccCccCeEEEEecCCcCc
Confidence            344555666666555567777765 8998 55443                 3456777777777888899999998664


Q ss_pred             CCCCccCcchhHHhh-hcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHH-HHHhhCCCHHHHhhh
Q psy3261         265 LPDRRESHLPLYMLK-KAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREE-IAFLTKRVPQKMYEF  338 (342)
Q Consensus       265 ~~~~~~~~~p~~llg-~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~e-l~~lSgGNP~~l~~l  338 (342)
                      ++.        -.+- .+-         +.+.+++.+++...+++....-++..|+.... +...++|..|+...+
T Consensus       162 ip~--------TIlSRcq~---------f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~Gs~RDalsl  220 (515)
T COG2812         162 IPN--------TILSRCQR---------FDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSL  220 (515)
T ss_pred             Cch--------hhhhcccc---------ccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCCChhhHHHH
Confidence            332        2222 222         57889999999999999999888874443322 445888888876543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.57  E-value=0.0016  Score=61.90  Aligned_cols=112  Identities=9%  Similarity=0.103  Sum_probs=60.3

Q ss_pred             EEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCc--chhHHhhhcCCC
Q psy3261         207 FVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESH--LPLYMLKKAGFE  284 (342)
Q Consensus       207 LvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~--~p~~llg~~g~~  284 (342)
                      ++.||++..+.....   +      .+..-.+...|+.++.....+-.||+|++...     ....  +...+..+  |.
T Consensus       124 vL~iDEi~~L~~~~~---~------~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~-----~~~~~~~np~L~sR--~~  187 (284)
T TIGR02880       124 VLFIDEAYYLYRPDN---E------RDYGQEAIEILLQVMENQRDDLVVILAGYKDR-----MDSFFESNPGFSSR--VA  187 (284)
T ss_pred             EEEEechhhhccCCC---c------cchHHHHHHHHHHHHhcCCCCEEEEEeCCcHH-----HHHHHhhCHHHHhh--CC
Confidence            677899976653311   0      01112456677777765444445555544221     0000  00111111  11


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHh--------hCCCHHHHhhhc
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFL--------TKRVPQKMYEFC  339 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~l--------SgGNP~~l~~lc  339 (342)
                           ..|+++.|+.+|...+++++....-.. +++....+.-.        .-||.|+++.+.
T Consensus       188 -----~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~v  246 (284)
T TIGR02880       188 -----HHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAI  246 (284)
T ss_pred             -----cEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHH
Confidence                 248999999999999999988764222 34333333221        249999998654

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.54  E-value=0.0066  Score=59.81  Aligned_cols=120  Identities=15%  Similarity=0.156  Sum_probs=73.3

Q ss_pred             chhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCC
Q psy3261         183 YASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPR  262 (342)
Q Consensus       183 ~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~  262 (342)
                      +..+.+..+.+.+...+ ....|.+|.||+...+    +              ..-...|++.+.....+..+|+.+...
T Consensus       121 I~VdqiR~l~~~~~~~~-~~~~~kVviIDead~m----~--------------~~aanaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        121 ITVDEVRELISFFGLTA-AEGGWRVVIVDTADEM----N--------------ANAANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             ccHHHHHHHHHHhCcCc-ccCCCEEEEEechHhc----C--------------HHHHHHHHHHHhcCCCCeEEEEEECCc
Confidence            34455556666655433 3456778999997543    2              345678888887666667677765543


Q ss_pred             CCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         263 ANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       263 ~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      ..+       +|. +.        .-...+.++.++.+|+..+++...  +.. .++....+..+|||||+....++.
T Consensus       182 ~~l-------lpt-i~--------SRc~~i~l~~l~~~~i~~~L~~~~--~~~-~~~~~~~l~~~s~Gsp~~Al~ll~  240 (365)
T PRK07471        182 ARL-------LPT-IR--------SRCRKLRLRPLAPEDVIDALAAAG--PDL-PDDPRAALAALAEGSVGRALRLAG  240 (365)
T ss_pred             hhc-------hHH-hh--------ccceEEECCCCCHHHHHHHHHHhc--ccC-CHHHHHHHHHHcCCCHHHHHHHhc
Confidence            311       111 10        001248999999999998886531  111 222223566699999998877753

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.52  E-value=0.0035  Score=61.44  Aligned_cols=98  Identities=7%  Similarity=0.064  Sum_probs=59.3

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      +-+|.||++..+-.                  .....|++.+........+|++++....        +...+..+ +  
T Consensus       109 ~kiviIDE~~~l~~------------------~~~~~ll~~le~~~~~~~~Il~~~~~~k--------l~~~l~sr-~--  159 (367)
T PRK14970        109 YKIYIIDEVHMLSS------------------AAFNAFLKTLEEPPAHAIFILATTEKHK--------IIPTILSR-C--  159 (367)
T ss_pred             cEEEEEeChhhcCH------------------HHHHHHHHHHhCCCCceEEEEEeCCccc--------CCHHHHhc-c--
Confidence            34689999854311                  1256677777665556666777654221        11122211 1  


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHh-CCC-ccCcchHHHHHHhhCCCHHHHhh
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYES-KKW-LQTSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~-l~~e~~~~el~~lSgGNP~~l~~  337 (342)
                           ..++++.++.+|+...+.-... .|. + +++..+.+-..++||++.+..
T Consensus       160 -----~~v~~~~~~~~~l~~~l~~~~~~~g~~i-~~~al~~l~~~~~gdlr~~~~  208 (367)
T PRK14970        160 -----QIFDFKRITIKDIKEHLAGIAVKEGIKF-EDDALHIIAQKADGALRDALS  208 (367)
T ss_pred             -----eeEecCCccHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHhCCCCHHHHHH
Confidence                 1378889999999988765544 454 3 455555566699999996544

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.52  E-value=0.0059  Score=63.49  Aligned_cols=119  Identities=13%  Similarity=0.125  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++++......++++ ++.||++..+ .  +               .-...|++.+...+.+.++|++|+.... 
T Consensus       102 d~ir~i~~~v~~~p~~~~~k-ViIIDE~~~L-t--~---------------~a~naLLKtLEepp~~~ifIlatt~~~k-  161 (559)
T PRK05563        102 DEIRDIRDKVKYAPSEAKYK-VYIIDEVHML-S--T---------------GAFNALLKTLEEPPAHVIFILATTEPHK-  161 (559)
T ss_pred             HHHHHHHHHHhhCcccCCeE-EEEEECcccC-C--H---------------HHHHHHHHHhcCCCCCeEEEEEeCChhh-
Confidence            44445555554332223444 5579998433 1  1               2355778888776677778888764321 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                             ++..+..+.        ..+++.+++.+|+...+++.... |+-..++....+-..++|+++.+..++
T Consensus       162 -------i~~tI~SRc--------~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G~~R~al~~L  221 (559)
T PRK05563        162 -------IPATILSRC--------QRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSIL  221 (559)
T ss_pred             -------CcHHHHhHh--------eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                   222232221        12678889999999999887665 432144444456669999999876554

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.51  E-value=0.0053  Score=59.49  Aligned_cols=119  Identities=13%  Similarity=0.136  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++++...+.-++.+ +|.||++..+-.                  .....|++.+.....+..+|++++...  
T Consensus       100 ~~~~~l~~~~~~~p~~~~~~-vviidea~~l~~------------------~~~~~Ll~~le~~~~~~~lIl~~~~~~--  158 (355)
T TIGR02397       100 DDIREILDNVKYAPSSGKYK-VYIIDEVHMLSK------------------SAFNALLKTLEEPPEHVVFILATTEPH--  158 (355)
T ss_pred             HHHHHHHHHHhcCcccCCce-EEEEeChhhcCH------------------HHHHHHHHHHhCCccceeEEEEeCCHH--
Confidence            33445566654332122333 666999854411                  124567777755445555566653211  


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                       +     ++..+..+ .       ..++++.++.+|....+..+... |+--+++....+.-.++|+|+.+...+
T Consensus       159 -~-----l~~~l~sr-~-------~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       159 -K-----IPATILSR-C-------QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             -H-----HHHHHHhh-e-------eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHH
Confidence             0     11122211 1       13788899999999888766554 542145445556679999999887654

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.48  E-value=0.0035  Score=65.39  Aligned_cols=116  Identities=9%  Similarity=0.123  Sum_probs=70.1

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++.++.....++++|+| ||++..+ +.                 .-...|++++..-..+..+|++|+....   
T Consensus       104 ir~l~~~~~~~p~~~~~KVvI-Idev~~L-t~-----------------~a~naLLk~LEepp~~~~fIl~t~~~~k---  161 (576)
T PRK14965        104 IRELRENVKYLPSRSRYKIFI-IDEVHML-ST-----------------NAFNALLKTLEEPPPHVKFIFATTEPHK---  161 (576)
T ss_pred             HHHHHHHHHhccccCCceEEE-EEChhhC-CH-----------------HHHHHHHHHHHcCCCCeEEEEEeCChhh---
Confidence            444555554433345677755 9998332 21                 2356888888776677888888865332   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                           ++.-+..+ .       ..+++..++.+|+...+..... .|+--.++....+-..++|+.+.+..+
T Consensus       162 -----l~~tI~SR-c-------~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G~lr~al~~  220 (576)
T PRK14965        162 -----VPITILSR-C-------QRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLST  220 (576)
T ss_pred             -----hhHHHHHh-h-------hhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                 23222222 1       1267888999999888866544 454324544555666999999976543

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.47  E-value=0.0074  Score=63.39  Aligned_cols=118  Identities=14%  Similarity=0.175  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++++......++++ +|.||+...+    +              -.-...|++++..-..+..+|++++....+
T Consensus       104 d~Ir~li~~~~~~P~~~~~K-VvIIdea~~L----s--------------~~a~naLLK~LEepp~~tifIL~tt~~~kI  164 (614)
T PRK14971        104 DDIRNLIEQVRIPPQIGKYK-IYIIDEVHML----S--------------QAAFNAFLKTLEEPPSYAIFILATTEKHKI  164 (614)
T ss_pred             HHHHHHHHHHhhCcccCCcE-EEEEECcccC----C--------------HHHHHHHHHHHhCCCCCeEEEEEeCCchhc
Confidence            44445556665432223445 4578886433    1              134678889988766677778877643211


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhh
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~l  338 (342)
                             +| .+..+ +.       .+++..++.+|+...+.+.....-+. .++....+-..+||+.+.+...
T Consensus       165 -------l~-tI~SR-c~-------iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~  222 (614)
T PRK14971        165 -------LP-TILSR-CQ-------IFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSI  222 (614)
T ss_pred             -------hH-HHHhh-hh-------eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                   11 12211 11       37889999999999998766553343 4444555667999999966543

>PRK04195 replication factor C large subunit; Provisional

Probab=97.46  E-value=0.0094  Score=60.81  Aligned_cols=103  Identities=15%  Similarity=0.155  Sum_probs=57.3

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .+-+|.||++..+....+              -.....|++++... +. .+|+++...... .      +..+ ...  
T Consensus        98 ~~kvIiIDEaD~L~~~~d--------------~~~~~aL~~~l~~~-~~-~iIli~n~~~~~-~------~k~L-rsr--  151 (482)
T PRK04195         98 RRKLILLDEVDGIHGNED--------------RGGARAILELIKKA-KQ-PIILTANDPYDP-S------LREL-RNA--  151 (482)
T ss_pred             CCeEEEEecCcccccccc--------------hhHHHHHHHHHHcC-CC-CEEEeccCcccc-c------hhhH-hcc--
Confidence            466899999977654322              34456677777532 23 344433322110 1      0111 111  


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhh
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~  337 (342)
                           ...++++.++.+++...+...... |+--.++....+--.++|+.|.+..
T Consensus       152 -----~~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain  201 (482)
T PRK04195        152 -----CLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAIN  201 (482)
T ss_pred             -----ceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence                 124899999999999988765543 4321444444555688888876643

>PLN03025 replication factor C subunit; Provisional

Probab=97.45  E-value=0.0027  Score=61.19  Aligned_cols=47  Identities=21%  Similarity=0.184  Sum_probs=34.5

Q ss_pred             eecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         292 IHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      ++++.++.+|....+..-..+ |.--+++....+-..++|+.|.+...
T Consensus       153 i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~gDlR~aln~  200 (319)
T PLN03025        153 VRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNN  200 (319)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            788999999999988776544 54325555566667899999887643

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.0064  Score=63.58  Aligned_cols=100  Identities=9%  Similarity=0.071  Sum_probs=60.7

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      ..+|.||++..+- .                 .....|++++.....+..+|++|+....        ++..+..+-   
T Consensus       120 ~kVIIIDEad~Lt-~-----------------~a~naLLk~LEEP~~~~ifILaTt~~~k--------ll~TI~SRc---  170 (624)
T PRK14959        120 YKVFIIDEAHMLT-R-----------------EAFNALLKTLEEPPARVTFVLATTEPHK--------FPVTIVSRC---  170 (624)
T ss_pred             ceEEEEEChHhCC-H-----------------HHHHHHHHHhhccCCCEEEEEecCChhh--------hhHHHHhhh---
Confidence            3467799996552 1                 2246678888765456667776654321        222222221   


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                           ..+++..++.+|+...+...... |+-.+++....+-.+|+|+.+....+
T Consensus       171 -----q~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~l  220 (624)
T PRK14959        171 -----QHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSL  220 (624)
T ss_pred             -----hccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                 12788999999999888665443 54214544445556999999966554

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.0053  Score=64.31  Aligned_cols=117  Identities=10%  Similarity=0.129  Sum_probs=69.3

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++.+......++++ ++.||++..+- ...                 ...|++.+..-.....+|++|+....   
T Consensus       109 iReli~~~~~~p~~g~~K-V~IIDEvh~Ls-~~a-----------------~NaLLKtLEEPP~~~~fIL~Ttd~~k---  166 (618)
T PRK14951        109 VQQLLEQAVYKPVQGRFK-VFMIDEVHMLT-NTA-----------------FNAMLKTLEEPPEYLKFVLATTDPQK---  166 (618)
T ss_pred             HHHHHHHHHhCcccCCce-EEEEEChhhCC-HHH-----------------HHHHHHhcccCCCCeEEEEEECCchh---
Confidence            344444443322234455 56899995542 211                 34677777665666677777754221   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ++.-++.+ +       ..+++..++.+|+...+.... ..|+-.+++....+...++|+++.+..++
T Consensus       167 -----il~TIlSR-c-------~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lL  226 (618)
T PRK14951        167 -----VPVTVLSR-C-------LQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLT  226 (618)
T ss_pred             -----hhHHHHHh-c-------eeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                 22222222 1       137899999999998887654 44544234344556679999999988764

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.43  E-value=0.0069  Score=64.96  Aligned_cols=129  Identities=12%  Similarity=0.202  Sum_probs=71.6

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC--CCCCeEEEEEeCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS--DWNNGAIVLALSPRANL  265 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~--~~~~G~vv~AtS~~~~~  265 (342)
                      +..+++..++     ..|.+|.+|++.+++..-. -   ...  ....=.++..|+..+.|  +-.+.+||+||+.... 
T Consensus       535 i~~~f~~A~~-----~~p~iifiDEid~l~~~r~-~---~~~--~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~-  602 (733)
T TIGR01243       535 IREIFRKARQ-----AAPAIIFFDEIDAIAPARG-A---RFD--TSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDI-  602 (733)
T ss_pred             HHHHHHHHHh-----cCCEEEEEEChhhhhccCC-C---CCC--ccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhh-
Confidence            3445555444     4688999999998876422 0   000  00011355555555554  2344455555543221 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                             +...+++.-.|+.     .+.|+..+.++-..++..+....-+..+....++-- ..|-++.++..+|.
T Consensus       603 -------ld~allRpgRfd~-----~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~~  666 (733)
T TIGR01243       603 -------LDPALLRPGRFDR-----LILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCR  666 (733)
T ss_pred             -------CCHhhcCCCccce-----EEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHHH
Confidence                   2234443223543     378888899999999887765443422222334443 45668888888884

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.42  E-value=0.0047  Score=65.56  Aligned_cols=120  Identities=13%  Similarity=0.219  Sum_probs=72.4

Q ss_pred             hHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCC
Q psy3261         185 SDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRAN  264 (342)
Q Consensus       185 ~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~  264 (342)
                      .+.+..+++++...+..++++ ++.||++..+ ..                 .-..+|++.+...+...++|++|+....
T Consensus       100 vd~IReLie~~~~~P~~g~~K-V~IIDEa~~L-T~-----------------~A~NALLKtLEEPP~~tifILaTte~~K  160 (725)
T PRK07133        100 VDEIRELIENVKNLPTQSKYK-IYIIDEVHML-SK-----------------SAFNALLKTLEEPPKHVIFILATTEVHK  160 (725)
T ss_pred             HHHHHHHHHHHHhchhcCCCE-EEEEEChhhC-CH-----------------HHHHHHHHHhhcCCCceEEEEEcCChhh
Confidence            344556666665443234555 5579998433 21                 2366788888776677777888754321


Q ss_pred             CCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         265 LPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       265 ~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                              ++..+..+-        .++++.+++.+|+...+.... ..|+-..++....+-.+|+|++|.+..++
T Consensus       161 --------Ll~TI~SRc--------q~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        161 --------IPLTILSRV--------QRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             --------hhHHHHhhc--------eeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                    222232221        138899999999998886543 44543233334446669999999776543

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.38  E-value=0.0051  Score=66.51  Aligned_cols=101  Identities=6%  Similarity=-0.022  Sum_probs=62.7

Q ss_pred             CCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         202 GVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       202 ~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ++++|+| ||++..+-                  -.-.+.|++++..-..+..+|++|+....        +...+ ...
T Consensus       119 ~~~KV~I-IDEad~lt------------------~~a~NaLLK~LEEpP~~~~fIl~tt~~~k--------Ll~TI-rSR  170 (824)
T PRK07764        119 SRYKIFI-IDEAHMVT------------------PQGFNALLKIVEEPPEHLKFIFATTEPDK--------VIGTI-RSR  170 (824)
T ss_pred             CCceEEE-EechhhcC------------------HHHHHHHHHHHhCCCCCeEEEEEeCChhh--------hhHHH-Hhh
Confidence            5677765 99995552                  23456899999887778888888754321        11111 111


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHH-HHhCCCccCcchHHHHHHhhCCCHHHHhh
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNL-YESKKWLQTSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~y-y~~~~~l~~e~~~~el~~lSgGNP~~l~~  337 (342)
                      ..       .+++..++.+++...+.. +...|+-..++....+-.++||+++.+..
T Consensus       171 c~-------~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~  220 (824)
T PRK07764        171 TH-------HYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLS  220 (824)
T ss_pred             ee-------EEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            11       267888999999887755 44556432333334455599999975543

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.32  E-value=0.019  Score=55.76  Aligned_cols=119  Identities=13%  Similarity=0.154  Sum_probs=74.2

Q ss_pred             chhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCC
Q psy3261         183 YASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPR  262 (342)
Q Consensus       183 ~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~  262 (342)
                      ...+.+..+++++...+..+..+|+| ||+...+    +              .+-...|++.+.....+..+|++|+..
T Consensus        86 i~id~iR~l~~~~~~~~~~~~~kv~i-I~~a~~m----~--------------~~aaNaLLK~LEEPp~~~~fiL~t~~~  146 (328)
T PRK05707         86 IKVDQVRELVSFVVQTAQLGGRKVVL-IEPAEAM----N--------------RNAANALLKSLEEPSGDTVLLLISHQP  146 (328)
T ss_pred             CCHHHHHHHHHHHhhccccCCCeEEE-ECChhhC----C--------------HHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence            33566666777776544356788885 7998555    2              456789999998777778888777664


Q ss_pred             CCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         263 ANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       263 ~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      ..+       +| -+.-+-        ..+.++..+.+|+...+..-.  +-. .++....+..+++|+|....+++
T Consensus       147 ~~l-------l~-TI~SRc--------~~~~~~~~~~~~~~~~L~~~~--~~~-~~~~~~~~l~la~Gsp~~A~~l~  204 (328)
T PRK05707        147 SRL-------LP-TIKSRC--------QQQACPLPSNEESLQWLQQAL--PES-DERERIELLTLAGGSPLRALQLH  204 (328)
T ss_pred             hhC-------cH-HHHhhc--------eeeeCCCcCHHHHHHHHHHhc--ccC-ChHHHHHHHHHcCCCHHHHHHHH
Confidence            321       11 111110        126778889998877775321  112 23333456679999998776654

>KOG2228|consensus

Probab=97.32  E-value=0.0079  Score=58.11  Aligned_cols=149  Identities=19%  Similarity=0.248  Sum_probs=91.8

Q ss_pred             hhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCccccccCCcceeccCCCCCccc
Q psy3261          48 NCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLRWFAYPKEVSHSLTKEGMVD  125 (342)
Q Consensus        48 ~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~  125 (342)
                      ++-.+|-..+++ +.--+..+.++|.||+|||||+++.++..-+.++  +.++++..                   |.+.
T Consensus        31 ~~~~~l~~~lkq-t~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Ln-------------------g~~~   90 (408)
T KOG2228|consen   31 DEQKHLSELLKQ-TILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLN-------------------GELQ   90 (408)
T ss_pred             HHHHHHHHHHHH-HHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEEC-------------------ccch
Confidence            345566667766 4344678899999999999999999999986654  56666651                   1121


Q ss_pred             c-HHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCc
Q psy3261         126 L-NIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVC  204 (342)
Q Consensus       126 q-P~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~  204 (342)
                      . -..-..+-+++...|....+                                . .-.-++.+..++.-|++-....+.
T Consensus        91 ~dk~al~~I~rql~~e~~~~~k--------------------------------~-~gsfte~l~~lL~~L~~~~~~t~~  137 (408)
T KOG2228|consen   91 TDKIALKGITRQLALELNRIVK--------------------------------S-FGSFTENLSKLLEALKKGDETTSG  137 (408)
T ss_pred             hhHHHHHHHHHHHHHHHhhhhe--------------------------------e-ecccchhHHHHHHHHhcCCCCCCc
Confidence            1 01222222233222211111                                0 001123344455555553334578


Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRA  263 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~  263 (342)
                      ||++..|+|.-|.+.+-              =++...+.++....-.-.+|++.|++-.
T Consensus       138 ~ViFIldEfDlf~~h~r--------------QtllYnlfDisqs~r~Piciig~Ttrld  182 (408)
T KOG2228|consen  138 KVIFILDEFDLFAPHSR--------------QTLLYNLFDISQSARAPICIIGVTTRLD  182 (408)
T ss_pred             eEEEEeehhhccccchh--------------hHHHHHHHHHHhhcCCCeEEEEeecccc
Confidence            99999999955555444              6888899999887667788888888755

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.31  E-value=0.011  Score=61.73  Aligned_cols=113  Identities=8%  Similarity=0.003  Sum_probs=67.9

Q ss_pred             HHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCc
Q psy3261         190 VLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRR  269 (342)
Q Consensus       190 ~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~  269 (342)
                      .+++++......++++ ++.||++..+ ..                 .-...|++.+.....+-.+|++|++...     
T Consensus       105 el~~~~~~~P~~~~~K-VvIIDEah~L-t~-----------------~A~NALLK~LEEpp~~~~fIL~tte~~k-----  160 (584)
T PRK14952        105 ELRDRAFYAPAQSRYR-IFIVDEAHMV-TT-----------------AGFNALLKIVEEPPEHLIFIFATTEPEK-----  160 (584)
T ss_pred             HHHHHHHhhhhcCCce-EEEEECCCcC-CH-----------------HHHHHHHHHHhcCCCCeEEEEEeCChHh-----
Confidence            3444443322223555 5689998433 21                 2456788888877778888888865321     


Q ss_pred             cCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhh
Q psy3261         270 ESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       270 ~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~  337 (342)
                         ++..+..+ +.       .+++..++.+|+...+.+.... |.-.+++....+...++|++|....
T Consensus       161 ---ll~TI~SR-c~-------~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~GdlR~aln  218 (584)
T PRK14952        161 ---VLPTIRSR-TH-------HYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLS  218 (584)
T ss_pred             ---hHHHHHHh-ce-------EEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence               22222222 21       3788899999999888776554 5432343334455699999995543

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

Probab=97.31  E-value=0.00053  Score=56.13  Aligned_cols=38  Identities=18%  Similarity=0.280  Sum_probs=30.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .....++|+|++|||||+++.++.......+.-|++++
T Consensus        17 ~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   54 (151)
T cd00009          17 PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLN   54 (151)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEe
Confidence            35678999999999999999999888775566666553

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

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.29  E-value=0.0087  Score=60.95  Aligned_cols=100  Identities=12%  Similarity=0.057  Sum_probs=62.1

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .+-+|.||++..+- ..                 ....|++.+.....+.++|+||+....        ++..+..+   
T Consensus       117 ~~kVvIIDE~h~Lt-~~-----------------a~~~LLk~LE~p~~~vv~Ilattn~~k--------l~~~L~SR---  167 (472)
T PRK14962        117 KYKVYIIDEVHMLT-KE-----------------AFNALLKTLEEPPSHVVFVLATTNLEK--------VPPTIISR---  167 (472)
T ss_pred             CeEEEEEEChHHhH-HH-----------------HHHHHHHHHHhCCCcEEEEEEeCChHh--------hhHHHhcC---
Confidence            34578899995542 11                 235667777665555666777763211        23333222   


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhh
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~  337 (342)
                           +..+++.+++.+|....++..... |+--+++....+-..++|+.|.+..
T Consensus       168 -----~~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln  217 (472)
T PRK14962        168 -----CQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALT  217 (472)
T ss_pred             -----cEEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence                 124888999999999999887643 5432555555666689999986543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.28  E-value=0.0077  Score=60.97  Aligned_cols=49  Identities=12%  Similarity=0.079  Sum_probs=36.7

Q ss_pred             eeecCCCCHHHHHHHHHHHHhC-CC-cc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESK-KW-LQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~-~~-l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+.+..++.++...+++...+. |+ +. +++....+...++||+|.|..+|
T Consensus       269 ~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL  320 (450)
T PRK14087        269 SIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSV  320 (450)
T ss_pred             eeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHH
Confidence            3678899999999999877765 53 12 45444446668999999998877

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

Probab=97.27  E-value=0.0037  Score=62.94  Aligned_cols=118  Identities=13%  Similarity=0.242  Sum_probs=64.1

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhh---cC-CCCCeE-EEEEeCCCCCCCCCccCcchhHH
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLV---QS-DWNNGA-IVLALSPRANLPDRRESHLPLYM  277 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~---~~-~~~~G~-vv~AtS~~~~~~~~~~~~~p~~l  277 (342)
                      ..|.++.+|++.+++....  ......     +-.+.+.++.++   .+ +-..++ ||+||..-.        .++..+
T Consensus       275 ~~P~ILfIDEID~l~~kR~--~~~sgg-----~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d--------~LDpaL  339 (438)
T PTZ00361        275 NAPSIVFIDEIDAIGTKRY--DATSGG-----EKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIE--------SLDPAL  339 (438)
T ss_pred             CCCcEEeHHHHHHHhccCC--CCCCcc-----cHHHHHHHHHHHHHHhhhcccCCeEEEEecCChH--------HhhHHh
Confidence            4688999999988875421  111111     112223333333   22 223344 455543211        133344


Q ss_pred             hhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHH-HhhCCCHHHHhhhcc
Q psy3261         278 LKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIA-FLTKRVPQKMYEFCS  340 (342)
Q Consensus       278 lg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~-~lSgGNP~~l~~lc~  340 (342)
                      ++...|+.     .|+++..+.++-..+++.|...--+..+....++- ...|-++.++..+|.
T Consensus       340 lRpGRfd~-----~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~  398 (438)
T PTZ00361        340 IRPGRIDR-----KIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICT  398 (438)
T ss_pred             ccCCeeEE-----EEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHH
Confidence            43222321     48999999999999999887654442121223333 466889999999884

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.27  E-value=0.011  Score=61.17  Aligned_cols=116  Identities=11%  Similarity=0.232  Sum_probs=67.9

Q ss_pred             HHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCC
Q psy3261         189 DVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDR  268 (342)
Q Consensus       189 ~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~  268 (342)
                      ..+++++......++ .-++.||+...+    +              -.-...|++++..-.....+|++|+....    
T Consensus       105 r~ii~~~~~~p~~g~-~kViIIDEa~~l----s--------------~~a~naLLK~LEepp~~v~fIL~Ttd~~k----  161 (546)
T PRK14957        105 KEILDNIQYMPSQGR-YKVYLIDEVHML----S--------------KQSFNALLKTLEEPPEYVKFILATTDYHK----  161 (546)
T ss_pred             HHHHHHHHhhhhcCC-cEEEEEechhhc----c--------------HHHHHHHHHHHhcCCCCceEEEEECChhh----
Confidence            344445443221233 457889998333    1              23456888888765667777888754321    


Q ss_pred             ccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         269 RESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       269 ~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                          ++.-+..+ .       ..+++..++.+|+...+..-.. .|+-..++....+-..|+|++|.+..++
T Consensus       162 ----il~tI~SR-c-------~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~GdlR~alnlL  221 (546)
T PRK14957        162 ----IPVTILSR-C-------IQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLL  221 (546)
T ss_pred             ----hhhhHHHh-e-------eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                12122211 1       1378999999999977766433 3543244444556669999999665543

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.27  E-value=0.0059  Score=63.00  Aligned_cols=119  Identities=10%  Similarity=0.137  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++++......+++ -++.||+...+ .                 -.-...|++.+.....+..+|++|+.... 
T Consensus       102 d~ir~l~~~~~~~p~~~~~-kVvIIDEad~l-s-----------------~~a~naLLK~LEepp~~~~fIL~t~d~~k-  161 (527)
T PRK14969        102 DAMRELLDNAQYAPTRGRF-KVYIIDEVHML-S-----------------KSAFNAMLKTLEEPPEHVKFILATTDPQK-  161 (527)
T ss_pred             HHHHHHHHHHhhCcccCCc-eEEEEcCcccC-C-----------------HHHHHHHHHHHhCCCCCEEEEEEeCChhh-
Confidence            3344444444322212333 46889998433 1                 12345788888776667778888754321 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHH-HHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNL-YESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~y-y~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                             ++.-+..+ .       ..+++..++.+|+...+.. ....|+-..++....+-..|+|+++....+|
T Consensus       162 -------il~tI~SR-c-------~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        162 -------IPVTVLSR-C-------LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             -------CchhHHHH-H-------HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                   11112211 1       1268888999999977754 4445643233333445569999999877665

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.24  E-value=0.014  Score=59.56  Aligned_cols=116  Identities=9%  Similarity=0.075  Sum_probs=67.4

Q ss_pred             HHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCC
Q psy3261         189 DVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDR  268 (342)
Q Consensus       189 ~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~  268 (342)
                      ..+.+.+......++ +-++.||++..+- .                 .....|++++.......++|++|+....    
T Consensus       105 r~I~~~~~~~P~~~~-~KVvIIDEad~Lt-~-----------------~a~naLLk~LEepp~~~v~Il~tt~~~k----  161 (486)
T PRK14953        105 RALRDAVSYTPIKGK-YKVYIIDEAHMLT-K-----------------EAFNALLKTLEEPPPRTIFILCTTEYDK----  161 (486)
T ss_pred             HHHHHHHHhCcccCC-eeEEEEEChhhcC-H-----------------HHHHHHHHHHhcCCCCeEEEEEECCHHH----
Confidence            344444443321223 4477899985331 1                 2245677888766667777777754221    


Q ss_pred             ccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         269 RESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       269 ~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                          ++..+..+ +       ..+.++.++.+|+...+...... |+-..++....+-..++||++.+..++
T Consensus       162 ----l~~tI~SR-c-------~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        162 ----IPPTILSR-C-------QRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             ----HHHHHHHh-c-------eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                22222222 1       13788899999999888765544 543233334445569999999766554

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.24  E-value=0.0006  Score=62.14  Aligned_cols=51  Identities=25%  Similarity=0.241  Sum_probs=38.8

Q ss_pred             HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        52 el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +++..++++.........++|+|++|||||.++..+...+...|+-+++|.
T Consensus        27 ~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~   77 (227)
T PRK08903         27 ELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLD   77 (227)
T ss_pred             HHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            345555553333345678999999999999999999988888888877764

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.21  E-value=0.0085  Score=62.69  Aligned_cols=116  Identities=8%  Similarity=0.103  Sum_probs=69.3

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++.+......++++| |.||+...+ .                 -.-...|++.+..-.....+|+++++...   
T Consensus       117 IReIie~~~~~P~~a~~KV-vIIDEad~L-s-----------------~~a~naLLKtLEePp~~~~fIl~tte~~k---  174 (598)
T PRK09111        117 IREIIESVRYRPVSARYKV-YIIDEVHML-S-----------------TAAFNALLKTLEEPPPHVKFIFATTEIRK---  174 (598)
T ss_pred             HHHHHHHHHhchhcCCcEE-EEEEChHhC-C-----------------HHHHHHHHHHHHhCCCCeEEEEEeCChhh---
Confidence            3444444433222235555 789997333 1                 12357888888776677777888754321   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                           ++.-+..+ .       ..+++..++.+|+...+.-.... |.-.+++....+...++|+++.+..+
T Consensus       175 -----ll~tI~SR-c-------q~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~  233 (598)
T PRK09111        175 -----VPVTVLSR-C-------QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSL  233 (598)
T ss_pred             -----hhHHHHhh-e-------eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                 22122211 1       13789999999999888665443 43224555555677999999987654

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.20  E-value=0.00066  Score=62.65  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=31.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      ....++|+|++|||||.++..+.+.+..+|.=|+|++-
T Consensus        44 ~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~   81 (235)
T PRK08084         44 HSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPL   81 (235)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEH
Confidence            34689999999999999999888888877877777643

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.18  E-value=0.014  Score=61.08  Aligned_cols=100  Identities=9%  Similarity=0.055  Sum_probs=59.8

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      .-+|.||++..+ ..                 .-...|++++.....+..+|++++....        +...+. ...  
T Consensus       121 ~kVvIIDEa~~L-~~-----------------~a~naLLk~LEepp~~tv~Il~t~~~~k--------ll~tI~-SR~--  171 (585)
T PRK14950        121 YKVYIIDEVHML-ST-----------------AAFNALLKTLEEPPPHAIFILATTEVHK--------VPATIL-SRC--  171 (585)
T ss_pred             eEEEEEeChHhC-CH-----------------HHHHHHHHHHhcCCCCeEEEEEeCChhh--------hhHHHH-hcc--
Confidence            346789998433 11                 2345678888766566677776643221        111111 111  


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                           ..+++..++..|+...+...... |+--+++....+-.+++||++.+...
T Consensus       172 -----~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~Gdlr~al~~  221 (585)
T PRK14950        172 -----QRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENL  221 (585)
T ss_pred             -----ceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                 13778889999999888766544 44214444555666999999977653

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.18  E-value=0.0011  Score=64.48  Aligned_cols=92  Identities=15%  Similarity=0.265  Sum_probs=61.5

Q ss_pred             EeCHHHHHHhhhcCCCChhhHHh-hhhcCCc----------eEEechhHHHHHHHHHhcc-CCCCCCCeEEEEccCCCcH
Q psy3261          13 TLPDEVRSAIFELGGITRVFNEQ-TQIFNES----------SILIRNCMLELVGYLKSMT-NFDRPSPRFVLYGEHGVGK   80 (342)
Q Consensus        13 ~~~~~~~~~l~~~g~l~~~~~~~-~~~~~~~----------~~lvR~~t~el~~~l~~~~-~~~~~~~r~vL~G~~GsGK   80 (342)
                      .+-...++.++..-++++.+.+. |+.|.--          ..--|+...++++...+++ ++......++|+|+.|+||
T Consensus       117 C~~q~~i~~~~~~S~i~~~~~~~~F~nf~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~f~~~f~~~~~~Lll~G~~GtGK  196 (329)
T PRK06835        117 CYKQKLINLYYKQSNLKEILKEENFSNFNLNYYSDEKDDDEPLSPRKNMEKILEKCKNFIENFDKNNENLLFYGNTGTGK  196 (329)
T ss_pred             chhHHHHHHHHHHcCCchHHHhCChhhCCccccCccccccCCCCHHHHHHHHHHHHHHHHHHHhccCCcEEEECCCCCcH
Confidence            34455677777777899877654 7777522          1134555445554333211 1223447799999999999


Q ss_pred             HHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          81 SMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        81 S~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      |.++.-+...+..+|.-|+|++..
T Consensus       197 ThLa~aIa~~l~~~g~~V~y~t~~  220 (329)
T PRK06835        197 TFLSNCIAKELLDRGKSVIYRTAD  220 (329)
T ss_pred             HHHHHHHHHHHHHCCCeEEEEEHH
Confidence            998888888888889989888654

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.015  Score=61.17  Aligned_cols=118  Identities=11%  Similarity=0.094  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      +.+..+++.+......++.+ +|.||++..+ .                 -.....|++++.....+.++|++|+...  
T Consensus       104 d~IReii~~a~~~p~~~~~K-ViIIDEad~L-t-----------------~~a~naLLK~LEePp~~tvfIL~t~~~~--  162 (620)
T PRK14948        104 DNIRELIERAQFAPVQARWK-VYVIDECHML-S-----------------TAAFNALLKTLEEPPPRVVFVLATTDPQ--  162 (620)
T ss_pred             HHHHHHHHHHhhChhcCCce-EEEEECcccc-C-----------------HHHHHHHHHHHhcCCcCeEEEEEeCChh--
Confidence            34444554443221123444 5679997444 1                 1345678888887666777777775321  


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                          . -+| .+..+-        ..+++..++.+|+...+...... |.-..++....+-..++|+++.+..+
T Consensus       163 ----~-llp-TIrSRc--------~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G~lr~A~~l  222 (620)
T PRK14948        163 ----R-VLP-TIISRC--------QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDAESL  222 (620)
T ss_pred             ----h-hhH-HHHhhe--------eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                1 112 222121        13678889999998887766554 43213444445666999999977654

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.12  E-value=0.021  Score=59.44  Aligned_cols=116  Identities=13%  Similarity=0.119  Sum_probs=68.2

Q ss_pred             HHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCC
Q psy3261         189 DVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDR  268 (342)
Q Consensus       189 ~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~  268 (342)
                      ..+++++......++++| +.||++..+ ..                 .....|++.+...+.+..+|++++.-..    
T Consensus       105 r~l~e~~~~~p~~~~~KV-vIIDEa~~L-s~-----------------~a~naLLK~LEepp~~~vfI~~tte~~k----  161 (563)
T PRK06647        105 RQIKEEIMFPPASSRYRV-YIIDEVHML-SN-----------------SAFNALLKTIEEPPPYIVFIFATTEVHK----  161 (563)
T ss_pred             HHHHHHHHhchhcCCCEE-EEEEChhhc-CH-----------------HHHHHHHHhhccCCCCEEEEEecCChHH----
Confidence            344445443322345565 559997433 11                 2356788888766667777887754221    


Q ss_pred             ccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         269 RESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       269 ~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                          ++..+..+ .       ..+++..++.+|....+.... ..|+-.+++....+-..++|+++.+..++
T Consensus       162 ----L~~tI~SR-c-------~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~GdlR~alslL  221 (563)
T PRK06647        162 ----LPATIKSR-C-------QHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLF  221 (563)
T ss_pred             ----hHHHHHHh-c-------eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                22223222 1       126788899999988886654 34433245445556679999999776543

>PF13245 AAA_19: Part of AAA domain

Probab=97.11  E-value=0.00082  Score=51.15  Aligned_cols=35  Identities=26%  Similarity=0.375  Sum_probs=28.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC----CeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN----NYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~----gwiVl~v  101 (342)
                      ...++|.|++|||||+++.+++.+...+    +.=|+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~   48 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVL   48 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEE
Confidence            4567779999999999999999988854    5555555

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.11  E-value=0.02  Score=56.97  Aligned_cols=113  Identities=11%  Similarity=0.096  Sum_probs=65.1

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++++...+..+.++ ++.||++..+-.                  .-...|++.+.....+..+|++|+....   
T Consensus       102 iR~l~~~~~~~p~~~~~k-ViiIDead~m~~------------------~aanaLLk~LEep~~~~~fIL~a~~~~~---  159 (394)
T PRK07940        102 VRELVTIAARRPSTGRWR-IVVIEDADRLTE------------------RAANALLKAVEEPPPRTVWLLCAPSPED---  159 (394)
T ss_pred             HHHHHHHHHhCcccCCcE-EEEEechhhcCH------------------HHHHHHHHHhhcCCCCCeEEEEECChHH---
Confidence            445555554332223444 566799966622                  2346688888766667777777665321   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ++.-+..+        ...+.++..+.+|+...+.-  ..| + .++....+-.+|+|+|....+++
T Consensus       160 -----llpTIrSR--------c~~i~f~~~~~~~i~~~L~~--~~~-~-~~~~a~~la~~s~G~~~~A~~l~  214 (394)
T PRK07940        160 -----VLPTIRSR--------CRHVALRTPSVEAVAEVLVR--RDG-V-DPETARRAARASQGHIGRARRLA  214 (394)
T ss_pred             -----ChHHHHhh--------CeEEECCCCCHHHHHHHHHH--hcC-C-CHHHHHHHHHHcCCCHHHHHHHh
Confidence                 11112111        12478888999998777751  224 3 24333345569999998776654

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.10  E-value=0.009  Score=59.43  Aligned_cols=84  Identities=7%  Similarity=0.030  Sum_probs=50.7

Q ss_pred             HHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccC
Q psy3261         239 TRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQT  317 (342)
Q Consensus       239 ~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~  317 (342)
                      ...|++++........+|++++....        +...+. ..+.       .+++..++.+|+...+..... .|.--+
T Consensus       144 ~~~LLk~LEep~~~t~~Il~t~~~~k--------l~~tl~-sR~~-------~v~f~~l~~~ei~~~l~~~~~~~g~~i~  207 (397)
T PRK14955        144 FNAFLKTLEEPPPHAIFIFATTELHK--------IPATIA-SRCQ-------RFNFKRIPLEEIQQQLQGICEAEGISVD  207 (397)
T ss_pred             HHHHHHHHhcCCCCeEEEEEeCChHH--------hHHHHH-HHHH-------HhhcCCCCHHHHHHHHHHHHHHcCCCCC
Confidence            45677887765556667777653211        111121 1111       267888999999988765543 343214


Q ss_pred             cchHHHHHHhhCCCHHHHhhh
Q psy3261         318 SEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       318 e~~~~el~~lSgGNP~~l~~l  338 (342)
                      ++....+-.+|||+++.+...
T Consensus       208 ~~al~~l~~~s~g~lr~a~~~  228 (397)
T PRK14955        208 ADALQLIGRKAQGSMRDAQSI  228 (397)
T ss_pred             HHHHHHHHHHcCCCHHHHHHH
Confidence            555556777999999976654

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

Probab=97.06  E-value=0.0057  Score=55.41  Aligned_cols=39  Identities=21%  Similarity=0.118  Sum_probs=33.4

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC------eEEEEeC
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENN------YLLVHIP  102 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g------wiVl~vP  102 (342)
                      -.+..-+.|+|++|||||+++.|++..+...+      .-|+||.
T Consensus        16 ~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~   60 (226)
T cd01393          16 IPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID   60 (226)
T ss_pred             CcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEe
Confidence            35678899999999999999999999887776      7788874

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.

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=97.02  E-value=0.0052  Score=61.31  Aligned_cols=243  Identities=19%  Similarity=0.189  Sum_probs=124.4

Q ss_pred             Eech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC-CccccccCC--------cce
Q psy3261          45 LIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP-WVLRWFAYP--------KEV  114 (342)
Q Consensus        45 lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP-~~~~~~~~~--------~~~  114 (342)
                      +=|+ ..-.|.+.|+..++  ..+.--++.|+-|||||.+|..+...|+++|++|.+|- ++....+++        .++
T Consensus        28 VGr~~e~~~l~~~l~~v~~--G~s~~kfi~G~YGsGKTf~l~~i~~~A~~~~fvvs~v~ls~e~~lh~~~g~~~~~Yr~l  105 (416)
T PF10923_consen   28 VGREREIEALDRDLDRVAD--GGSSFKFIRGEYGSGKTFFLRLIRERALEKGFVVSEVDLSPERPLHGTGGQLEALYREL  105 (416)
T ss_pred             echHHHHHHHHHHHHHHhC--CCCeEEEEEeCCCCcHHHHHHHHHHHHHHcCCEEEEEecCCCcccccccccHHHHHHHH
Confidence            4455 45566667776332  33444556699999999999999999999999999982 334444421        111


Q ss_pred             eccCC---C-CCccccHHHHHHHHHHHHHhCcccc---------CC--CCc----c-ccc---ce---------------
Q psy3261         115 SHSLT---K-EGMVDLNIDAAMWLRHFQKQNTKWL---------ED--PRL----T-TSQ---EY---------------  156 (342)
Q Consensus       115 ~~s~~---~-~~~~~qP~~a~~~L~~~~~~N~~~L---------~~--~~l----~-~s~---~~---------------  156 (342)
                      ..+-.   . +| =-.+....+|+..+.....+.-         +.  ..|    . +++   .+               
T Consensus       106 ~~nL~t~~~p~G-~al~~ild~wi~~~~~~~~~~~~~~~~~~~~~~v~~~I~~~L~~l~~~~~~~~Fa~~l~~Y~~a~~~  184 (416)
T PF10923_consen  106 MRNLSTKTKPEG-GALRSILDRWIYNLEEEVAAEGGIEPDEGFEEAVEELIEERLASLSELVHGPDFAAALRAYYRAYVE  184 (416)
T ss_pred             HHhcCCCCCCCc-hHHHHHHHHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHHHHHHcccCChhHHHHHHHHHHHHhc
Confidence            11110   1 11 0123344555555532111100         00  000    0 010   11               


Q ss_pred             ----------ecCCCCCCCCCCCHHHHH-Hhhcccc---cchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCc
Q psy3261         157 ----------VWSPREKSEANIPLAALI-EHGITRV---KYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTN  222 (342)
Q Consensus       157 ----------~~~~~e~~~~g~tL~dlv-~~gi~~~---~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~  222 (342)
                                .|-..    +..+-.+.- +.|+...   ..+.+-+..+.+=++. .  +-.-++|.+|++=.++.....
T Consensus       185 gd~~~~~~~l~WL~G----e~~~kt~ar~~lGV~~~Idd~~~~~~Lk~L~~~lr~-a--Gy~GLlI~lDE~e~l~kl~~~  257 (416)
T PF10923_consen  185 GDEELADAALRWLRG----EYNTKTEARRALGVRGIIDDDNAYDFLKGLARFLRD-A--GYKGLLILLDELENLYKLRND  257 (416)
T ss_pred             CCHHHHHHHHHHHcC----CCccHHHHHHHcCCCeeeCchHHHHHHHHHHHHHHH-c--CCCceEEEEechHHHHhcCCh
Confidence                      12222    223334444 3566533   2233334434433433 2  566799999999777766431


Q ss_pred             C-CCCCCCcccCCcc-chHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCcc---Ccchh-HHhhhcCC---CCCCCcc-ee
Q psy3261         223 C-KPEDKSKVLPSRV-TLTRSVINLVQSDWNNGAIVLALSPRANLPDRRE---SHLPL-YMLKKAGF---ESIDPFV-PI  292 (342)
Q Consensus       223 y-~~~~~~~I~~~~l-~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~---~~~p~-~llg~~g~---~~~dP~~-~i  292 (342)
                      - |+        ..+ .|=+++-++.+|..++-.+|.+-+... .-+++.   +|-|. ..+....+   ...||.. .|
T Consensus       258 ~~R~--------~~ye~lr~lidd~~~G~~~gL~~~~~gTPef-~eD~rrGv~sY~AL~~RL~~~~~~~~~~~n~~~pvI  328 (416)
T PF10923_consen  258 QARE--------KNYEALRQLIDDIDQGRAPGLYFVFAGTPEF-FEDGRRGVYSYEALAQRLAEEFFADDGFDNLRAPVI  328 (416)
T ss_pred             HHHH--------HHHHHHHHHHHHHhcCCCCceEEEEeeCHHH-hhCccccccccHHHHHHHhccccccccccCccCcee
Confidence            2 11        123 233344455568888888877766543 212222   33221 11221111   1345544 47


Q ss_pred             ecCCCCHHHHHHHH
Q psy3261         293 HVPELNDEEFHNLL  306 (342)
Q Consensus       293 ~v~~~s~~E~~~ll  306 (342)
                      ++.+|+.+|+..++
T Consensus       329 rL~~l~~eel~~l~  342 (416)
T PF10923_consen  329 RLQPLTPEELLELL  342 (416)
T ss_pred             cCCCCCHHHHHHHH
Confidence            89999999998776

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>KOG0731|consensus

Probab=97.01  E-value=0.016  Score=61.56  Aligned_cols=124  Identities=18%  Similarity=0.223  Sum_probs=77.0

Q ss_pred             CCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         202 GVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       202 ~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ...|.+|.||++.++-..-.  ..-.+..=.-.+.++-.++.++..-....|+||.|.+...   +-    +-.+|++.-
T Consensus       401 ~~aP~iifideida~~~~r~--G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~---d~----ld~allrpG  471 (774)
T KOG0731|consen  401 KNAPSIIFIDEIDAVGRKRG--GKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRP---DI----LDPALLRPG  471 (774)
T ss_pred             ccCCeEEEeccccccccccc--ccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCc---cc----cCHHhcCCC
Confidence            37899999999977654421  0011223344567999999999987777888888877643   21    123455443


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcc-hHHHHHHhhCC-CHHHHhhhc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSE-GREEIAFLTKR-VPQKMYEFC  339 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~-~~~el~~lSgG-NP~~l~~lc  339 (342)
                      .|+.     .|.++-=+..+=+++++++.+..-+..|+ .-..+-.+|-| .+.+|..+|
T Consensus       472 Rfdr-----~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~  526 (774)
T KOG0731|consen  472 RFDR-----QIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLC  526 (774)
T ss_pred             cccc-----ceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhh
Confidence            3542     26666667788889999998887773111 11224444444 456676666

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.98  E-value=0.0037  Score=63.26  Aligned_cols=117  Identities=21%  Similarity=0.235  Sum_probs=79.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccc-cCCcceeccCCCCCccccHHHHHHHHHHHHHhCcc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWF-AYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTK  143 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~-~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~  143 (342)
                      .+.-=++++||.||||||+|..++.+....+--|+.|-++-++. .+..-+.-++ +-|+     .-+..|+.|+...-+
T Consensus       256 ~p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~~~~gI~Q~qVN~-k~gl-----tfa~~LRa~LRqDPD  329 (500)
T COG2804         256 RPQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEYQLPGINQVQVNP-KIGL-----TFARALRAILRQDPD  329 (500)
T ss_pred             CCCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeeeecCCcceeeccc-ccCC-----CHHHHHHHHhccCCC
Confidence            46778899999999999999999999998777799997777763 3444444443 3333     235667888554444


Q ss_pred             ccCCCCc------------ccccceecCCCCCCCCCCCHHHHHHhhcccccchhHH
Q psy3261         144 WLEDPRL------------TTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDV  187 (342)
Q Consensus       144 ~L~~~~l------------~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~  187 (342)
                      ++==+.|            .++...+++--....+..++..|.++|+..-..+...
T Consensus       330 vImVGEIRD~ETAeiavqAalTGHLVlSTlHtnda~~ai~RL~~mGv~~~~l~s~l  385 (500)
T COG2804         330 VIMVGEIRDLETAEIAVQAALTGHLVLSTLHTNDAPGAITRLLEMGVEPYLLASSL  385 (500)
T ss_pred             eEEEeccCCHHHHHHHHHHHhcCCeEeeecccCchHHHHHHHHHcCCCHHHHHHHH
Confidence            3310001            2355566665555567789999999999865555543

>PRK12377 putative replication protein; Provisional

Probab=96.98  E-value=0.0016  Score=60.79  Aligned_cols=38  Identities=16%  Similarity=0.167  Sum_probs=33.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ...++|+|++|||||.++.-+...+.++|.-|++++-.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~  138 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVP  138 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHH
Confidence            46799999999999999999999999999888877543

>PRK08116 hypothetical protein; Validated

Probab=96.95  E-value=0.0024  Score=60.22  Aligned_cols=79  Identities=13%  Similarity=0.199  Sum_probs=48.7

Q ss_pred             HHHhhhcCCCChhhHH-hhhhcCCceEEechhH---HHHH-HHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          19 RSAIFELGGITRVFNE-QTQIFNESSILIRNCM---LELV-GYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        19 ~~~l~~~g~l~~~~~~-~~~~~~~~~~lvR~~t---~el~-~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ++.++...++|+++.+ .|+.|..     .+..   ...+ ++++++......+..++|+|+.|||||.++..+...+.+
T Consensus        66 ~~~l~~~s~i~~~~~~~tFdnf~~-----~~~~~~a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThLa~aia~~l~~  140 (268)
T PRK08116         66 IERLKSNSLLDEKFRNSTFENFLF-----DKGSEKAYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYLAACIANELIE  140 (268)
T ss_pred             HHHHHHhcCCCHHHHhcchhcccC-----ChHHHHHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4455656567766543 3555542     1222   2222 233332222234567999999999999999998888888


Q ss_pred             CCeEEEEeC
Q psy3261          94 NNYLLVHIP  102 (342)
Q Consensus        94 ~gwiVl~vP  102 (342)
                      +|--|++++
T Consensus       141 ~~~~v~~~~  149 (268)
T PRK08116        141 KGVPVIFVN  149 (268)
T ss_pred             cCCeEEEEE
Confidence            787777764

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

Probab=96.94  E-value=0.05  Score=50.46  Aligned_cols=98  Identities=18%  Similarity=0.241  Sum_probs=60.9

Q ss_pred             HHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC---CCCeEEEEEeCCCCCCC
Q psy3261         190 VLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD---WNNGAIVLALSPRANLP  266 (342)
Q Consensus       190 ~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~---~~~G~vv~AtS~~~~~~  266 (342)
                      .++++|+..    ..+++|.+||+ +|=.-.+                --+.++.++.|.   .+.-+++.|||.+.++ 
T Consensus       129 ~l~~~Lr~~----~~kFIlFcDDL-SFe~gd~----------------~yK~LKs~LeG~ve~rP~NVl~YATSNRRHL-  186 (287)
T COG2607         129 DLVELLRAR----PEKFILFCDDL-SFEEGDD----------------AYKALKSALEGGVEGRPANVLFYATSNRRHL-  186 (287)
T ss_pred             HHHHHHhcC----CceEEEEecCC-CCCCCch----------------HHHHHHHHhcCCcccCCCeEEEEEecCCccc-
Confidence            355678764    68999999999 4433222                235677888775   3556788898876532 


Q ss_pred             CCccCcchhHHhhhcCCC-CCCC-------------cc-eeecCCCCHHHHHHHHHHHHhCCCc
Q psy3261         267 DRRESHLPLYMLKKAGFE-SIDP-------------FV-PIHVPELNDEEFHNLLNLYESKKWL  315 (342)
Q Consensus       267 ~~~~~~~p~~llg~~g~~-~~dP-------------~~-~i~v~~~s~~E~~~ll~yy~~~~~l  315 (342)
                            +|.......++. .+.|             |- -+.....+.+|.-.+++.|.+.=-|
T Consensus       187 ------l~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l  244 (287)
T COG2607         187 ------LPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGL  244 (287)
T ss_pred             ------ccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCC
Confidence                  222222222221 2222             21 2556689999999999999876544

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

Probab=96.94  E-value=0.074  Score=50.89  Aligned_cols=228  Identities=14%  Similarity=0.137  Sum_probs=117.5

Q ss_pred             HHhhhhcCCceEEechhHHHHHHHHHhccCC--CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccC
Q psy3261          33 NEQTQIFNESSILIRNCMLELVGYLKSMTNF--DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAY  110 (342)
Q Consensus        33 ~~~~~~~~~~~~lvR~~t~el~~~l~~~~~~--~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~  110 (342)
                      ..-.....++.++-=..+.++++.|+.....  ...-..++|+|+.|.|||+++.+...   ...      |. .+.-..
T Consensus        25 ~eRI~~i~~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~---~hp------~~-~d~~~~   94 (302)
T PF05621_consen   25 EERIAYIRADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRR---LHP------PQ-SDEDAE   94 (302)
T ss_pred             HHHHHHHhcCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHH---HCC------CC-CCCCCc
Confidence            3344566678888888888999998873332  23446799999999999998866553   211      10 010000


Q ss_pred             CcceeccCCCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHH
Q psy3261         111 PKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDV  190 (342)
Q Consensus       111 ~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~  190 (342)
                      ...+.+-. -+..=+...+-..+|..+           ..+.            ....+..++-...+           .
T Consensus        95 ~~PVv~vq-~P~~p~~~~~Y~~IL~~l-----------gaP~------------~~~~~~~~~~~~~~-----------~  139 (302)
T PF05621_consen   95 RIPVVYVQ-MPPEPDERRFYSAILEAL-----------GAPY------------RPRDRVAKLEQQVL-----------R  139 (302)
T ss_pred             cccEEEEe-cCCCCChHHHHHHHHHHh-----------Cccc------------CCCCCHHHHHHHHH-----------H
Confidence            00000000 011112222334444444           2321            11122222221111           2


Q ss_pred             HHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCC-CCCCCc
Q psy3261         191 LFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRA-NLPDRR  269 (342)
Q Consensus       191 l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~-~~~~~~  269 (342)
                      +++++       + +=++.||+++.+..-+.  +          +=.-+-.++++++++++=..|.+-|.... +..+  
T Consensus       140 llr~~-------~-vrmLIIDE~H~lLaGs~--~----------~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~--  197 (302)
T PF05621_consen  140 LLRRL-------G-VRMLIIDEFHNLLAGSY--R----------KQREFLNALKFLGNELQIPIVGVGTREAYRALRT--  197 (302)
T ss_pred             HHHHc-------C-CcEEEeechHHHhcccH--H----------HHHHHHHHHHHHhhccCCCeEEeccHHHHHHhcc--
Confidence            33322       2 23677999988766542  1          12333444555567776666544443221 0000  


Q ss_pred             cCcchhHHhhhcCCCCCCCcceeecCCCC-HHHHHHHHHHHHhCCCcc------CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         270 ESHLPLYMLKKAGFESIDPFVPIHVPELN-DEEFHNLLNLYESKKWLQ------TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       270 ~~~~p~~llg~~g~~~~dP~~~i~v~~~s-~~E~~~ll~yy~~~~~l~------~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                         . .++..+  |      .|+.+++.. .+||+.++.-+...=-|+      .++-...++-+|+|+-.++.++.
T Consensus       198 ---D-~QLa~R--F------~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~ll  262 (302)
T PF05621_consen  198 ---D-PQLASR--F------EPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSRLL  262 (302)
T ss_pred             ---C-HHHHhc--c------CCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHHHH
Confidence               1 123333  3      345555332 458999998887766666      22223457779999999998864

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

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.92  E-value=0.013  Score=63.82  Aligned_cols=95  Identities=9%  Similarity=0.069  Sum_probs=53.2

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++|++..    ..++++.||++..+.+... -.    ..     ......|+.++...  .-.+|+||+...-  .
T Consensus       268 lk~ii~e~~~~----~~~~ILfIDEih~l~~~g~-~~----~~-----~d~~n~Lkp~l~~G--~l~~IgaTT~~e~--~  329 (852)
T TIGR03345       268 LKSVIDEVKAS----PQPIILFIDEAHTLIGAGG-QA----GQ-----GDAANLLKPALARG--ELRTIAATTWAEY--K  329 (852)
T ss_pred             HHHHHHHHHhc----CCCeEEEEeChHHhccCCC-cc----cc-----ccHHHHhhHHhhCC--CeEEEEecCHHHH--h
Confidence            44566677642    4689999999988876532 10    01     12334455555421  2346888775321  1


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHH
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLY  309 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy  309 (342)
                      +. ......+.++  |      .+|.|+..|.+|...++.-+
T Consensus       330 ~~-~~~d~AL~rR--f------~~i~v~eps~~~~~~iL~~~  362 (852)
T TIGR03345       330 KY-FEKDPALTRR--F------QVVKVEEPDEETAIRMLRGL  362 (852)
T ss_pred             hh-hhccHHHHHh--C------eEEEeCCCCHHHHHHHHHHH
Confidence            00 0111233332  3      35999999999988886433

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.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=96.89  E-value=0.001  Score=58.37  Aligned_cols=30  Identities=20%  Similarity=0.340  Sum_probs=25.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      +++|||++|+||||++..++..+..+|.-|
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l~~~~~~v   30 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEELKKKGLPV   30 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHHHHTCGGE
T ss_pred             CEEEECcCCCCHHHHHHHHHHHhhccCCcc
Confidence            689999999999999999999998765443

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.

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=96.88  E-value=0.0048  Score=55.25  Aligned_cols=69  Identities=17%  Similarity=0.132  Sum_probs=41.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh----CCeEEEEe-CCccccccCCcceeccCCCC--CccccHHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE----NNYLLVHI-PWVLRWFAYPKEVSHSLTKE--GMVDLNIDAAMWLRHFQK  139 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~----~gwiVl~v-P~~~~~~~~~~~~~~s~~~~--~~~~qP~~a~~~L~~~~~  139 (342)
                      ...+++.|..|||||++|..++..+..    .++-|.-| |...+|..-    ...+...  -.-+.+..+.++|+.+..
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~l~~~~~p~~~~l~iiD~k~~~l~~~----~~~~~~~~~~~~~~~~~~~~~l~~l~~  113 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLSLALTYSPDDVQLYIIDPKGSDLAPL----ADLPHVAAVAVATDPEEILRLLEELVE  113 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSSCCGGG----TT-TTBSS-S-B-SHHHHHHHHHHHHH
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHHHhcCCccEEEEEcCCccccchh----hhhhhhccccccccHHHHHHHHHHHHH
Confidence            458999999999999999998888777    45444433 443333222    1111111  145688899999988843

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>PF13173 AAA_14: AAA domain

Probab=96.88  E-value=0.0013  Score=54.57  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=22.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .-++|+|+||||||+++.|++..-.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~   27 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL   27 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc
Confidence            4689999999999999999987655

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.88  E-value=0.077  Score=54.84  Aligned_cols=101  Identities=11%  Similarity=0.077  Sum_probs=64.3

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      .-+|.||+...+    +              -....+|++.+.....+..+|++++....        ++..+.-+ .  
T Consensus       118 ~KVvIIDEad~L----t--------------~~A~NALLK~LEEpp~~t~FIL~ttd~~k--------L~~tI~SR-c--  168 (535)
T PRK08451        118 FKIFIIDEVHML----T--------------KEAFNALLKTLEEPPSYVKFILATTDPLK--------LPATILSR-T--  168 (535)
T ss_pred             eEEEEEECcccC----C--------------HHHHHHHHHHHhhcCCceEEEEEECChhh--------CchHHHhh-c--
Confidence            346689998333    1              23356788888776677777777743221        22222222 1  


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ..+++..++.+++...+..-. ..|+-.+++....+-..++|++|.+..+|
T Consensus       169 -----~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlL  219 (535)
T PRK08451        169 -----QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLL  219 (535)
T ss_pred             -----eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence                 137889999999988886654 44554245445556679999999887765

>PRK08181 transposase; Validated

Probab=96.86  E-value=0.0023  Score=60.37  Aligned_cols=37  Identities=22%  Similarity=0.246  Sum_probs=32.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ....++|+|++|||||.++.-+...|.++|+-|+|++
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~  141 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTR  141 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeee
Confidence            3556999999999999999999999999999998885

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.85  E-value=0.042  Score=55.70  Aligned_cols=101  Identities=13%  Similarity=0.114  Sum_probs=61.4

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .+-+|.||+...+-.                  .....|++++.....+..+|+++++...        +...+..+ ..
T Consensus       121 ~~kvvIIdead~lt~------------------~~~n~LLk~lEep~~~~~~Il~t~~~~k--------l~~tI~sR-c~  173 (451)
T PRK06305        121 RYKIYIIDEVHMLTK------------------EAFNSLLKTLEEPPQHVKFFLATTEIHK--------IPGTILSR-CQ  173 (451)
T ss_pred             CCEEEEEecHHhhCH------------------HHHHHHHHHhhcCCCCceEEEEeCChHh--------cchHHHHh-ce
Confidence            344678999844421                  1246788888765556667777643221        11112211 11


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHH-HhCCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLY-ESKKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy-~~~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                             .+++..++.+|+...+.-. ...|+-..++....+-..++||.+.+..+
T Consensus       174 -------~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~  222 (451)
T PRK06305        174 -------KMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESL  222 (451)
T ss_pred             -------EEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence                   3889999999999877655 44465324545556777999999976554

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.81  E-value=0.095  Score=50.83  Aligned_cols=114  Identities=12%  Similarity=0.164  Sum_probs=63.6

Q ss_pred             hHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCC
Q psy3261         185 SDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRAN  264 (342)
Q Consensus       185 ~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~  264 (342)
                      .+.+..+++++...+..+.++| +.||+...+    +              -.-...|++.+...+.+..+|+.|+....
T Consensus        92 id~ir~l~~~~~~~~~~~~~kv-viI~~a~~~----~--------------~~a~NaLLK~LEEPp~~~~~Il~t~~~~~  152 (329)
T PRK08058         92 KDQIRYLKEEFSKSGVESNKKV-YIIEHADKM----T--------------ASAANSLLKFLEEPSGGTTAILLTENKHQ  152 (329)
T ss_pred             HHHHHHHHHHHhhCCcccCceE-EEeehHhhh----C--------------HHHHHHHHHHhcCCCCCceEEEEeCChHh
Confidence            4455556666654332345555 778887333    2              34567899999887778877877664321


Q ss_pred             CCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         265 LPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       265 ~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +       +| -+.-+ .       ..+++..++.+|+...+   .+.|+-  ++ ...+....+|+|....++.
T Consensus       153 l-------l~-TIrSR-c-------~~i~~~~~~~~~~~~~L---~~~gi~--~~-~~~~l~~~~g~~~~A~~l~  205 (329)
T PRK08058        153 I-------LP-TILSR-C-------QVVEFRPLPPESLIQRL---QEEGIS--ES-LATLLAGLTNSVEEALALS  205 (329)
T ss_pred             C-------cH-HHHhh-c-------eeeeCCCCCHHHHHHHH---HHcCCC--hH-HHHHHHHHcCCHHHHHHHh
Confidence            1       11 11111 1       13778888888875555   345532  22 2233333356787776654

>PRK06921 hypothetical protein; Provisional

Probab=96.81  E-value=0.0032  Score=59.36  Aligned_cols=85  Identities=20%  Similarity=0.302  Sum_probs=52.7

Q ss_pred             HHHHhhhcCCCChhhH-HhhhhcCCce--EEechhHHHH-HHHHHhccC-CCCCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          18 VRSAIFELGGITRVFN-EQTQIFNESS--ILIRNCMLEL-VGYLKSMTN-FDRPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        18 ~~~~l~~~g~l~~~~~-~~~~~~~~~~--~lvR~~t~el-~~~l~~~~~-~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ....++..-++|..+. ..|+.|....  -.++. +.+. .+++++... .......++|+|++|+|||.++.-+...+.
T Consensus        64 ~~~~~~~~s~i~~~~~~~~F~nf~~~~~~~~~~~-~~~~~~~~~~~f~~~~~~~~~~l~l~G~~G~GKThLa~aia~~l~  142 (266)
T PRK06921         64 KIERLLKASEITEAFRKLTFKNFKTEGKPQAIKD-AYECAVEYVKDFEKIQESRKNSIALLGQPGSGKTHLLTAAANELM  142 (266)
T ss_pred             HHHHHHHHcCCCHHHHhhhhhcCccCCccHHHHH-HHHHHHHHHHHHHHhcccCCCeEEEECCCCCcHHHHHHHHHHHHh
Confidence            4555555568888653 3466666321  01111 1111 234444111 112467899999999999999988888888


Q ss_pred             hC-CeEEEEeCC
Q psy3261          93 EN-NYLLVHIPW  103 (342)
Q Consensus        93 ~~-gwiVl~vP~  103 (342)
                      ++ |.-|+|++.
T Consensus       143 ~~~g~~v~y~~~  154 (266)
T PRK06921        143 RKKGVPVLYFPF  154 (266)
T ss_pred             hhcCceEEEEEH
Confidence            77 899999874

>PLN03210 Resistant to P

Probab=96.81  E-value=0.095  Score=59.15  Aligned_cols=49  Identities=16%  Similarity=-0.000  Sum_probs=33.4

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc---CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ---TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~---~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .++|+.++.+|+..++..++-.+-..   .++-..++--.+||.|-.+.-+.
T Consensus       345 ~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlg  396 (1153)
T PLN03210        345 IYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLG  396 (1153)
T ss_pred             EEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHH
Confidence            47899999999999998876543221   11123345568999998876554

syringae 6; Provisional

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.80  E-value=0.017  Score=61.56  Aligned_cols=49  Identities=14%  Similarity=0.219  Sum_probs=34.9

Q ss_pred             ceEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          42 SSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        42 ~~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      ...++|.   .|++.|.+ +   ....-++|.-|.|.||||+++|... -...||-|
T Consensus        19 ~~~v~R~---rL~~~L~~-~---~~~RL~li~APAGfGKttl~aq~~~-~~~~~~~v   67 (894)
T COG2909          19 DNYVVRP---RLLDRLRR-A---NDYRLILISAPAGFGKTTLLAQWRE-LAADGAAV   67 (894)
T ss_pred             ccccccH---HHHHHHhc-C---CCceEEEEeCCCCCcHHHHHHHHHH-hcCcccce
Confidence            3667777   56788877 1   2245678889999999999999876 23445444

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

Probab=96.78  E-value=0.021  Score=61.06  Aligned_cols=48  Identities=15%  Similarity=0.263  Sum_probs=35.9

Q ss_pred             eecCCCCHHHHHHHHHHHHh-------CCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         292 IHVPELNDEEFHNLLNLYES-------KKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~-------~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +.++.++.++...+++....       ..-+. +++....|...++||.|++..+.
T Consensus       163 ~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~L  218 (725)
T PRK13341        163 FRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNAL  218 (725)
T ss_pred             eecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            78999999999999988765       11122 45555667778999999987753

>PRK06851 hypothetical protein; Provisional

Probab=96.78  E-value=0.0022  Score=63.03  Aligned_cols=39  Identities=26%  Similarity=0.257  Sum_probs=34.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      -..+|+|.|++|+|||+++.++...|.++|+-|.+..++
T Consensus       213 ~~~~~~i~G~pG~GKstl~~~i~~~a~~~G~~v~~~hC~  251 (367)
T PRK06851        213 VKNRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCG  251 (367)
T ss_pred             cceEEEEeCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence            356899999999999999999999999999988766443

>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=96.78  E-value=0.0021  Score=52.23  Aligned_cols=32  Identities=16%  Similarity=0.200  Sum_probs=27.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      +++|.|++||||||+..++....   |+.++++.+
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~---~~~~i~~d~   32 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL---GFPVISMDD   32 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH---TCEEEEEHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH---CCeEEEecc
Confidence            48999999999999999987643   888888755

...

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.76  E-value=0.0014  Score=52.82  Aligned_cols=29  Identities=14%  Similarity=0.116  Sum_probs=26.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ...++|+|++|||||+++..+.......+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~   30 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPG   30 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCC
Confidence            56899999999999999999988887776

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.

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

Probab=96.75  E-value=0.18  Score=47.04  Aligned_cols=114  Identities=18%  Similarity=0.226  Sum_probs=72.6

Q ss_pred             CCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCC-eEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         202 GVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNN-GAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       202 ~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~-G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ++.||.+.||+. ...+.++              +.--|.|.+.....-+. ++|+.+-.+-.  ++.+   .|  .+.+
T Consensus       129 g~r~v~l~vdEa-h~L~~~~--------------le~Lrll~nl~~~~~~~l~ivL~Gqp~L~--~~lr---~~--~l~e  186 (269)
T COG3267         129 GKRPVVLMVDEA-HDLNDSA--------------LEALRLLTNLEEDSSKLLSIVLIGQPKLR--PRLR---LP--VLRE  186 (269)
T ss_pred             CCCCeEEeehhH-hhhChhH--------------HHHHHHHHhhcccccCceeeeecCCcccc--hhhc---hH--HHHh
Confidence            589999999999 4455566              88888888887643222 23332211111  1111   11  1222


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc----CcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ----TSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~----~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      .+... +  +.|++++|+.+|.+.++.+--+.+-..    +++....++.-|.|=|+..-.+|.
T Consensus       187 ~~~R~-~--ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         187 LEQRI-D--IRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             hhheE-E--EEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            11110 1  237899999999999999887766322    555677899999999999888774

>PRK09183 transposase/IS protein; Provisional

Probab=96.73  E-value=0.0028  Score=59.42  Aligned_cols=50  Identities=22%  Similarity=0.205  Sum_probs=38.7

Q ss_pred             HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        52 el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +.+..|.. ..+-.....++|+|++|||||+++..+...|..+|.=|++++
T Consensus        88 ~~i~~L~~-~~~i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~  137 (259)
T PRK09183         88 KQLQSLRS-LSFIERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT  137 (259)
T ss_pred             HHHHHHhc-CCchhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            45555654 333445678999999999999999999888888888887774

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.69  E-value=0.0034  Score=59.73  Aligned_cols=61  Identities=16%  Similarity=0.247  Sum_probs=47.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMW  133 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~  133 (342)
                      .+.-=++++||.||||||+|+-.+.|--+ ..-.|+.|-++.++++.+        +..+..|-+....-
T Consensus       123 ~~~GLILVTGpTGSGKSTTlAamId~iN~~~~~HIlTIEDPIE~vh~s--------kkslI~QREvG~dT  184 (353)
T COG2805         123 SPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIEDPIEYVHES--------KKSLINQREVGRDT  184 (353)
T ss_pred             CCCceEEEeCCCCCcHHHHHHHHHHHHhccCCcceEEecCchHhhhcc--------hHhhhhHHHhcccH
Confidence            46778899999999999999999999864 588899999998888774        33455555544443

>KOG1970|consensus

Probab=96.69  E-value=0.012  Score=60.04  Aligned_cols=141  Identities=15%  Similarity=0.074  Sum_probs=76.7

Q ss_pred             HHHHHHHHHh--ccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCC-----CC
Q psy3261          50 MLELVGYLKS--MTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTK-----EG  122 (342)
Q Consensus        50 t~el~~~l~~--~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~-----~~  122 (342)
                      --|+-.+|+.  +....-++.-++|+||.||||||++.-+   |.+.|.      ...+|.|....-.+...+     -+
T Consensus        91 I~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvL---skelg~------~~~Ew~Npi~~~~~~~~h~~t~~~~  161 (634)
T KOG1970|consen   91 ISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVL---SKELGY------QLIEWSNPINLKEPENLHNETSFLM  161 (634)
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHH---HHhhCc------eeeeecCCccccccccccccchhcc
Confidence            4466667773  2334456678999999999999997543   455554      345777665544444211     12


Q ss_pred             ccccHHHH--HHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhcccc
Q psy3261         123 MVDLNIDA--AMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLST  200 (342)
Q Consensus       123 ~~~qP~~a--~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~  200 (342)
                      .+++...+  ..+|.+..+-|.=...  +.++..+-++-         =+-||=++...   -+...|+.+++++...  
T Consensus       162 ~~~~s~L~~fesFler~~kyg~l~~~--g~~~~~~~~li---------LveDLPn~~~~---d~~~~f~evL~~y~s~--  225 (634)
T KOG1970|consen  162 FPYQSQLAVFESFLLRATKYGSLQMS--GDDLRTDKKLI---------LVEDLPNQFYR---DDSETFREVLRLYVSI--  225 (634)
T ss_pred             cchhhHHHHHHHHHHHHHhhchhhhc--ccccccCceEE---------Eeeccchhhhh---hhHHHHHHHHHHHHhc--
Confidence            22333332  3455555333332222  22222111110         01122222221   1567888899987765  


Q ss_pred             CCCceEEEEEeCcccc
Q psy3261         201 EGVCRTFVCVDGYNSF  216 (342)
Q Consensus       201 ~~~~pVLvavD~~n~~  216 (342)
                       +.+|+++.|=|.++-
T Consensus       226 -g~~PlIf~iTd~~~~  240 (634)
T KOG1970|consen  226 -GRCPLIFIITDSLSN  240 (634)
T ss_pred             -CCCcEEEEEeccccC
Confidence             699999999888764

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

Probab=96.68  E-value=0.0037  Score=55.34  Aligned_cols=48  Identities=25%  Similarity=0.400  Sum_probs=33.6

Q ss_pred             HHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          54 VGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        54 ~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ++.+.. ..+-.....++|+|+.|+|||.+..-+...|..+|.-|+|+.
T Consensus        35 ~~~l~~-~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~   82 (178)
T PF01695_consen   35 IAQLAA-LEFIENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFIT   82 (178)
T ss_dssp             HHHHHH-H-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             HHHHhc-CCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEee
Confidence            444433 333445678999999999999999999988989998888874

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.67  E-value=0.064  Score=57.58  Aligned_cols=118  Identities=13%  Similarity=0.174  Sum_probs=60.1

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC-CCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW-NNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~-~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.++.+|++.++.....    ....   ..+-.++..|+.++.+-. .+.++|.+++...   .    .++..+....
T Consensus       270 ~~p~il~iDEid~l~~~r~----~~~~---~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~---~----~ld~al~r~g  335 (733)
T TIGR01243       270 NAPSIIFIDEIDAIAPKRE----EVTG---EVEKRVVAQLLTLMDGLKGRGRVIVIGATNRP---D----ALDPALRRPG  335 (733)
T ss_pred             cCCcEEEeehhhhhccccc----CCcc---hHHHHHHHHHHHHhhccccCCCEEEEeecCCh---h----hcCHHHhCch
Confidence            3577888999988765421    0001   112356777888876643 2344455444321   1    1222232222


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhh-CCCHHHHhhhc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLT-KRVPQKMYEFC  339 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lS-gGNP~~l~~lc  339 (342)
                      .|+.     .+.++..+.++-..++..+...--+..+....++--.+ |-.+.++..+|
T Consensus       336 Rfd~-----~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~  389 (733)
T TIGR01243       336 RFDR-----EIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALA  389 (733)
T ss_pred             hccE-----EEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHH
Confidence            2322     26677778888888888665433332222233444333 33455555554

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.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.67  E-value=0.06  Score=56.65  Aligned_cols=82  Identities=7%  Similarity=0.078  Sum_probs=52.3

Q ss_pred             HHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CC-cc
Q psy3261         239 TRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KW-LQ  316 (342)
Q Consensus       239 ~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~-l~  316 (342)
                      ...|++++..-....++|++++....        +...+. ..+.       .+++..++.+|+...+...... |. + 
T Consensus       144 ~naLLK~LEePp~~tv~IL~t~~~~k--------Ll~TI~-SRc~-------~vef~~l~~~ei~~~L~~i~~~egi~I-  206 (620)
T PRK14954        144 FNAFLKTLEEPPPHAIFIFATTELHK--------IPATIA-SRCQ-------RFNFKRIPLDEIQSQLQMICRAEGIQI-  206 (620)
T ss_pred             HHHHHHHHhCCCCCeEEEEEeCChhh--------hhHHHH-hhce-------EEecCCCCHHHHHHHHHHHHHHcCCCC-
Confidence            56788888776666777777654221        111121 2221       3788999999999888765544 54 3 


Q ss_pred             CcchHHHHHHhhCCCHHHHhh
Q psy3261         317 TSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       317 ~e~~~~el~~lSgGNP~~l~~  337 (342)
                      +++....+-.++||+.+.+..
T Consensus       207 ~~eal~~La~~s~Gdlr~al~  227 (620)
T PRK14954        207 DADALQLIARKAQGSMRDAQS  227 (620)
T ss_pred             CHHHHHHHHHHhCCCHHHHHH
Confidence            455455566699999996554

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.66  E-value=0.0095  Score=54.27  Aligned_cols=37  Identities=19%  Similarity=0.118  Sum_probs=29.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC------CeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN------NYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~------gwiVl~v  101 (342)
                      .+..-+.|+|++|||||+++.|+...+...      +.-|+||
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi   59 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYI   59 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEE
Confidence            567889999999999999999999876543      2556666

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 .

>TIGR00763 lon ATP-dependent protease La

Probab=96.66  E-value=0.036  Score=59.86  Aligned_cols=31  Identities=26%  Similarity=0.423  Sum_probs=21.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYL   97 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi   97 (342)
                      +...++|+|++|||||++ +++++.+.....+
T Consensus       346 ~~~~lll~GppG~GKT~l-Ak~iA~~l~~~~~  376 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSL-GKSIAKALNRKFV  376 (775)
T ss_pred             CCceEEEECCCCCCHHHH-HHHHHHHhcCCeE
Confidence            455799999999999854 5555555543333

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.66  E-value=0.045  Score=53.96  Aligned_cols=187  Identities=13%  Similarity=0.075  Sum_probs=97.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC----eEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHh
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN----YLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQ  140 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g----wiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~  140 (342)
                      .+..|.+|+|++|||||++|.++......+.    .+++.|.+...                      ...++++.++. 
T Consensus       131 GkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~----------------------EV~df~~~i~~-  187 (380)
T PRK12608        131 GKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPE----------------------EVTDMRRSVKG-  187 (380)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCC----------------------CHHHHHHHHhh-
Confidence            4678999999999999999999777655442    45556654322                      11234444421 


Q ss_pred             CccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCC
Q psy3261         141 NTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEK  220 (342)
Q Consensus       141 N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s  220 (342)
                              .+-.+          +....+... +        .+..++....+.+..+    ...|+|.+|++..+-.--
T Consensus       188 --------~Vvas----------t~de~~~~~-~--------~v~~~~~~~Ae~f~~~----GkdVVLvlDsltr~A~A~  236 (380)
T PRK12608        188 --------EVYAS----------TFDRPPDEH-I--------RVAELVLERAKRLVEQ----GKDVVILLDSLTRLARAY  236 (380)
T ss_pred             --------hEEee----------cCCCCHHHH-H--------HHHHHHHHHHHHHHHc----CCCEEEEEeCcHHHHHHH
Confidence                    11100          000111110 0        1113344455566654    689999999997664421


Q ss_pred             C-----cCCCCCCCcccCCccchHHHHHHhhcCCCCCeEE---EEEeCCCCCCC-CC----------ccCcchhHHhhhc
Q psy3261         221 T-----NCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAI---VLALSPRANLP-DR----------RESHLPLYMLKKA  281 (342)
Q Consensus       221 ~-----~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~v---v~AtS~~~~~~-~~----------~~~~~p~~llg~~  281 (342)
                      -     .=+.+. +=++|.-|..++-|..-.++--.+|.+   -++.-.+++.- ++          -...|.+.|+.+.
T Consensus       237 rei~~~~G~~~s-~G~~~s~~~~~~rl~~~A~~~~~~GSiT~i~TvLvetg~~mdd~I~ee~kg~~dg~ivLsR~lA~~~  315 (380)
T PRK12608        237 NNEVESSGRTLS-GGVDARALQRPKRLFGAARNIEEGGSLTIIATALVDTGSRMDEVIFEEFKGTGNMEIVLDRELADKR  315 (380)
T ss_pred             HhhhcccCCCCC-CCcChHHHhhhHHHHHhcCCCCCCcchhheEEEEEecCCCCCcchHHHhcccCCCeEEECHHHHhCC
Confidence            0     023344 457777777777777666543224432   11112212111 11          1155667777776


Q ss_pred             CCCCCCCcce--eecC-CCCHHHHHHHH
Q psy3261         282 GFESIDPFVP--IHVP-ELNDEEFHNLL  306 (342)
Q Consensus       282 g~~~~dP~~~--i~v~-~~s~~E~~~ll  306 (342)
                      -|..+|+..-  -.++ -++++|.+.+.
T Consensus       316 ~fPAIDi~~S~sR~~~~l~~~~~~~~~~  343 (380)
T PRK12608        316 VFPAIDIAKSGTRREELLLDSKELEKVR  343 (380)
T ss_pred             CCCccCcccccCcchhhcCCHHHHHHHH
Confidence            6777777531  1222 45556655443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.65  E-value=0.069  Score=51.81  Aligned_cols=183  Identities=12%  Similarity=0.105  Sum_probs=104.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKW  144 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~  144 (342)
                      .-..-++++|++|+||+++..++..+....+      |....         ++           -...-.+.+...|..-
T Consensus        22 rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~------~~~~~---------~C-----------g~C~sC~~~~~g~HPD   75 (325)
T PRK06871         22 LGHHALLFKADSGLGTEQLIRALAQWLMCQT------PQGDQ---------PC-----------GQCHSCHLFQAGNHPD   75 (325)
T ss_pred             CcceeEEeECCCCCCHHHHHHHHHHHHcCCC------CCCCC---------CC-----------CCCHHHHHHhcCCCCC
Confidence            4467899999999999999998888766543      11100         11           1112244444434333


Q ss_pred             cCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCC
Q psy3261         145 LEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCK  224 (342)
Q Consensus       145 L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~  224 (342)
                      +-  -+.           + ..|.             ....+.+-.+.+++...+..+..+|.| ||+...+-       
T Consensus        76 ~~--~i~-----------p-~~~~-------------~I~id~iR~l~~~~~~~~~~g~~KV~i-I~~a~~m~-------  120 (325)
T PRK06871         76 FH--ILE-----------P-IDNK-------------DIGVDQVREINEKVSQHAQQGGNKVVY-IQGAERLT-------  120 (325)
T ss_pred             EE--EEc-----------c-ccCC-------------CCCHHHHHHHHHHHhhccccCCceEEE-EechhhhC-------
Confidence            33  221           0 0121             134566667777776655456777776 88885542       


Q ss_pred             CCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHH
Q psy3261         225 PEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHN  304 (342)
Q Consensus       225 ~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~  304 (342)
                                 -.-...|++.+...+.+..+|+.++....+       +| -+.-+-        ..+.+..++.+++..
T Consensus       121 -----------~~AaNaLLKtLEEPp~~~~fiL~t~~~~~l-------lp-TI~SRC--------~~~~~~~~~~~~~~~  173 (325)
T PRK06871        121 -----------EAAANALLKTLEEPRPNTYFLLQADLSAAL-------LP-TIYSRC--------QTWLIHPPEEQQALD  173 (325)
T ss_pred             -----------HHHHHHHHHHhcCCCCCeEEEEEECChHhC-------ch-HHHhhc--------eEEeCCCCCHHHHHH
Confidence                       345689999998888888888877654321       11 111110        126777888888876


Q ss_pred             HHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         305 LLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       305 ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .++-   .+.. .++....+..+++|+|....++.
T Consensus       174 ~L~~---~~~~-~~~~~~~~~~l~~g~p~~A~~~~  204 (325)
T PRK06871        174 WLQA---QSSA-EISEILTALRINYGRPLLALTFL  204 (325)
T ss_pred             HHHH---Hhcc-ChHHHHHHHHHcCCCHHHHHHHh
Confidence            6642   2222 12112234458888887655543

>CHL00206 ycf2 Ycf2; Provisional

Probab=96.63  E-value=0.074  Score=61.57  Aligned_cols=122  Identities=7%  Similarity=0.114  Sum_probs=63.2

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC----CCCeEEEEEeCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD----WNNGAIVLALSPRA  263 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~----~~~G~vv~AtS~~~  263 (342)
                      +..+++.-++     ..|.+|-||++-++....            ...+++ ..|++.++|+    -.+|++|.|+|...
T Consensus      1721 Ir~lFelARk-----~SPCIIFIDEIDaL~~~d------------s~~ltL-~qLLneLDg~~~~~s~~~VIVIAATNRP 1782 (2281)
T CHL00206       1721 ITLQFELAKA-----MSPCIIWIPNIHDLNVNE------------SNYLSL-GLLVNSLSRDCERCSTRNILVIASTHIP 1782 (2281)
T ss_pred             HHHHHHHHHH-----CCCeEEEEEchhhcCCCc------------cceehH-HHHHHHhccccccCCCCCEEEEEeCCCc
Confidence            3445555444     569999999998775431            222344 4455556553    24677666655432


Q ss_pred             CCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHH-HhCCCccCcc--hHHHHHH-hhCCCHHHHhhhc
Q psy3261         264 NLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLY-ESKKWLQTSE--GREEIAF-LTKRVPQKMYEFC  339 (342)
Q Consensus       264 ~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy-~~~~~l~~e~--~~~el~~-lSgGNP~~l~~lc  339 (342)
                         +    .+..+|++.-.|+.     -|.|+..+..+=+..+.-. ..+|+-..++  ...++-. ..|-++++|..+|
T Consensus      1783 ---D----~LDPALLRPGRFDR-----~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLv 1850 (2281)
T CHL00206       1783 ---Q----KVDPALIAPNKLNT-----CIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALT 1850 (2281)
T ss_pred             ---c----cCCHhHcCCCCCCe-----EEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHH
Confidence               1    13345665444543     2566655544333333321 2233211111  1223333 5688899998887

>PRK06526 transposase; Provisional

Probab=96.63  E-value=0.0021  Score=60.14  Aligned_cols=39  Identities=18%  Similarity=0.180  Sum_probs=32.7

Q ss_pred             CCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          62 NFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        62 ~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ++-.....++|+|++|||||.++..+...|...|+-|++
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f  131 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF  131 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhh
Confidence            333456789999999999999999999998888887766

>PRK05642 DNA replication initiation factor; Validated

Probab=96.60  E-value=0.0053  Score=56.59  Aligned_cols=37  Identities=27%  Similarity=0.331  Sum_probs=28.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .+.++|+|++|||||.+|.-+.+.+.++|--|+|++-
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~   81 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL   81 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH
Confidence            4789999999999999977666666666666677753

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=96.60  E-value=0.054  Score=57.34  Aligned_cols=122  Identities=14%  Similarity=0.084  Sum_probs=64.5

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.||++.++...-.....    .-+...-.....|+.-+.+- -+.+++|.+++...   +    .+...+++..
T Consensus       243 ~~P~IifIDEiD~l~~~r~~~~~----g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p---~----~lD~Al~Rpg  311 (644)
T PRK10733        243 AAPCIIFIDEIDAVGRQRGAGLG----GGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRP---D----VLDPALLRPG  311 (644)
T ss_pred             cCCcEEEehhHhhhhhccCCCCC----CCchHHHHHHHHHHHhhhcccCCCCeeEEEecCCh---h----hcCHHHhCCc
Confidence            46888899999888654221110    00111123334444334432 23455555555432   1    1223343322


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHH-HhhCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIA-FLTKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~-~lSgGNP~~l~~lc~  340 (342)
                      .|+.     .+.|+.-+.++-..++..|....-+..+.....+- ...|-+|.++..+|.
T Consensus       312 Rfdr-----~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~  366 (644)
T PRK10733        312 RFDR-----QVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  366 (644)
T ss_pred             ccce-----EEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHH
Confidence            2432     36777778889999999887765443121112222 356778889998884

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

Probab=96.56  E-value=0.026  Score=60.64  Aligned_cols=96  Identities=11%  Similarity=0.160  Sum_probs=54.8

Q ss_pred             HHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCC
Q psy3261         187 VVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLP  266 (342)
Q Consensus       187 ~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~  266 (342)
                      .+..+++++.+     ..++++.||++..+++... .   ...     ...+...++.++...  .-.||+||+...- .
T Consensus       266 rl~~l~~~l~~-----~~~~ILfIDEIh~L~g~g~-~---~~g-----~~d~~nlLkp~L~~g--~i~vIgATt~~E~-~  328 (758)
T PRK11034        266 RFKALLKQLEQ-----DTNSILFIDEIHTIIGAGA-A---SGG-----QVDAANLIKPLLSSG--KIRVIGSTTYQEF-S  328 (758)
T ss_pred             HHHHHHHHHHh-----cCCCEEEeccHHHHhccCC-C---CCc-----HHHHHHHHHHHHhCC--CeEEEecCChHHH-H
Confidence            45567777764     3477888999988877532 1   111     234556666666421  2345666664320 0


Q ss_pred             CCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHH
Q psy3261         267 DRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLY  309 (342)
Q Consensus       267 ~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy  309 (342)
                      +  -......+.++  |      .+|.|+..|.+|...++.-+
T Consensus       329 ~--~~~~D~AL~rR--F------q~I~v~ePs~~~~~~IL~~~  361 (758)
T PRK11034        329 N--IFEKDRALARR--F------QKIDITEPSIEETVQIINGL  361 (758)
T ss_pred             H--HhhccHHHHhh--C------cEEEeCCCCHHHHHHHHHHH
Confidence            0  00011233332  3      35999999999999998743

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.56  E-value=0.23  Score=48.35  Aligned_cols=185  Identities=11%  Similarity=0.061  Sum_probs=106.3

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCcc
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTK  143 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~  143 (342)
                      +.-..-++++|+.|+||+++......+-.-.+      |....         ++           -...=.+.+...|..
T Consensus        21 ~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~------~~~~~---------~C-----------g~C~sC~~~~~g~HP   74 (334)
T PRK07993         21 GRGHHALLIQALPGMGDDALIYALSRWLMCQQ------PQGHK---------SC-----------GHCRGCQLMQAGTHP   74 (334)
T ss_pred             CCcceEEeeECCCCCCHHHHHHHHHHHHcCCC------CCCCC---------CC-----------CCCHHHHHHHcCCCC
Confidence            35567899999999999999888877654321      11100         01           001113444444444


Q ss_pred             ccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcC
Q psy3261         144 WLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNC  223 (342)
Q Consensus       144 ~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y  223 (342)
                      -+.  -+.             |.+.           ......+.+..+.+.+...+..+..+|. .||+...+    +  
T Consensus        75 D~~--~i~-------------p~~~-----------~~~I~idqiR~l~~~~~~~~~~g~~kV~-iI~~ae~m----~--  121 (334)
T PRK07993         75 DYY--TLT-------------PEKG-----------KSSLGVDAVREVTEKLYEHARLGGAKVV-WLPDAALL----T--  121 (334)
T ss_pred             CEE--EEe-------------cccc-----------cccCCHHHHHHHHHHHhhccccCCceEE-EEcchHhh----C--
Confidence            443  221             1111           0124567777778887765545666664 46766443    2  


Q ss_pred             CCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHH
Q psy3261         224 KPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFH  303 (342)
Q Consensus       224 ~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~  303 (342)
                                  -+-...|++.+...+.+..+|+.++....+       +| -+.-+-        ..+.++..+.+++.
T Consensus       122 ------------~~AaNaLLKtLEEPp~~t~fiL~t~~~~~l-------Lp-TIrSRC--------q~~~~~~~~~~~~~  173 (334)
T PRK07993        122 ------------DAAANALLKTLEEPPENTWFFLACREPARL-------LA-TLRSRC--------RLHYLAPPPEQYAL  173 (334)
T ss_pred             ------------HHHHHHHHHHhcCCCCCeEEEEEECChhhC-------hH-HHHhcc--------ccccCCCCCHHHHH
Confidence                        456789999998888888888887764321       11 111110        02677778888888


Q ss_pred             HHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         304 NLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       304 ~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      ..+.-  ..+ + .++....+..+++|+|....++.
T Consensus       174 ~~L~~--~~~-~-~~~~a~~~~~la~G~~~~Al~l~  205 (334)
T PRK07993        174 TWLSR--EVT-M-SQDALLAALRLSAGAPGAALALL  205 (334)
T ss_pred             HHHHH--ccC-C-CHHHHHHHHHHcCCCHHHHHHHh
Confidence            76642  113 3 23323345569999998766553

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.54  E-value=0.0051  Score=61.22  Aligned_cols=37  Identities=27%  Similarity=0.304  Sum_probs=31.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP  102 (342)
                      ..+.++|+|++|+|||.++..+...+.++  |+-|+|++
T Consensus       135 ~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       135 AYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             cCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            35679999999999999998887777766  78888884

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).

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.53  E-value=0.0033  Score=52.83  Aligned_cols=34  Identities=15%  Similarity=0.209  Sum_probs=29.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      ++|+|++|||||+++.+++..+..+|--|+++.-
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~   35 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDI   35 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEEC
Confidence            6899999999999999999998887777777753

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.

>PRK08727 hypothetical protein; Validated

Probab=96.48  E-value=0.0051  Score=56.66  Aligned_cols=37  Identities=22%  Similarity=0.220  Sum_probs=32.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ....++|+|+.|||||.++.-+.+.+.++|--|+|+|
T Consensus        40 ~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~   76 (233)
T PRK08727         40 SSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP   76 (233)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            3456999999999999999988888888888888886

>PRK06893 DNA replication initiation factor; Validated

Probab=96.47  E-value=0.0054  Score=56.28  Aligned_cols=37  Identities=27%  Similarity=0.316  Sum_probs=29.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ..+.++|+|++|||||.++.-+.+.+.++|-=|+|++
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~   74 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIP   74 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEee
Confidence            3456899999999999999888888777665555554

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=96.46  E-value=0.0035  Score=56.04  Aligned_cols=23  Identities=22%  Similarity=0.325  Sum_probs=20.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      -.+|.||+|||||++++.+++.+
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHHHh
Confidence            48999999999999999999998

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.45  E-value=0.0037  Score=54.65  Aligned_cols=32  Identities=19%  Similarity=0.113  Sum_probs=28.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|++|||||++..|+++.+.++|==|+|+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~   33 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYV   33 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            68999999999999999999888887777777

A related protein is found in archaea.

>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=96.44  E-value=0.0097  Score=54.36  Aligned_cols=52  Identities=19%  Similarity=0.203  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh--CCeEEEEeC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE--NNYLLVHIP  102 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~--~gwiVl~vP  102 (342)
                      .+...++.+-+  +.....+.++|+|+.|+|||-+|..+.+.+.+  .+--|+|++
T Consensus        18 ~a~~~~~~ia~--~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~   71 (219)
T PF00308_consen   18 LAYAAAKAIAE--NPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS   71 (219)
T ss_dssp             HHHHHHHHHHH--STTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE
T ss_pred             HHHHHHHHHHh--cCCCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec
Confidence            44455555544  22234567999999999999987777777664  355666664

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.

>KOG0734|consensus

Probab=96.44  E-value=0.048  Score=55.73  Aligned_cols=126  Identities=17%  Similarity=0.200  Sum_probs=73.3

Q ss_pred             HHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCC
Q psy3261         189 DVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDR  268 (342)
Q Consensus       189 ~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~  268 (342)
                      -.|+.+-++     +-|.+|.||++.+.=+.-.      .+..|--+-+|-.++.++..-.-+-|+||.+.+...   + 
T Consensus       386 RdLF~aAk~-----~APcIIFIDEiDavG~kR~------~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfp---e-  450 (752)
T KOG0734|consen  386 RDLFAAAKA-----RAPCIIFIDEIDAVGGKRN------PSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFP---E-  450 (752)
T ss_pred             HHHHHHHHh-----cCCeEEEEechhhhcccCC------ccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCCh---h-
Confidence            345555554     6799999999977654422      233433334788888888765666677655544321   1 


Q ss_pred             ccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH--hhCCCHHHHhhh
Q psy3261         269 RESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF--LTKRVPQKMYEF  338 (342)
Q Consensus       269 ~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~--lSgGNP~~l~~l  338 (342)
                         .|-..|.+.-.|+.     .|.||.=+-..=..++++|...-.+ .++-...+..  .+|-++.+|..+
T Consensus       451 ---~LD~AL~RPGRFD~-----~v~Vp~PDv~GR~eIL~~yl~ki~~-~~~VD~~iiARGT~GFsGAdLaNl  513 (752)
T KOG0734|consen  451 ---ALDKALTRPGRFDR-----HVTVPLPDVRGRTEILKLYLSKIPL-DEDVDPKIIARGTPGFSGADLANL  513 (752)
T ss_pred             ---hhhHHhcCCCccce-----eEecCCCCcccHHHHHHHHHhcCCc-ccCCCHhHhccCCCCCchHHHHHH
Confidence               12234444444542     2777777777777888888764444 3321222222  566677776654

>KOG2543|consensus

Probab=96.42  E-value=0.058  Score=53.03  Aligned_cols=48  Identities=21%  Similarity=0.244  Sum_probs=30.8

Q ss_pred             ceEEechhH-HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          42 SSILIRNCM-LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        42 ~~~lvR~~t-~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      |-+.-|+.. ..+...|-+  +...-..-++|+|..|||||.++.|+.-..
T Consensus         6 ~~v~~Re~qi~~L~~Llg~--~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~   54 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGN--NSCTIPSIVHIYGHSGTGKTYLVRQLLRKL   54 (438)
T ss_pred             cCccchHHHHHHHHHHhCC--CCcccceeEEEeccCCCchhHHHHHHHhhc
Confidence            445567744 334444433  111223445999999999999999998765

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.42  E-value=0.0087  Score=55.71  Aligned_cols=36  Identities=17%  Similarity=0.173  Sum_probs=31.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ...++|+|++|||||.++..+..++...|--|++++
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it  134 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT  134 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            358999999999999999999999988887777773

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

Probab=96.41  E-value=0.087  Score=56.61  Aligned_cols=95  Identities=13%  Similarity=0.102  Sum_probs=52.6

Q ss_pred             HHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCC
Q psy3261         187 VVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLP  266 (342)
Q Consensus       187 ~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~  266 (342)
                      -+..+++|++.     ..|+++.||++-.+++... .   ...     .......|+..+..  ..-.+|+||+...  .
T Consensus       262 ~l~~i~~~~~~-----~~~~ILfiDEih~l~~~g~-~---~~~-----~~~~~~~L~~~l~~--g~i~~IgaTt~~e--~  323 (731)
T TIGR02639       262 RLKAVVSEIEK-----EPNAILFIDEIHTIVGAGA-T---SGG-----SMDASNLLKPALSS--GKLRCIGSTTYEE--Y  323 (731)
T ss_pred             HHHHHHHHHhc-----cCCeEEEEecHHHHhccCC-C---CCc-----cHHHHHHHHHHHhC--CCeEEEEecCHHH--H
Confidence            34456667754     2488899999988876421 0   011     12234556555542  1234678877532  0


Q ss_pred             CCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHH
Q psy3261         267 DRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNL  308 (342)
Q Consensus       267 ~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~y  308 (342)
                      .+. ......+..+  |      .+|+|+..|.+|...+++-
T Consensus       324 ~~~-~~~d~al~rR--f------~~i~v~~p~~~~~~~il~~  356 (731)
T TIGR02639       324 KNH-FEKDRALSRR--F------QKIDVGEPSIEETVKILKG  356 (731)
T ss_pred             HHH-hhhhHHHHHh--C------ceEEeCCCCHHHHHHHHHH
Confidence            100 0011233332  3      2489999999999999973

>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=96.41  E-value=0.0049  Score=51.50  Aligned_cols=34  Identities=15%  Similarity=0.136  Sum_probs=25.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .++|+|++|||||++..++.+.. ...+++++++.
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~-~~~~~~i~~~~   34 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL-GRPVIRINCSS   34 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH-TCEEEEEE-TT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh-hcceEEEEecc
Confidence            37999999999999988877766 55666666543

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.

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

Probab=96.39  E-value=0.0087  Score=56.00  Aligned_cols=73  Identities=16%  Similarity=0.160  Sum_probs=50.0

Q ss_pred             CCCChhhHHhhhhcC-CceEEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          26 GGITRVFNEQTQIFN-ESSILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        26 g~l~~~~~~~~~~~~-~~~~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .++|..  +.++.|. +....+++ .-.++....+. .+   ....++|+|++|+|||.++.-+...+...||=|++++-
T Consensus        68 a~~p~~--k~~~~~d~~~~~~~~~~~l~~~~~~~~~-~~---~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~  141 (254)
T COG1484          68 ASFPAK--KTFEEFDFEFQPGIDKKALEDLASLVEF-FE---RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITA  141 (254)
T ss_pred             hcCCcc--CCcccccccCCcchhHHHHHHHHHHHHH-hc---cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEH
Confidence            467774  5555554 12222444 33334444434 22   68899999999999999999999988888999999865


Q ss_pred             c
Q psy3261         104 V  104 (342)
Q Consensus       104 ~  104 (342)
                      +
T Consensus       142 ~  142 (254)
T COG1484         142 P  142 (254)
T ss_pred             H
Confidence            5

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

Probab=96.39  E-value=0.058  Score=50.37  Aligned_cols=29  Identities=14%  Similarity=0.074  Sum_probs=24.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      .++.|.+|.|++|||||+++..+......
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            46889999999999999988777765544

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.38  E-value=0.17  Score=48.89  Aligned_cols=119  Identities=13%  Similarity=0.202  Sum_probs=70.4

Q ss_pred             chhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCC
Q psy3261         183 YASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPR  262 (342)
Q Consensus       183 ~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~  262 (342)
                      ...+-+..+.+.+...+..++++| +.||+...+    +              -.-...|++.+...+ ++.+|+.++..
T Consensus       104 I~id~ir~i~~~l~~~p~~~~~kV-vII~~ae~m----~--------------~~aaNaLLK~LEEPp-~~~fILi~~~~  163 (314)
T PRK07399        104 IRLEQIREIKRFLSRPPLEAPRKV-VVIEDAETM----N--------------EAAANALLKTLEEPG-NGTLILIAPSP  163 (314)
T ss_pred             CcHHHHHHHHHHHccCcccCCceE-EEEEchhhc----C--------------HHHHHHHHHHHhCCC-CCeEEEEECCh
Confidence            445556666666665443345554 556776222    2              345778999997655 77777776543


Q ss_pred             CCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         263 ANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       263 ~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      ..       -+| -+.-+ .       ..+.++.++.+++...++......-.  +.....+..+++|+|+....+.
T Consensus       164 ~~-------Ll~-TI~SR-c-------q~i~f~~l~~~~~~~~L~~~~~~~~~--~~~~~~l~~~a~Gs~~~al~~l  222 (314)
T PRK07399        164 ES-------LLP-TIVSR-C-------QIIPFYRLSDEQLEQVLKRLGDEEIL--NINFPELLALAQGSPGAAIANI  222 (314)
T ss_pred             Hh-------CcH-HHHhh-c-------eEEecCCCCHHHHHHHHHHhhccccc--hhHHHHHHHHcCCCHHHHHHHH
Confidence            21       122 11111 1       13788999999998888754221111  1113467889999999887654

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.28  E-value=0.04  Score=60.09  Aligned_cols=123  Identities=14%  Similarity=0.063  Sum_probs=73.2

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      -++...+.....    .+.|+++.+||+ +|....+              |.+.+.+++-+.    .|+.   .......
T Consensus       140 ~~~~~~i~~~~~----~~~plVi~leDl-hWaD~~S--------------L~lL~~lm~~~~----~~~~---~~n~v~~  193 (849)
T COG3899         140 LAFLRFIQVFTA----EEHPLVIVLEDL-HWADSAS--------------LKLLQLLMDRIA----IGAY---RDNEVLL  193 (849)
T ss_pred             HHHHHHHHHHHh----ccCCeEEEEecc-cccChhH--------------HHHHHHHHHhcc----hhhh---hcccccc
Confidence            455556666554    367999999999 8888877              888888888876    1221   0100001


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      ..|....++.-.  + +.   .....|.+.+||..+...++.---.+........-.++.-.|.|||.=+.++|.
T Consensus       194 ~h~~~~~~~~~~--~-~~---~~i~~I~L~PL~~~d~~~lV~~~l~~~~~~~~p~~~~i~~kt~GnPfFi~e~lk  262 (849)
T COG3899         194 LHPLRPTLGEIL--K-SA---TNITTITLAPLSRADTNQLVAATLGCTKLLPAPLLELIFEKTKGNPFFIEEFLK  262 (849)
T ss_pred             CCCccchhhHHh--h-cC---CceeEEecCcCchhhHHHHHHHHhCCcccccchHHHHHHHHhcCCCccHHHHHH
Confidence            111111111111  1 11   112248999999999999996555554332222333566689999988777764

>PTZ00202 tuzin; Provisional

Probab=96.27  E-value=0.023  Score=57.18  Aligned_cols=48  Identities=19%  Similarity=0.129  Sum_probs=31.2

Q ss_pred             eEEechhHH-HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          43 SILIRNCML-ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        43 ~~lvR~~t~-el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+.=|+.-+ +|...|.. .+... ..-.+|+|+.|||||+++..++..+.
T Consensus       263 ~FVGReaEla~Lr~VL~~-~d~~~-privvLtG~~G~GKTTLlR~~~~~l~  311 (550)
T PTZ00202        263 QFVSREAEESWVRQVLRR-LDTAH-PRIVVFTGFRGCGKSSLCRSAVRKEG  311 (550)
T ss_pred             CCCCcHHHHHHHHHHHhc-cCCCC-ceEEEEECCCCCCHHHHHHHHHhcCC
Confidence            445566333 34444444 33222 24678999999999999999997654

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.24  E-value=0.052  Score=59.06  Aligned_cols=92  Identities=13%  Similarity=0.169  Sum_probs=52.0

Q ss_pred             HHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc-CCCCCeEEEEEeCCCCCC
Q psy3261         187 VVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ-SDWNNGAIVLALSPRANL  265 (342)
Q Consensus       187 ~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~-~~~~~G~vv~AtS~~~~~  265 (342)
                      -+..+++|++.     ..|+++.||++-.+++...  .  ++      ...+...|+.++. |+   -.+|+||+...- 
T Consensus       259 rl~~i~~~~~~-----~~~~ILfiDEih~l~~~g~--~--~g------~~~~a~lLkp~l~rg~---l~~IgaTt~~ey-  319 (821)
T CHL00095        259 RLKRIFDEIQE-----NNNIILVIDEVHTLIGAGA--A--EG------AIDAANILKPALARGE---LQCIGATTLDEY-  319 (821)
T ss_pred             HHHHHHHHHHh-----cCCeEEEEecHHHHhcCCC--C--CC------cccHHHHhHHHHhCCC---cEEEEeCCHHHH-
Confidence            35566777754     4689999999988876532  1  11      1245666666664 32   346777764320 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHH
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLN  307 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~  307 (342)
                       ... ......+..+        |.++.+...+.+|...++.
T Consensus       320 -~~~-ie~D~aL~rR--------f~~I~v~ep~~~e~~aILr  351 (821)
T CHL00095        320 -RKH-IEKDPALERR--------FQPVYVGEPSVEETIEILF  351 (821)
T ss_pred             -HHH-HhcCHHHHhc--------ceEEecCCCCHHHHHHHHH
Confidence             000 0000111111        3358888899999877774

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.24  E-value=0.0074  Score=52.54  Aligned_cols=41  Identities=22%  Similarity=0.340  Sum_probs=34.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE--EEeCCcc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLL--VHIPWVL  105 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV--l~vP~~~  105 (342)
                      +...|+.++|++|+||||++.-+....+++|+=|  ++.|...
T Consensus         3 ~~~mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR   45 (179)
T COG1618           3 KMAMKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVR   45 (179)
T ss_pred             CcceEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeee
Confidence            3467999999999999999999999999998777  5556654

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=96.20  E-value=0.0041  Score=54.72  Aligned_cols=26  Identities=27%  Similarity=0.349  Sum_probs=23.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++-++.|+||.|||||++|.++...
T Consensus        27 ~~Ge~iaitGPSG~GKStllk~va~L   52 (223)
T COG4619          27 RAGEFIAITGPSGCGKSTLLKIVASL   52 (223)
T ss_pred             cCCceEEEeCCCCccHHHHHHHHHhc
Confidence            46889999999999999999998764

>TIGR00750 lao LAO/AO transport system ATPase

Probab=96.15  E-value=0.0049  Score=58.96  Aligned_cols=38  Identities=21%  Similarity=0.140  Sum_probs=32.8

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..+...+.|.|++|||||+++..+..++.+.|+-|..|
T Consensus        31 ~~~~~~i~i~G~~G~GKttl~~~l~~~~~~~~~~v~~i   68 (300)
T TIGR00750        31 TGNAHRVGITGTPGAGKSTLLEALGMELRRRGLKVAVI   68 (300)
T ss_pred             cCCceEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            35688999999999999999999999998888766554

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.15  E-value=0.011  Score=56.97  Aligned_cols=75  Identities=16%  Similarity=0.092  Sum_probs=46.0

Q ss_pred             cCCCChhhH-HhhhhcCCceEEechhHHHH-HHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          25 LGGITRVFN-EQTQIFNESSILIRNCMLEL-VGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        25 ~g~l~~~~~-~~~~~~~~~~~lvR~~t~el-~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .-+||+.+. ..++.|.-.. .-|..+.+. .+++++ .........++|+|+.|+|||.++.-+...+.++|+=|.++
T Consensus       114 ~a~~p~~~~~atf~~~~~~~-~~~~~~~~~~~~fi~~-~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~  190 (306)
T PRK08939        114 SIYMPKDLLQASLADIDLDD-RDRLDALMAALDFLEA-YPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLL  190 (306)
T ss_pred             HcCCCHhHhcCcHHHhcCCC-hHHHHHHHHHHHHHHH-hhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            347887554 2344443111 123322222 334444 22223457899999999999999999999988888766554

>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=96.14  E-value=0.005  Score=50.24  Aligned_cols=65  Identities=15%  Similarity=0.242  Sum_probs=38.0

Q ss_pred             HHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCC--CeEEEEEeCCC
Q psy3261         187 VVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWN--NGAIVLALSPR  262 (342)
Q Consensus       187 ~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~--~G~vv~AtS~~  262 (342)
                      .+..++++.+..    ..|.++.+||+-.++...+       ..-...+-.+.+.|++.+.....  +.++|.+|+..
T Consensus        45 ~i~~~~~~~~~~----~~~~vl~iDe~d~l~~~~~-------~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~  111 (132)
T PF00004_consen   45 KIRDFFKKAKKS----AKPCVLFIDEIDKLFPKSQ-------PSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNS  111 (132)
T ss_dssp             HHHHHHHHHHHT----STSEEEEEETGGGTSHHCS-------TSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESS
T ss_pred             cccccccccccc----ccceeeeeccchhcccccc-------cccccccccccceeeecccccccccccceeEEeeCC
Confidence            344455555442    2489999999988877641       11222334677788888876543  44555555543

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 ....

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.13  E-value=0.0084  Score=55.17  Aligned_cols=38  Identities=16%  Similarity=0.180  Sum_probs=33.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+...++|.|+.|||||++..|++.-+.++|+-++||.
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            45779999999999999999999988878898887775

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

Probab=96.10  E-value=0.0094  Score=50.68  Aligned_cols=34  Identities=18%  Similarity=0.284  Sum_probs=29.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++.+.|+.|||||+++..++.++.++|+=|.+|
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~i   34 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRRGYRVAVI   34 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHcCCceEEE
Confidence            3688999999999999999999999999988766

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.06  E-value=0.019  Score=51.45  Aligned_cols=36  Identities=19%  Similarity=0.176  Sum_probs=29.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...-.+|.|++|||||++|..+.......|+-|+.+
T Consensus        17 ~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~   52 (196)
T PF13604_consen   17 GDRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGL   52 (196)
T ss_dssp             TCSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEE
T ss_pred             CCeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            456688899999999999999998888888777666

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.01  E-value=0.016  Score=58.55  Aligned_cols=38  Identities=26%  Similarity=0.330  Sum_probs=31.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPW  103 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~  103 (342)
                      ..+.++|+|++|||||.++..+...+.++  +.-|+|++.
T Consensus       147 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~  186 (450)
T PRK00149        147 AYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTS  186 (450)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            44679999999999999998888888776  566777743

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.01  E-value=0.0073  Score=52.06  Aligned_cols=27  Identities=26%  Similarity=0.372  Sum_probs=21.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      |++|+|..||||||++.++..+    |+.++
T Consensus         1 rI~i~G~~stGKTTL~~~L~~~----g~~~v   27 (163)
T PF13521_consen    1 RIVITGGPSTGKTTLIEALAAR----GYPVV   27 (163)
T ss_dssp             -EEEE--TTSHHHHHHHHHHHH----T-EEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHc----CCeEE
Confidence            7899999999999999999877    88876

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.01  E-value=0.0094  Score=55.59  Aligned_cols=38  Identities=13%  Similarity=0.181  Sum_probs=35.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+...++++|++|||||++..|.+.-..+.|+-|+||.
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            56889999999999999999999999999999999993

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.99  E-value=0.0094  Score=55.83  Aligned_cols=38  Identities=11%  Similarity=0.077  Sum_probs=33.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|.|++|||||++..|++..+.++|.=|+||.
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            46788999999999999999999888878899888884

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.99  E-value=0.011  Score=54.14  Aligned_cols=38  Identities=8%  Similarity=0.179  Sum_probs=33.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP  102 (342)
                      .++.-++|.|++|+|||+++.|++..+..+ |+-|+|+.
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s   49 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFS   49 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEe
Confidence            567789999999999999999998877766 99999985

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=95.98  E-value=0.48  Score=45.86  Aligned_cols=118  Identities=10%  Similarity=0.061  Sum_probs=71.3

Q ss_pred             chhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCC
Q psy3261         183 YASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPR  262 (342)
Q Consensus       183 ~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~  262 (342)
                      ...+.+..+.+.+...+..++.+ ++.||+...+    +              .+-...|++.+.....+..+|+.++..
T Consensus        93 I~idqIR~l~~~~~~~p~~g~~k-V~iI~~ae~m----~--------------~~AaNaLLKtLEEPp~~~~fiL~~~~~  153 (319)
T PRK08769         93 IVIEQVREISQKLALTPQYGIAQ-VVIVDPADAI----N--------------RAACNALLKTLEEPSPGRYLWLISAQP  153 (319)
T ss_pred             ccHHHHHHHHHHHhhCcccCCcE-EEEeccHhhh----C--------------HHHHHHHHHHhhCCCCCCeEEEEECCh
Confidence            44555666666665543334445 4557777544    2              456789999998877888787777654


Q ss_pred             CCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         263 ANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       263 ~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                      ..+       +|- +.-+        -..+.++..+.+|+...+.   +.|.-  ++...++..+++|+|....+++.
T Consensus       154 ~~l-------LpT-IrSR--------Cq~i~~~~~~~~~~~~~L~---~~~~~--~~~a~~~~~l~~G~p~~A~~~~~  210 (319)
T PRK08769        154 ARL-------PAT-IRSR--------CQRLEFKLPPAHEALAWLL---AQGVS--ERAAQEALDAARGHPGLAAQWLR  210 (319)
T ss_pred             hhC-------chH-HHhh--------heEeeCCCcCHHHHHHHHH---HcCCC--hHHHHHHHHHcCCCHHHHHHHhc
Confidence            321       111 1111        0126777788888776664   34432  33344667799999988777653

>KOG2859|consensus

Probab=95.94  E-value=0.038  Score=50.42  Aligned_cols=162  Identities=12%  Similarity=0.137  Sum_probs=92.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh------CCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE------NNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQK  139 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~------~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~  139 (342)
                      .+.-+=++||.|||||..|.|++++|.-      -+|.|+.|.--.+                 ||--..++.+=.++++
T Consensus        37 aG~~vEi~Gp~~sgKt~vL~ql~a~CilPk~~GGl~~~VLfidld~~-----------------fd~lrL~~~l~hrL~q   99 (293)
T KOG2859|consen   37 AGTLVEISGPGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDHK-----------------FDRLRLAKSLRHRLKQ   99 (293)
T ss_pred             cCcEEEEeCCCCccHHHHHHHHHHHeecccccCCceeEEEEEecccc-----------------ccHHHHHHHHHHHHHH
Confidence            4567889999999999999999999973      3899998843222                 5555667666667777


Q ss_pred             hCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccc----hh-HHHHHHHHHHhccccCCCceEEEEEeCcc
Q psy3261         140 QNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKY----AS-DVVDVLFTEIKKLSTEGVCRTFVCVDGYN  214 (342)
Q Consensus       140 ~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~----a~-~~~~~l~~EL~~~~~~~~~pVLvavD~~n  214 (342)
                      .|   +.  +.-+.+         -|..+.+.||+..++.+-.+    ++ +.+.-++.-=..-. ++.--.|+++|.+.
T Consensus       100 ~~---~~--e~~~~~---------c~te~~~eEi~~~Cm~Rf~~v~C~~s~~ll~sL~~l~y~i~-~~p~~cll~~Dsls  164 (293)
T KOG2859|consen  100 YS---VG--EVIAAK---------CPTEEQLEEIAGECMSRFRFVNCFASDDLLTSLIDLRYAII-NDPGICLLAMDSLS  164 (293)
T ss_pred             hh---hh--hhhhhc---------CCcHhHHHHHHHHHHhhEEEEEeeccHHHHHHHHHHHHHHh-cCCceeEEeecchh
Confidence            66   44  222111         12344788999888877543    22 33333332211111 01113499999998


Q ss_pred             ccccCCCcCCCCCCCcccCCcc-chHHHHHHhhcCCCCCeEEEEEeCCCC
Q psy3261         215 SFFAEKTNCKPEDKSKVLPSRV-TLTRSVINLVQSDWNNGAIVLALSPRA  263 (342)
Q Consensus       215 ~~~~~s~~y~~~~~~~I~~~~l-~l~~~~~~~~~~~~~~G~vv~AtS~~~  263 (342)
                      +|+=... .+.-+..+-...++ .+..-+.++...   -..|++||.++.
T Consensus       165 aFyW~Dr-~~~le~~n~~~~~lr~~~q~LeKL~~d---~~lv~~aT~~ti  210 (293)
T KOG2859|consen  165 AFYWLDR-PKILEKRNSMYRHLRLLQQRLEKLCKD---AILVGMATVETI  210 (293)
T ss_pred             hheeecc-cchHhhhhhHHHHHHHHHHHHHHHHhh---heeeeeeehhHH
Confidence            7765432 33211112112222 233333333322   347788888754

>PRK04296 thymidine kinase; Provisional

Probab=95.93  E-value=0.011  Score=52.81  Aligned_cols=33  Identities=21%  Similarity=0.231  Sum_probs=28.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -.+++|+.|+|||+++.+.+..+...|--|+.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            468999999999999999999988888777766

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.91  E-value=0.011  Score=55.08  Aligned_cols=38  Identities=21%  Similarity=0.127  Sum_probs=33.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP  102 (342)
                      .+..-++|.|++|+|||+++.|+...+..+ |+-|+|+.
T Consensus        28 ~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS   66 (271)
T cd01122          28 RKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS   66 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEE
Confidence            467789999999999999999998877655 99999984

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

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

Probab=95.90  E-value=0.29  Score=48.39  Aligned_cols=24  Identities=21%  Similarity=0.360  Sum_probs=19.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++...++|+||+|||||.+...+.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA  169 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVF  169 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHH
Confidence            677889999999999998755443

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=95.84  E-value=0.3  Score=49.84  Aligned_cols=119  Identities=17%  Similarity=0.208  Sum_probs=69.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|..|.+|++-+++..-+ ....      .....++..|+..+.| +-..+++|.+++...   +    .+...+++.-
T Consensus       334 ~~p~iiFiDEiDs~~~~r~-~~~~------~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p---~----~ld~a~lR~g  399 (494)
T COG0464         334 LAPSIIFIDEIDSLASGRG-PSED------GSGRRVVGQLLTELDGIEKAEGVLVIAATNRP---D----DLDPALLRPG  399 (494)
T ss_pred             CCCcEEEEEchhhhhccCC-CCCc------hHHHHHHHHHHHHhcCCCccCceEEEecCCCc---c----ccCHhhcccC
Confidence            5689999999999987733 1100      0004677778877765 344555555544432   1    1223444432


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc--CcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ--TSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~--~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      .|+.     .+.|+.-+.+|-..++..+....-..  .+-...++-- ..|-.+.++..+|.
T Consensus       400 Rfd~-----~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~  456 (494)
T COG0464         400 RFDR-----LIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVR  456 (494)
T ss_pred             ccce-----EeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHH
Confidence            3443     37899999999999998888743321  1222223333 44556777776663

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.80  E-value=0.02  Score=52.12  Aligned_cols=39  Identities=13%  Similarity=0.073  Sum_probs=33.2

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      -.+..-++|.|++|||||+++.|++..+.++|.=|+||.
T Consensus        17 i~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881        17 IPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             CcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            357889999999999999999998877777888778774

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.78  E-value=0.011  Score=58.40  Aligned_cols=37  Identities=19%  Similarity=0.342  Sum_probs=33.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      -+..-++|-|++|.||||+|+|+.+-..+++ =||||.
T Consensus        91 V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVs  127 (456)
T COG1066          91 VPGSVILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVS  127 (456)
T ss_pred             ccccEEEEccCCCCCHHHHHHHHHHHHHhcC-cEEEEe
Confidence            3678899999999999999999999887777 999995

>cd04155 Arl3 Arl3 subfamily

Probab=95.75  E-value=0.0096  Score=51.08  Aligned_cols=25  Identities=24%  Similarity=0.406  Sum_probs=22.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|+.|||||+++.++..
T Consensus        12 ~~~~~v~i~G~~g~GKStLl~~l~~   36 (173)
T cd04155          12 SEEPRILILGLDNAGKTTILKQLAS   36 (173)
T ss_pred             CCccEEEEEccCCCCHHHHHHHHhc
Confidence            4578999999999999999998854

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.

>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=95.75  E-value=0.014  Score=50.78  Aligned_cols=34  Identities=21%  Similarity=0.328  Sum_probs=28.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+++.|++|+|||++...+...+.++|.-|+.|.
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~   35 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVA   35 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            4689999999999999999988888887666664

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.73  E-value=0.017  Score=51.78  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=32.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-+.|+|++|||||++..|+...+..+|-=|+||.
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~   47 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYID   47 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            45778899999999999999999998887787777774

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

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.71  E-value=0.012  Score=59.41  Aligned_cols=37  Identities=22%  Similarity=0.344  Sum_probs=31.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ..+.++|+|++|+|||.++..+...+.++|.-|+|++
T Consensus       140 ~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~  176 (445)
T PRK12422        140 PFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVR  176 (445)
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEee
Confidence            3478999999999999998888888877787777775

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.70  E-value=0.017  Score=52.50  Aligned_cols=37  Identities=24%  Similarity=0.201  Sum_probs=33.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|.|++|+|||++..|++..+.++|.-|+||
T Consensus        14 ~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~   50 (224)
T TIGR03880        14 PEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYI   50 (224)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            4678899999999999999999999998889999988

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>cd01394 radB RadB

Probab=95.69  E-value=0.024  Score=51.20  Aligned_cols=37  Identities=16%  Similarity=0.155  Sum_probs=32.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|+|++|||||++..|++..+..+|-=|+||
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi   53 (218)
T cd01394          17 ERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYI   53 (218)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            4567788999999999999999999888777777777

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

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.63  E-value=0.022  Score=52.45  Aligned_cols=38  Identities=18%  Similarity=0.079  Sum_probs=33.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-++|.|++|||||++..|++..+..+|==++||.
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            57888999999999999999999988778887777773

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.56  E-value=0.033  Score=54.18  Aligned_cols=47  Identities=23%  Similarity=0.136  Sum_probs=36.6

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      +.+|++.+..   ...+..++-|+|++||||||++..++.+....||=|.
T Consensus        42 ~~~l~~~~~~---~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~~g~~v~   88 (332)
T PRK09435         42 AQELLDALLP---HTGNALRIGITGVPGVGKSTFIEALGMHLIEQGHKVA   88 (332)
T ss_pred             HHHHHHHHhh---cCCCcEEEEEECCCCCCHHHHHHHHHHHHHHCCCeEE
Confidence            4456665543   2356789999999999999999999999998877443

>PRK07667 uridine kinase; Provisional

Probab=95.56  E-value=0.041  Score=49.04  Aligned_cols=51  Identities=16%  Similarity=0.162  Sum_probs=37.1

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCC
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPW  103 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~  103 (342)
                      +-+|++.|.+ ..  .....+-|+|..|||||++...+...-...  ++.+++.++
T Consensus         3 ~~~~~~~~~~-~~--~~~~iIgI~G~~gsGKStla~~L~~~l~~~~~~~~~i~~Dd   55 (193)
T PRK07667          3 TNELINIMKK-HK--ENRFILGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHIDD   55 (193)
T ss_pred             HHHHHHHHHh-cC--CCCEEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEEcCc
Confidence            4466777765 22  233677899999999999998888776655  477887765

>PRK13695 putative NTPase; Provisional

Probab=95.54  E-value=0.021  Score=49.82  Aligned_cols=30  Identities=23%  Similarity=0.432  Sum_probs=25.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      +++|+|+.|||||+++.++.......|.-+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~~G~~~   31 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKEEGYKV   31 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeE
Confidence            689999999999999999888776666543

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.53  E-value=1.3  Score=43.36  Aligned_cols=115  Identities=12%  Similarity=0.112  Sum_probs=72.5

Q ss_pred             chhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCC
Q psy3261         183 YASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPR  262 (342)
Q Consensus       183 ~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~  262 (342)
                      +..+-+..+.+.+...+..++.+|+| ||+...+    +              .+-...|++.+...+.+..+|+.|+..
T Consensus       112 I~idqiR~l~~~~~~~~~~~~~kV~i-I~~ae~m----~--------------~~AaNaLLKtLEEPp~~t~fiL~t~~~  172 (342)
T PRK06964        112 IKIEQVRALLDFCGVGTHRGGARVVV-LYPAEAL----N--------------VAAANALLKTLEEPPPGTVFLLVSARI  172 (342)
T ss_pred             cCHHHHHHHHHHhccCCccCCceEEE-Eechhhc----C--------------HHHHHHHHHHhcCCCcCcEEEEEECCh
Confidence            44566777777776544345666554 6777444    2              456789999998777888888888764


Q ss_pred             CCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         263 ANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       263 ~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      ..+       +| -+..+-        ..+.++..+.+|+...+.-   .|.-  +  ...+..+++|+|....++.
T Consensus       173 ~~L-------Lp-TI~SRc--------q~i~~~~~~~~~~~~~L~~---~~~~--~--~~~~l~~~~Gsp~~Al~~~  226 (342)
T PRK06964        173 DRL-------LP-TILSRC--------RQFPMTVPAPEAAAAWLAA---QGVA--D--ADALLAEAGGAPLAALALA  226 (342)
T ss_pred             hhC-------cH-HHHhcC--------EEEEecCCCHHHHHHHHHH---cCCC--h--HHHHHHHcCCCHHHHHHHH
Confidence            421       11 111110        1278888999888877753   3432  2  2245668999998776654

>PRK09087 hypothetical protein; Validated

Probab=95.53  E-value=0.033  Score=51.18  Aligned_cols=47  Identities=9%  Similarity=-0.033  Sum_probs=31.6

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhh
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~  337 (342)
                      .+++..++.++...+++...+..-+. .++-...|---+.|+.+.+..
T Consensus       147 ~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l~~  194 (226)
T PRK09087        147 VVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAAQT  194 (226)
T ss_pred             eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHHHH
Confidence            37889999999999997776654333 454333344466777777764

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.53  E-value=0.034  Score=52.32  Aligned_cols=42  Identities=19%  Similarity=0.287  Sum_probs=32.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      +..-+++.|+.||||||+|..++.+-...+.-|+.|-+..++
T Consensus        79 ~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~  120 (264)
T cd01129          79 PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEY  120 (264)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCcee
Confidence            345689999999999999998887765566677777555444

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.

>CHL00181 cbbX CbbX; Provisional

Probab=95.53  E-value=0.019  Score=54.77  Aligned_cols=114  Identities=8%  Similarity=0.111  Sum_probs=63.0

Q ss_pred             EEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCC
Q psy3261         207 FVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESI  286 (342)
Q Consensus       207 LvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~  286 (342)
                      ++.||++-.++....   +.      ...-.....|+.++.....+-+||+|++...  -+.. ......+..+  |.. 
T Consensus       125 VLfIDE~~~l~~~~~---~~------~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~--~~~~-~~~np~L~sR--~~~-  189 (287)
T CHL00181        125 VLFIDEAYYLYKPDN---ER------DYGSEAIEILLQVMENQRDDLVVIFAGYKDR--MDKF-YESNPGLSSR--IAN-  189 (287)
T ss_pred             EEEEEccchhccCCC---cc------chHHHHHHHHHHHHhcCCCCEEEEEeCCcHH--HHHH-HhcCHHHHHh--CCc-
Confidence            677999976654311   00      0112566777777765555556666654321  0000 0001123332  211 


Q ss_pred             CCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHH-h-------hCCCHHHHhhhc
Q psy3261         287 DPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAF-L-------TKRVPQKMYEFC  339 (342)
Q Consensus       287 dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~-l-------SgGNP~~l~~lc  339 (342)
                          .++++.|+.+|...+++.+....-.. ++++...+.- +       .-||.|++++++
T Consensus       190 ----~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~v  247 (287)
T CHL00181        190 ----HVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNAL  247 (287)
T ss_pred             ----eEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHH
Confidence                38999999999999998887654322 4544433332 1       228999998875

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=95.51  E-value=0.017  Score=52.47  Aligned_cols=33  Identities=18%  Similarity=0.174  Sum_probs=27.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH--HhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA--HENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A--~~~gwiVl   99 (342)
                      ..+++|+|+.|+|||++|.++..-+  .+.||.|.
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~   63 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVP   63 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeE
Confidence            3889999999999999999998544  45688664

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

>PF13479 AAA_24: AAA domain

Probab=95.51  E-value=0.029  Score=50.92  Aligned_cols=35  Identities=17%  Similarity=0.241  Sum_probs=29.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLR  106 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~  106 (342)
                      ...+++|||++|+|||+++..+      .+.++|.+-....
T Consensus         2 ~~~~~lIyG~~G~GKTt~a~~~------~k~l~id~E~g~~   36 (213)
T PF13479_consen    2 KPIKILIYGPPGSGKTTLAASL------PKPLFIDTENGSD   36 (213)
T ss_pred             CceEEEEECCCCCCHHHHHHhC------CCeEEEEeCCCcc
Confidence            4679999999999999999888      8888888855533

>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=95.50  E-value=0.02  Score=51.48  Aligned_cols=35  Identities=20%  Similarity=0.220  Sum_probs=29.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .-++|.|+.|+||||+++-+.++...+|+=|.-|.
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis   36 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLKGKKVALIS   36 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhccccceeec
Confidence            35789999999999999999999998898887773

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 ....

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.49  E-value=0.023  Score=51.64  Aligned_cols=38  Identities=21%  Similarity=0.214  Sum_probs=33.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-+.|+|++|+|||++..|++..+..+|.-|+||.
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            45778899999999999999999998888888888884

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.49  E-value=0.027  Score=56.90  Aligned_cols=37  Identities=24%  Similarity=0.357  Sum_probs=29.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~  103 (342)
                      .+.++|||+.|||||.++..+.+.+.++  +.-|+|++.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            4679999999999999887777776664  567788753

>PRK04328 hypothetical protein; Provisional

Probab=95.47  E-value=0.021  Score=53.10  Aligned_cols=38  Identities=21%  Similarity=0.081  Sum_probs=34.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-++|.|++|||||++..|.+..+.++|.-++||.
T Consensus        21 p~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis   58 (249)
T PRK04328         21 PERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA   58 (249)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            56888999999999999999999998888898888883

>PRK05973 replicative DNA helicase; Provisional

Probab=95.44  E-value=0.024  Score=52.50  Aligned_cols=37  Identities=19%  Similarity=0.142  Sum_probs=32.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++.-++|.|++|+|||++..|++..+.++|-=|+|+
T Consensus        62 ~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyf   98 (237)
T PRK05973         62 KPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFF   98 (237)
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            4678899999999999999999999888888777777

>PF12846 AAA_10: AAA-like domain

Probab=95.44  E-value=0.02  Score=53.34  Aligned_cols=35  Identities=23%  Similarity=0.327  Sum_probs=31.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++.|+.|||||+++..++..+...|.-|+.+
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l~~~~~~~g~~~~i~   35 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNLLEQLIRRGPRVVIF   35 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHcCCCEEEE
Confidence            35689999999999999999999999988888777

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

Probab=95.41  E-value=0.025  Score=52.93  Aligned_cols=37  Identities=19%  Similarity=0.092  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh------CCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE------NNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~------~gwiVl~v  101 (342)
                      ....-.=|+|++|||||.++.|+...+..      .+--|+||
T Consensus        36 ~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyi   78 (256)
T PF08423_consen   36 PTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYI   78 (256)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEE
T ss_pred             CCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEE
Confidence            34566679999999999999999887642      24456666

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 ....

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.40  E-value=0.025  Score=49.71  Aligned_cols=28  Identities=14%  Similarity=0.111  Sum_probs=24.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      +..-.+|.|++|+|||+++.|++.....
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~   58 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALAT   58 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            5678999999999999999999886553

>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=95.37  E-value=0.024  Score=49.64  Aligned_cols=35  Identities=20%  Similarity=0.223  Sum_probs=30.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ++|.|+.||||||++..+..+....|+-|+.++..
T Consensus         3 I~ieG~~GsGKtT~~~~L~~~l~~~g~~v~~~~~~   37 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAERLEARGYEVVLTREP   37 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence            68999999999999999998888888888777543

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.37  E-value=0.06  Score=53.70  Aligned_cols=145  Identities=14%  Similarity=0.239  Sum_probs=90.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHH-HHhCcc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHF-QKQNTK  143 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~-~~~N~~  143 (342)
                      .+...+++.|=.||||||+..-+..|-.+.|.=|+-|..-             .++|.-|+|       |+.+ .+.+-+
T Consensus        98 ~~P~vImmvGLQGsGKTTt~~KLA~~lkk~~~kvllVaaD-------------~~RpAA~eQ-------L~~La~q~~v~  157 (451)
T COG0541          98 KPPTVILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAAD-------------TYRPAAIEQ-------LKQLAEQVGVP  157 (451)
T ss_pred             CCCeEEEEEeccCCChHhHHHHHHHHHHHcCCceEEEecc-------------cCChHHHHH-------HHHHHHHcCCc
Confidence            3567799999999999999999999999988877766321             124544544       6666 222322


Q ss_pred             ccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccch------------hHHHHHHHHHHhccccC-CCceEEEEE
Q psy3261         144 WLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYA------------SDVVDVLFTEIKKLSTE-GVCRTFVCV  210 (342)
Q Consensus       144 ~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a------------~~~~~~l~~EL~~~~~~-~~~pVLvav  210 (342)
                      ++.                 ...+.+-.+++..|+...+..            -..=..+|+||++-... .-.-+|++|
T Consensus       158 ~f~-----------------~~~~~~Pv~Iak~al~~ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVv  220 (451)
T COG0541         158 FFG-----------------SGTEKDPVEIAKAALEKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVV  220 (451)
T ss_pred             eec-----------------CCCCCCHHHHHHHHHHHHHHcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEE
Confidence            222                 123445667888887754322            12225688888765421 123489999


Q ss_pred             eCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc----------CCCCCeEEEEEeCCCC
Q psy3261         211 DGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ----------SDWNNGAIVLALSPRA  263 (342)
Q Consensus       211 D~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~----------~~~~~G~vv~AtS~~~  263 (342)
                      |..   .+..-              ...++.|.+.+.          |+-++|+.+.+.+.++
T Consensus       221 Dam---~GQdA--------------~~~A~aF~e~l~itGvIlTKlDGdaRGGaALS~~~~tg  266 (451)
T COG0541         221 DAM---IGQDA--------------VNTAKAFNEALGITGVILTKLDGDARGGAALSARAITG  266 (451)
T ss_pred             ecc---cchHH--------------HHHHHHHhhhcCCceEEEEcccCCCcchHHHhhHHHHC
Confidence            954   66665              677888887774          4445565555544443

>TIGR02012 tigrfam_recA protein RecA

Probab=95.37  E-value=0.022  Score=55.14  Aligned_cols=37  Identities=19%  Similarity=0.214  Sum_probs=32.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-+.|+|++|||||++..|++..+..+|=-|+||
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yI   89 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFI   89 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            5667888999999999999999999888877777788

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.

>PHA03133 thymidine kinase; Provisional

Probab=95.35  E-value=0.017  Score=56.37  Aligned_cols=41  Identities=17%  Similarity=0.248  Sum_probs=32.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      ...|++|+|+-|.||||++.++...+...+= |+|||++-.+
T Consensus        39 ~~~rvYlDG~~GvGKTTt~~~l~~a~~~~~~-vl~~pEPM~Y   79 (368)
T PHA03133         39 ALLRIYVDGPHGLGKTTTAAALAAALGRRDD-IEYVPEPMAY   79 (368)
T ss_pred             eEEEEEEeCCCcCCHHHHHHHHHHhhCCCCC-eEEecCcHHH
Confidence            5679999999999999999888886543322 8999987653

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.32  E-value=0.036  Score=50.70  Aligned_cols=39  Identities=21%  Similarity=0.152  Sum_probs=34.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .+..-++|+|++|||||++..|+++-+..+|-=|+|+.-
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            567889999999999999999998887778888888854

>PRK14974 cell division protein FtsY; Provisional

Probab=95.31  E-value=0.025  Score=55.08  Aligned_cols=36  Identities=22%  Similarity=0.368  Sum_probs=31.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+++.|+.|+||||+++.+.++...+|+-|+.+
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li  174 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIA  174 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            356899999999999999999999999988766555

>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=95.30  E-value=0.023  Score=47.28  Aligned_cols=31  Identities=23%  Similarity=0.224  Sum_probs=22.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      +++.|++|||||++..++   +...++.++....
T Consensus         2 ii~~G~pgsGKSt~a~~l---~~~~~~~~i~~D~   32 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRL---AKRLGAVVISQDE   32 (143)
T ss_dssp             EEEEESTTSSHHHHHHHH---HHHSTEEEEEHHH
T ss_pred             EEEECCCCCCHHHHHHHH---HHHCCCEEEeHHH
Confidence            689999999999997665   4455666655433

...

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.30  E-value=0.027  Score=53.24  Aligned_cols=36  Identities=14%  Similarity=0.217  Sum_probs=31.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+++.|+.|+||||+++.+..++.+.|+=|+-|
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li  106 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLA  106 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            456788999999999999999999998888877666

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=95.29  E-value=0.024  Score=58.38  Aligned_cols=50  Identities=22%  Similarity=0.339  Sum_probs=34.8

Q ss_pred             chhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          47 RNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        47 R~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .+-..||-++|+.+....++..-++|+||.|||||+++.-   .|.+.|+=|+
T Consensus        25 kkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~---La~elg~~v~   74 (519)
T PF03215_consen   25 KKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKV---LAKELGFEVQ   74 (519)
T ss_pred             HHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHH---HHHHhCCeeE
Confidence            3456688888887434444456788899999999998854   3456666554

>PRK06696 uridine kinase; Validated

Probab=95.28  E-value=0.05  Score=49.59  Aligned_cols=38  Identities=11%  Similarity=0.054  Sum_probs=30.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .....+.|.|..||||||+..++.......|.-|++++
T Consensus        20 ~~~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~   57 (223)
T PRK06696         20 TRPLRVAIDGITASGKTTFADELAEEIKKRGRPVIRAS   57 (223)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            45678899999999999999888877666676665544

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=95.27  E-value=0.025  Score=56.36  Aligned_cols=55  Identities=22%  Similarity=0.275  Sum_probs=35.0

Q ss_pred             HHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcc
Q psy3261          54 VGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKE  113 (342)
Q Consensus        54 ~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~  113 (342)
                      ++.|+.|.. +.++.-+|+.||+||||+.+..+-+-.-+.+   ||+|. |..+++..+|
T Consensus         5 ~~~L~~wL~-e~~~TFIvV~GPrGSGK~elV~d~~L~~r~~---vL~ID-C~~i~~ar~D   59 (431)
T PF10443_consen    5 IEQLKSWLN-ENPNTFIVVQGPRGSGKRELVMDHVLKDRKN---VLVID-CDQIVKARGD   59 (431)
T ss_pred             HHHHHHHHh-cCCCeEEEEECCCCCCccHHHHHHHHhCCCC---EEEEE-ChHhhhccCh
Confidence            344444322 2567899999999999999984433333555   77774 4466665433

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=95.25  E-value=0.013  Score=42.82  Aligned_cols=22  Identities=27%  Similarity=0.265  Sum_probs=17.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+|+|+.|||||++|--+..
T Consensus        24 ~~tli~G~nGsGKSTllDAi~~   45 (62)
T PF13555_consen   24 DVTLITGPNGSGKSTLLDAIQT   45 (62)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4699999999999999864443

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.22  E-value=0.028  Score=49.04  Aligned_cols=57  Identities=28%  Similarity=0.226  Sum_probs=41.1

Q ss_pred             hhHHhhhhcCCceEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          31 VFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        31 ~~~~~~~~~~~~~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++.+..+.++-+.+.+...+-+-++.|+...    ++...+|.|+.|+|||++++.++-.+
T Consensus         3 ~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l----~~k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen    3 ELLEQYEKLGYPVFFISAKTGEGIEELKELL----KGKTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             HHHHHHHHTTSEEEE-BTTTTTTHHHHHHHH----TTSEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             HHHHHHHHcCCcEEEEeCCCCcCHHHHHHHh----cCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3455666677777777766666666665522    24789999999999999999988764

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.

>KOG0780|consensus

Probab=95.22  E-value=0.13  Score=50.61  Aligned_cols=145  Identities=17%  Similarity=0.215  Sum_probs=85.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWL  145 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L  145 (342)
                      +..-+++.|=.|+||||++.-..+|-..+||=+.-|-  -           ++.++|-|||-       +    .|+...
T Consensus       100 kpsVimfVGLqG~GKTTtc~KlA~y~kkkG~K~~Lvc--a-----------DTFRagAfDQL-------k----qnA~k~  155 (483)
T KOG0780|consen  100 KPSVIMFVGLQGSGKTTTCTKLAYYYKKKGYKVALVC--A-----------DTFRAGAFDQL-------K----QNATKA  155 (483)
T ss_pred             CCcEEEEEeccCCCcceeHHHHHHHHHhcCCceeEEe--e-----------cccccchHHHH-------H----HHhHhh
Confidence            5678889999999999999999999999999887661  1           12256667662       1    222222


Q ss_pred             CCCCcccccceecCCCCCCCCCCCHHHHHHhhccccc------------chhHHHHHHHHHHhccccCCC-ceEEEEEeC
Q psy3261         146 EDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVK------------YASDVVDVLFTEIKKLSTEGV-CRTFVCVDG  212 (342)
Q Consensus       146 ~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~------------~a~~~~~~l~~EL~~~~~~~~-~pVLvavD~  212 (342)
                         +++.--.|.-         .--..++..|+.+-+            -+-..=..+++|+++-+..-+ --|++++|.
T Consensus       156 ---~iP~ygsyte---------~dpv~ia~egv~~fKke~fdvIIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDa  223 (483)
T KOG0780|consen  156 ---RVPFYGSYTE---------ADPVKIASEGVDRFKKENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDA  223 (483)
T ss_pred             ---CCeeEecccc---------cchHHHHHHHHHHHHhcCCcEEEEeCCCchhhhHHHHHHHHHHHhhcCCCeEEEEEec
Confidence               2443333221         112355555554321            122223457788777653222 237888885


Q ss_pred             ccccccCCCcCCCCCCCcccCCccchHHHHHHhhc----------CCCCCeEEEEEeCCCC
Q psy3261         213 YNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ----------SDWNNGAIVLALSPRA  263 (342)
Q Consensus       213 ~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~----------~~~~~G~vv~AtS~~~  263 (342)
                      -   .+...              ...+++|..-+.          |.-++|..+.|.--+.
T Consensus       224 s---iGQaa--------------e~Qa~aFk~~vdvg~vIlTKlDGhakGGgAlSaVaaTk  267 (483)
T KOG0780|consen  224 S---IGQAA--------------EAQARAFKETVDVGAVILTKLDGHAKGGGALSAVAATK  267 (483)
T ss_pred             c---ccHhH--------------HHHHHHHHHhhccceEEEEecccCCCCCceeeehhhhC
Confidence            3   44444              567777777664          4456776655554443

>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=95.19  E-value=0.019  Score=46.09  Aligned_cols=25  Identities=24%  Similarity=0.367  Sum_probs=20.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      |+++.|++|||||+++.+++..-..
T Consensus         1 kI~V~G~~g~GKTsLi~~l~~~~~~   25 (119)
T PF08477_consen    1 KIVVLGDSGVGKTSLIRRLCGGEFP   25 (119)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS--
T ss_pred             CEEEECcCCCCHHHHHHHHhcCCCc
Confidence            6899999999999999998865433

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.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.18  E-value=0.016  Score=52.50  Aligned_cols=35  Identities=17%  Similarity=0.215  Sum_probs=32.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      -++|+|.+|||||+.-.+++.--++++|-|+++-.
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~~~i~~vi~l~k   37 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEK   37 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHHHhhhhccccch
Confidence            37899999999999999999999999999999854

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.16  E-value=0.027  Score=48.13  Aligned_cols=32  Identities=19%  Similarity=0.096  Sum_probs=27.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|.+|||||++...+..+....|+-++++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i   33 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVL   33 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            68999999999999999999888888766655

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK06851 hypothetical protein; Provisional

Probab=95.13  E-value=0.029  Score=55.27  Aligned_cols=36  Identities=25%  Similarity=0.290  Sum_probs=30.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ....++|+|++|+|||+++.++...+.+.|+-|-++
T Consensus        29 ~~~~~il~G~pGtGKStl~~~i~~~~~~~g~~Ve~~   64 (367)
T PRK06851         29 ANRIFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFL   64 (367)
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            456799999999999999999999988888876443

>PRK06620 hypothetical protein; Validated

Probab=95.12  E-value=0.028  Score=51.22  Aligned_cols=48  Identities=17%  Similarity=0.010  Sum_probs=31.7

Q ss_pred             eeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         291 PIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      .+++...+.++...++..... .|+--.++-..-|---++|+.+.+...
T Consensus       141 ~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~d~r~l~~~  189 (214)
T PRK06620        141 SILLNSPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPREYSKIIEI  189 (214)
T ss_pred             eEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHH
Confidence            378899999999999966655 554214443333444677887777654

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=95.07  E-value=0.039  Score=44.31  Aligned_cols=26  Identities=19%  Similarity=0.323  Sum_probs=23.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .++|.|+.|+|||+++...+.+....
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~   27 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDS   27 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhc
Confidence            57999999999999999999988754

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK13764 ATPase; Provisional

Probab=95.05  E-value=0.034  Score=58.09  Aligned_cols=43  Identities=12%  Similarity=0.106  Sum_probs=36.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccccc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFA  109 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~  109 (342)
                      ...++++|++||||||+|..++.+.-.++-+|+.+=++.++..
T Consensus       257 ~~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~~  299 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQV  299 (602)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEECCCccccC
Confidence            4569999999999999999988888888999988876666643

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.05  E-value=0.031  Score=55.25  Aligned_cols=38  Identities=18%  Similarity=0.298  Sum_probs=33.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|+|||+++.|+.+....+|.=|+||.
T Consensus        80 ~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs  117 (372)
T cd01121          80 VPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVS  117 (372)
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            45678899999999999999999988877877888884

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.

>PHA03135 thymidine kinase; Provisional

Probab=95.03  E-value=0.025  Score=54.82  Aligned_cols=42  Identities=17%  Similarity=0.203  Sum_probs=31.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      ..-.|++|+|+-|+||||++.++..... +|--|+|||++-.+
T Consensus         8 ~~~~rIYlDG~~GvGKTT~~~~l~~~~~-~~~~vl~vpEPM~Y   49 (343)
T PHA03135          8 AQLIRVYLDGPFGIGKTSMLNEMPDHSP-DGVPVLKVFEPMKY   49 (343)
T ss_pred             ceEEEEEEECCCCCCHHHHHHHHHHhcC-CCCceEEecCcHHH
Confidence            4567999999999999999966665433 33338888876543

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.03  E-value=0.026  Score=52.68  Aligned_cols=48  Identities=13%  Similarity=0.135  Sum_probs=32.7

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHH----------hhCCCHHHHhhh
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAF----------LTKRVPQKMYEF  338 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~----------lSgGNP~~l~~l  338 (342)
                      .++++.|+.+|...+++.+....-.. +++....+.-          -+.||.|.++.+
T Consensus       172 ~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n~  230 (261)
T TIGR02881       172 SIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNI  230 (261)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHHH
Confidence            37899999999999998887754333 4443333311          246898888765

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.02  E-value=0.039  Score=49.45  Aligned_cols=33  Identities=27%  Similarity=0.464  Sum_probs=24.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      -++|.|+.||||||+|..++.+.... +--|+.+
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~   36 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTI   36 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEE
Confidence            47899999999999998887776543 3334444

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.

>KOG0743|consensus

Probab=95.01  E-value=0.015  Score=58.13  Aligned_cols=60  Identities=18%  Similarity=0.324  Sum_probs=36.3

Q ss_pred             HHHHHhhcCCCCCe----EEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC
Q psy3261         240 RSVINLVQSDWNNG----AIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK  312 (342)
Q Consensus       240 ~~~~~~~~~~~~~G----~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~  312 (342)
                      ..|++++.|=|...    .||.+|..-.    +    |-..|++.-..+     .-|+|+.=+.+.|+.|...|-..
T Consensus       322 SGLLNfiDGlwSscg~ERIivFTTNh~E----k----LDPALlRpGRmD-----mhI~mgyCtf~~fK~La~nYL~~  385 (457)
T KOG0743|consen  322 SGLLNFLDGLWSSCGDERIIVFTTNHKE----K----LDPALLRPGRMD-----MHIYMGYCTFEAFKTLASNYLGI  385 (457)
T ss_pred             HHhhhhhccccccCCCceEEEEecCChh----h----cCHhhcCCCcce-----eEEEcCCCCHHHHHHHHHHhcCC
Confidence            45778888877543    4566654422    1    123455432222     13889999999999999655544

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=94.98  E-value=0.033  Score=50.60  Aligned_cols=37  Identities=16%  Similarity=0.195  Sum_probs=30.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      .++.-++|.|++|||||++..|.+..+.++ |==|+||
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyv   54 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYV   54 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEE
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEE
Confidence            567889999999999999999999887776 7777776

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>cd03114 ArgK-like The function of this protein family is unkown

Probab=94.97  E-value=0.039  Score=47.24  Aligned_cols=33  Identities=15%  Similarity=0.130  Sum_probs=27.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++.+.|+.|||||+++.++..+..+.|+=|+.+
T Consensus         1 ~i~~~G~~GsGKTt~~~~l~~~~~~~g~~v~ii   33 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITALRARGKRVAVL   33 (148)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            367889999999999999999888887755544

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

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

Probab=94.95  E-value=0.034  Score=53.93  Aligned_cols=38  Identities=18%  Similarity=0.207  Sum_probs=32.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-+.|+|++|||||++..|++..+..+|=.++||.
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            45667789999999999999999998887776777874

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR00235 udk uridine kinase

Probab=94.94  E-value=0.028  Score=50.52  Aligned_cols=37  Identities=11%  Similarity=0.072  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++..+.|.|+.||||||++..+.......++.+++.
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~l~~~~~~~i~~   40 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQLGKLEIVIISQ   40 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHhcccCCeEecc
Confidence            3456778999999999999988877654444545443

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

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.94  E-value=0.051  Score=50.93  Aligned_cols=34  Identities=18%  Similarity=0.210  Sum_probs=26.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +..++|.|++|||||++..++. .+....++.++.
T Consensus        21 g~~vLL~G~~GtGKT~lA~~la-~~lg~~~~~i~~   54 (262)
T TIGR02640        21 GYPVHLRGPAGTGKTTLAMHVA-RKRDRPVMLING   54 (262)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHH-HHhCCCEEEEeC
Confidence            6789999999999999887664 355556666655

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).

>PRK00889 adenylylsulfate kinase; Provisional

Probab=94.92  E-value=0.046  Score=47.62  Aligned_cols=36  Identities=17%  Similarity=0.154  Sum_probs=30.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++.-++|.|.+|||||++..++.......|+=|++|
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~i   38 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVL   38 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            456789999999999999999999888888656555

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

Probab=94.91  E-value=0.033  Score=44.83  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=20.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      +.|+|++|+|||++...+.....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            47999999999999999777665

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

>smart00763 AAA_PrkA PrkA AAA domain

Probab=94.91  E-value=0.045  Score=53.70  Aligned_cols=48  Identities=23%  Similarity=0.270  Sum_probs=34.0

Q ss_pred             echhHHHHHHHHHhccCC-CCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          46 IRNCMLELVGYLKSMTNF-DRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        46 vR~~t~el~~~l~~~~~~-~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ..+.-.+++++++.++.. ..+..-++|.||+|||||++...+......
T Consensus        56 ~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       56 MEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            445667788888874433 234455699999999999988777665543

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

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=94.90  E-value=0.022  Score=49.75  Aligned_cols=25  Identities=44%  Similarity=0.631  Sum_probs=21.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ..-.+|+|+.|+|||++| .++.||.
T Consensus        19 ~g~~vi~G~Ng~GKStil-~ai~~~L   43 (202)
T PF13476_consen   19 PGLNVIYGPNGSGKSTIL-EAIRYAL   43 (202)
T ss_dssp             SEEEEEEESTTSSHHHHH-HHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH-HHHHHHH
Confidence            357799999999999999 7778876

>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=94.89  E-value=0.059  Score=49.54  Aligned_cols=72  Identities=14%  Similarity=0.156  Sum_probs=45.3

Q ss_pred             eEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCC
Q psy3261         253 GAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRV  331 (342)
Q Consensus       253 G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGN  331 (342)
                      =.+|+||++.+.+..|.        ..+-|+       ..++.-|+.+|...++..-...--+. .+++..|+-.-|.|.
T Consensus       150 FTligATTr~g~ls~pL--------rdRFgi-------~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGt  214 (233)
T PF05496_consen  150 FTLIGATTRAGLLSSPL--------RDRFGI-------VLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGT  214 (233)
T ss_dssp             -EEEEEESSGCCTSHCC--------CTTSSE-------EEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTS
T ss_pred             ceEeeeeccccccchhH--------Hhhcce-------ecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCC
Confidence            36799999877433321        112121       24788899999999998765443332 777888899999999


Q ss_pred             HHHHhhhc
Q psy3261         332 PQKMYEFC  339 (342)
Q Consensus       332 P~~l~~lc  339 (342)
                      ||-.-+++
T Consensus       215 PRiAnrll  222 (233)
T PF05496_consen  215 PRIANRLL  222 (233)
T ss_dssp             HHHHHHHH
T ss_pred             hHHHHHHH
Confidence            99877764

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.

>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=94.88  E-value=0.053  Score=50.75  Aligned_cols=85  Identities=14%  Similarity=0.095  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC--eEEEEe-CCccccccCC-----cceeccCCC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENN--YLLVHI-PWVLRWFAYP-----KEVSHSLTK  120 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g--wiVl~v-P~~~~~~~~~-----~~~~~s~~~  120 (342)
                      ...+|++.+-.   .+.++.++=|||++|+|||+++..++.+.++.|  --||-| |+. .++-|.     .-...-..+
T Consensus        14 ~~~~ll~~l~~---~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSS-p~tGGAlLGDRiRM~~~~~d   89 (266)
T PF03308_consen   14 EARELLKRLYP---HTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSS-PFTGGALLGDRIRMQELSRD   89 (266)
T ss_dssp             HHHHHHHHHGG---GTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGG-GCC---SS--GGGCHHHHTS
T ss_pred             HHHHHHHHHHh---hcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCC-CCCCCcccccHHHhcCcCCC
Confidence            45566666644   335678999999999999999999999888765  556777 543 333321     111111125


Q ss_pred             CCccccHHHHHHHHHHH
Q psy3261         121 EGMVDLNIDAAMWLRHF  137 (342)
Q Consensus       121 ~~~~~qP~~a~~~L~~~  137 (342)
                      ++.|.-|+.++--|=-+
T Consensus        90 ~~vfIRS~atRG~lGGl  106 (266)
T PF03308_consen   90 PGVFIRSMATRGSLGGL  106 (266)
T ss_dssp             TTEEEEEE---SSHHHH
T ss_pred             CCEEEeecCcCCCCCCc
Confidence            67776666655544444

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.

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=94.88  E-value=0.072  Score=45.68  Aligned_cols=28  Identities=18%  Similarity=0.245  Sum_probs=24.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ...+++|.++.|||||.++..++.....
T Consensus        24 ~~~~~ll~~~tGsGKT~~~~~~~~~l~~   51 (184)
T PF04851_consen   24 EERRVLLNAPTGSGKTIIALALILELAR   51 (184)
T ss_dssp             GCSEEEEEESTTSSHHHHHHHHHHHHHC
T ss_pred             CCCCEEEEECCCCCcChhhhhhhhcccc
Confidence            5789999999999999999987776666

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=94.87  E-value=0.039  Score=52.39  Aligned_cols=37  Identities=22%  Similarity=0.177  Sum_probs=29.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-C-eEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-N-YLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-g-wiVl~vP  102 (342)
                      ....++|.|+.|+||||+++.+..++..+ | +=|..|.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            35578899999999999999999988764 4 6666553

>PRK10263 DNA translocase FtsK; Provisional

Probab=94.86  E-value=0.35  Score=54.40  Aligned_cols=67  Identities=22%  Similarity=0.206  Sum_probs=40.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH-Hh--CCeEEEEe--CCccccccCCcceeccCC-CCCccccHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA-HE--NNYLLVHI--PWVLRWFAYPKEVSHSLT-KEGMVDLNIDAAMWLRHF  137 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A-~~--~gwiVl~v--P~~~~~~~~~~~~~~s~~-~~~~~~qP~~a~~~L~~~  137 (342)
                      ..+++|.|-.|||||++|..++.-. ..  -+-+=+++  |..-++...    .--+. -....+.+..+.+.|+.+
T Consensus      1010 ~PHLLIAGaTGSGKSv~LntLIlSLl~~~sPeeVrl~LIDPK~vELs~y----e~LPHl~~~VvtD~eka~~aLr~l 1082 (1355)
T PRK10263       1010 MPHLLVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPKMLELSVY----EGIPHLLTEVVTDMKDAANALRWC 1082 (1355)
T ss_pred             CCcEEEecCCCCCHHHHHHHHHHHHHHhCCccceEEEEECCCccchhhh----ccCccccceeecCHHHHHHHHHHH
Confidence            4799999999999999999988733 22  24555555  333222221    11111 112345577888888877

>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=94.86  E-value=0.049  Score=47.71  Aligned_cols=51  Identities=18%  Similarity=0.223  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH--hCCeEEEEeC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH--ENNYLLVHIP  102 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~--~~gwiVl~vP  102 (342)
                      ...++++.+++++   .....++|+|++||||+.+...+.....  ...+|.|+-.
T Consensus         7 ~m~~~~~~~~~~a---~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~   59 (168)
T PF00158_consen    7 AMKRLREQAKRAA---SSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCA   59 (168)
T ss_dssp             HHHHHHHHHHHHT---TSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETT
T ss_pred             HHHHHHHHHHHHh---CCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehh
Confidence            4567777777733   3458999999999999987555555443  3457777774

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 ....

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=94.83  E-value=0.045  Score=50.08  Aligned_cols=46  Identities=15%  Similarity=0.153  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      -...|.+.|.+......+...+.|.|+.||||||+...+...-...
T Consensus        15 ~~~~l~~~~~~~~~~~~~~~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         15 VHKPLLRRLAALQAEPQRRTIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            4456667776644444667889999999999999999888776654

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=94.82  E-value=0.056  Score=53.18  Aligned_cols=40  Identities=20%  Similarity=0.311  Sum_probs=33.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CCc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PWV  104 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~~  104 (342)
                      .....++|+|+.|||||+++..+.++++..+=.|+.+ |.+
T Consensus        20 ~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg   60 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTG   60 (364)
T ss_pred             cCCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchH
Confidence            5678999999999999999999999999876666655 543

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=94.81  E-value=1.7  Score=42.18  Aligned_cols=113  Identities=11%  Similarity=0.091  Sum_probs=66.4

Q ss_pred             hHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCC
Q psy3261         185 SDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRAN  264 (342)
Q Consensus       185 ~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~  264 (342)
                      .+.+..+.+.+...+..+..+| +.||+...+    +              .+-...|++.+...+.+..+|+.++....
T Consensus        90 vdqiR~l~~~~~~~~~~~~~kV-~iI~~ae~m----~--------------~~AaNaLLKtLEEPp~~t~fiL~t~~~~~  150 (319)
T PRK06090         90 VEQIRQCNRLAQESSQLNGYRL-FVIEPADAM----N--------------ESASNALLKTLEEPAPNCLFLLVTHNQKR  150 (319)
T ss_pred             HHHHHHHHHHHhhCcccCCceE-EEecchhhh----C--------------HHHHHHHHHHhcCCCCCeEEEEEECChhh
Confidence            4444444445443322345565 456777444    2              45678999999988888888888775432


Q ss_pred             CCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         265 LPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       265 ~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +       +|- +.-+-        ..+.++..+.+++...+.   +.|.-  .  ...+..+++|+|....++.
T Consensus       151 l-------LpT-I~SRC--------q~~~~~~~~~~~~~~~L~---~~~~~--~--~~~~l~l~~G~p~~A~~~~  202 (319)
T PRK06090        151 L-------LPT-IVSRC--------QQWVVTPPSTAQAMQWLK---GQGIT--V--PAYALKLNMGSPLKTLAMM  202 (319)
T ss_pred             C-------hHH-HHhcc--------eeEeCCCCCHHHHHHHHH---HcCCc--h--HHHHHHHcCCCHHHHHHHh
Confidence            1       121 11110        126777888888776553   44432  1  2356668999998877664

>PRK09354 recA recombinase A; Provisional

Probab=94.79  E-value=0.04  Score=53.88  Aligned_cols=38  Identities=18%  Similarity=0.194  Sum_probs=32.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-+.|+|+.|||||++..|++.-|...|=.++||.
T Consensus        58 p~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId   95 (349)
T PRK09354         58 PRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   95 (349)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEC
Confidence            45667779999999999999999999888887888883

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=94.79  E-value=0.2  Score=53.98  Aligned_cols=37  Identities=19%  Similarity=0.249  Sum_probs=31.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-+.|+|+.|||||+++.|++.-|...|=-|+||
T Consensus        58 p~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yI   94 (790)
T PRK09519         58 PRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFI   94 (790)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            4577788999999999999999998887777667776

>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=94.78  E-value=0.029  Score=53.03  Aligned_cols=37  Identities=24%  Similarity=0.411  Sum_probs=29.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ....++|.|+.|||||+++.+.+.--....|++..++
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~   68 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITIN   68 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEE
T ss_pred             cCCcEEEECCCCCchhHHHHhhhccCCccccceeEee
Confidence            3678999999999999999998864445567766653

>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=94.76  E-value=0.053  Score=40.06  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=19.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      +.|.|++|||||++...+...-
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999888775

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.

>PRK01184 hypothetical protein; Provisional

Probab=94.76  E-value=0.032  Score=48.99  Aligned_cols=30  Identities=23%  Similarity=0.148  Sum_probs=23.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++|+|++||||||+ +.   .|.+.|+-++...
T Consensus         3 ~i~l~G~~GsGKsT~-a~---~~~~~g~~~i~~~   32 (184)
T PRK01184          3 IIGVVGMPGSGKGEF-SK---IAREMGIPVVVMG   32 (184)
T ss_pred             EEEEECCCCCCHHHH-HH---HHHHcCCcEEEhh
Confidence            578999999999995 44   4677888777663

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.75  E-value=0.055  Score=55.27  Aligned_cols=37  Identities=19%  Similarity=0.206  Sum_probs=33.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|.|++|+|||+++.|.+..+.++|==++||
T Consensus       261 ~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~  297 (484)
T TIGR02655       261 FKDSIILATGATGTGKTLLVSKFLENACANKERAILF  297 (484)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            5788999999999999999999999998888777776

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PHA03138 thymidine kinase; Provisional

Probab=94.73  E-value=0.035  Score=53.85  Aligned_cols=40  Identities=28%  Similarity=0.153  Sum_probs=29.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVL  105 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~  105 (342)
                      ...|++|+|+-|+||||++.+.+++....+=-|++||++-
T Consensus        11 ~~~riYleG~~GvGKTT~~~~~l~~~~~~~~~vl~vpEPm   50 (340)
T PHA03138         11 CILRIYLDGAFGIGKTTAAEAFLHGFAINPNRIFFIGEPL   50 (340)
T ss_pred             cEEEEEEECCCCcCHHhHHHHHHHhhhcCCCceEEeeCch
Confidence            4579999999999999999988777655432244555443

>KOG0735|consensus

Probab=94.71  E-value=0.25  Score=52.23  Aligned_cols=96  Identities=13%  Similarity=0.151  Sum_probs=55.4

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc--CCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ--SDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~--~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      -|-+|..||+-.+++-+.    .++.+-.-..=.|..++-+++.  ++.++-+.+.||.++-.       .+++.|...+
T Consensus       494 ~PSiIvLDdld~l~~~s~----~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~q-------tl~~~L~s~~  562 (952)
T KOG0735|consen  494 APSIIVLDDLDCLASASS----NENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQ-------TLNPLLVSPL  562 (952)
T ss_pred             CCcEEEEcchhhhhccCc----ccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhh-------hcChhhcCcc
Confidence            488999999999998322    2233322222234444445543  34456656667665531       1222232222


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWL  315 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l  315 (342)
                      -|.     ..+.+++....+=..++.+.-+.+.+
T Consensus       563 ~Fq-----~~~~L~ap~~~~R~~IL~~~~s~~~~  591 (952)
T KOG0735|consen  563 LFQ-----IVIALPAPAVTRRKEILTTIFSKNLS  591 (952)
T ss_pred             ceE-----EEEecCCcchhHHHHHHHHHHHhhhh
Confidence            221     24778888898888899888777763

>PRK11823 DNA repair protein RadA; Provisional

Probab=94.70  E-value=0.042  Score=55.61  Aligned_cols=38  Identities=18%  Similarity=0.274  Sum_probs=32.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|+|||+++.|+.+.+.++|-=|+||.
T Consensus        78 ~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs  115 (446)
T PRK11823         78 VPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVS  115 (446)
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            45678899999999999999999987777787888884

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=94.68  E-value=0.04  Score=57.59  Aligned_cols=39  Identities=23%  Similarity=0.299  Sum_probs=33.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh--CCeEEEEeCCc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE--NNYLLVHIPWV  104 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~--~gwiVl~vP~~  104 (342)
                      ..+.++|+|+.|||||.+|.-+.+++.+  .|.-|+|++..
T Consensus       313 ~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitae  353 (617)
T PRK14086        313 AYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSE  353 (617)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH
Confidence            3456999999999999999999998875  48889999754

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=94.65  E-value=0.048  Score=50.94  Aligned_cols=42  Identities=19%  Similarity=0.149  Sum_probs=32.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      ....+++.|+.||||||+|..++.+.-..+.-|+.|=+..++
T Consensus       126 ~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~  167 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPEL  167 (270)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S
T ss_pred             cceEEEEECCCccccchHHHHHhhhccccccceEEeccccce
Confidence            367899999999999999999988777775777777444333

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>KOG1514|consensus

Probab=94.64  E-value=2.1  Score=45.36  Aligned_cols=209  Identities=12%  Similarity=0.158  Sum_probs=113.0

Q ss_pred             ech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH---hCCeEEEEeCCccccccCCcceeccCCCC
Q psy3261          46 IRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH---ENNYLLVHIPWVLRWFAYPKEVSHSLTKE  121 (342)
Q Consensus        46 vR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~---~~gwiVl~vP~~~~~~~~~~~~~~s~~~~  121 (342)
                      -|+ +-.+|-++++........+..++|.|-+|||||.+..-+|---.   ++|=              ...|.|-..+.
T Consensus       400 cRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e--------------~p~f~yveINg  465 (767)
T KOG1514|consen  400 CRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKE--------------LPKFDYVEING  465 (767)
T ss_pred             chhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcC--------------CCCccEEEEcc
Confidence            355 66677788877333334556899999999999999988876322   1110              00111111122


Q ss_pred             CccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHH-HHHHHHHHhcccc
Q psy3261         122 GMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDV-VDVLFTEIKKLST  200 (342)
Q Consensus       122 ~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~-~~~l~~EL~~~~~  200 (342)
                      ....-|..+..|+..=            +                            .-....+.+ +.+|-.-.. ...
T Consensus       466 m~l~~~~~~Y~~I~~~------------l----------------------------sg~~~~~~~al~~L~~~f~-~~k  504 (767)
T KOG1514|consen  466 LRLASPREIYEKIWEA------------L----------------------------SGERVTWDAALEALNFRFT-VPK  504 (767)
T ss_pred             eeecCHHHHHHHHHHh------------c----------------------------ccCcccHHHHHHHHHHhhc-cCC
Confidence            2233344444444322            2                            111111111 111111111 223


Q ss_pred             CCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhh-
Q psy3261         201 EGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLK-  279 (342)
Q Consensus       201 ~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg-  279 (342)
                      +.+.|.+|.||+.-.+.+.+.               .+...|.++..-. +--.+|.++..+-        .||..++. 
T Consensus       505 ~~~~~~VvLiDElD~Lvtr~Q---------------dVlYn~fdWpt~~-~sKLvvi~IaNTm--------dlPEr~l~n  560 (767)
T KOG1514|consen  505 PKRSTTVVLIDELDILVTRSQ---------------DVLYNIFDWPTLK-NSKLVVIAIANTM--------DLPERLLMN  560 (767)
T ss_pred             CCCCCEEEEeccHHHHhcccH---------------HHHHHHhcCCcCC-CCceEEEEecccc--------cCHHHHhcc
Confidence            568999999999999988865               3344444444322 2335666666543        25655554 


Q ss_pred             ----hcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH----hhCCCHHHHhhhcc
Q psy3261         280 ----KAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF----LTKRVPQKMYEFCS  340 (342)
Q Consensus       280 ----~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~----lSgGNP~~l~~lc~  340 (342)
                          +.|+.      .+.+..|+..|...++.-=.. |.-.++.+.-||--    .-.|.-+...++|.
T Consensus       561 rvsSRlg~t------Ri~F~pYth~qLq~Ii~~RL~-~~~~f~~~aielvarkVAavSGDaRraldic~  622 (767)
T KOG1514|consen  561 RVSSRLGLT------RICFQPYTHEQLQEIISARLK-GLDAFENKAIELVARKVAAVSGDARRALDICR  622 (767)
T ss_pred             chhhhccce------eeecCCCCHHHHHHHHHHhhc-chhhcchhHHHHHHHHHHhccccHHHHHHHHH
Confidence                34553      378889999999888743221 22114554444332    55677787778774

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=94.63  E-value=0.033  Score=47.81  Aligned_cols=29  Identities=28%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|++|||||++...+....   |+.++..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l---~~~~v~~   29 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL---GAKFIEG   29 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc---CCeEEeC
Confidence            4789999999998877766553   5655543

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.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=94.62  E-value=0.053  Score=46.83  Aligned_cols=32  Identities=16%  Similarity=0.294  Sum_probs=29.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +.|.|+.|||||+++..++......|+=|..|
T Consensus         2 i~i~G~~gsGKTtl~~~l~~~l~~~G~~V~vi   33 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVKALKARGYRVATI   33 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            56889999999999999999999999988777

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.

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

Probab=94.60  E-value=0.99  Score=48.99  Aligned_cols=25  Identities=28%  Similarity=0.307  Sum_probs=19.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+...++|.|++|||||++...+..
T Consensus       347 ~~g~~i~l~GppG~GKTtl~~~ia~  371 (784)
T PRK10787        347 IKGPILCLVGPPGVGKTSLGQSIAK  371 (784)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHH
Confidence            3567899999999999976665554

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.60  E-value=0.043  Score=46.33  Aligned_cols=28  Identities=21%  Similarity=0.183  Sum_probs=22.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ++|+|++|||||++..++...   .|+.++.
T Consensus         2 i~l~G~~GsGKST~a~~l~~~---~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAER---LGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhh---cCCEEEe
Confidence            689999999999999887554   4665553

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK07261 topology modulation protein; Provisional

Probab=94.58  E-value=0.032  Score=48.87  Aligned_cols=31  Identities=26%  Similarity=0.319  Sum_probs=23.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .|++|.|+.||||||+..++..   ..|.-+++.
T Consensus         1 ~ri~i~G~~GsGKSTla~~l~~---~~~~~~i~~   31 (171)
T PRK07261          1 MKIAIIGYSGSGKSTLARKLSQ---HYNCPVLHL   31 (171)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH---HhCCCeEec
Confidence            3799999999999999988743   345555555

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.58  E-value=0.05  Score=54.87  Aligned_cols=37  Identities=16%  Similarity=0.264  Sum_probs=32.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +...++++|+.||||||+++.+..+..++|+=|+.|.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~  130 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVA  130 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEec
Confidence            4568899999999999999999999999998887773

>TIGR00416 sms DNA repair protein RadA

Probab=94.58  E-value=0.043  Score=55.66  Aligned_cols=38  Identities=21%  Similarity=0.344  Sum_probs=32.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|.|++|+|||+++.|+...+..+|-=|+||.
T Consensus        92 ~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs  129 (454)
T TIGR00416        92 VPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVS  129 (454)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            56778999999999999999999887777766677873

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=94.58  E-value=0.067  Score=40.59  Aligned_cols=33  Identities=21%  Similarity=0.239  Sum_probs=29.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +++.|..|+|||++..++.....+.|.=|+.+.
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~   34 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence            578899999999999999999888887777776

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PHA00729 NTP-binding motif containing protein

Probab=94.57  E-value=0.077  Score=48.82  Aligned_cols=25  Identities=20%  Similarity=0.351  Sum_probs=20.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ..++|+|++|+|||++...+...+.
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4799999999999998877776543

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.54  E-value=0.056  Score=52.29  Aligned_cols=36  Identities=14%  Similarity=0.141  Sum_probs=30.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+.|.|+.|+||||++..+..+....|.=|+-+
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li  148 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLA  148 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEE
Confidence            456888999999999999999999998888766555

>PRK14532 adenylate kinase; Provisional

Probab=94.54  E-value=0.044  Score=48.23  Aligned_cols=30  Identities=17%  Similarity=0.328  Sum_probs=23.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|.|++||||||....+   |...||..+..
T Consensus         2 ~i~~~G~pGsGKsT~a~~l---a~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRL---VEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHcCCeEEeC
Confidence            5899999999999987666   45568777654

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=94.52  E-value=0.063  Score=54.94  Aligned_cols=42  Identities=19%  Similarity=0.284  Sum_probs=31.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      +..-++++|+.||||||+|..++..-...+--|+.|-++.++
T Consensus       241 ~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~  282 (486)
T TIGR02533       241 PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEY  282 (486)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeee
Confidence            344689999999999999988877665556667777555544

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>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=94.52  E-value=0.043  Score=48.20  Aligned_cols=31  Identities=19%  Similarity=0.243  Sum_probs=23.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      |++|.|++|||||++...+..   .-|+.++.+.
T Consensus         1 ~I~i~G~pGsGKst~a~~La~---~~~~~~i~~~   31 (194)
T cd01428           1 RILLLGPPGSGKGTQAERLAK---KYGLPHISTG   31 (194)
T ss_pred             CEEEECCCCCCHHHHHHHHHH---HcCCeEEECc
Confidence            589999999999988777654   3477776653

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>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=94.51  E-value=0.036  Score=44.85  Aligned_cols=22  Identities=18%  Similarity=0.117  Sum_probs=20.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++|.|.+||||||++..+....
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            5899999999999999998876

...

>PHA03134 thymidine kinase; Provisional

Probab=94.49  E-value=0.04  Score=53.41  Aligned_cols=42  Identities=21%  Similarity=0.143  Sum_probs=32.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      ..-.|++|+|+-|.||||++.++.+.+. .|--|+|||++-.+
T Consensus        11 ~~~~rvYlDG~~GvGKTT~~~~l~~~~~-~~~~vl~~pEPM~Y   52 (340)
T PHA03134         11 VRIVRIYLDGAYGIGKSTTGRVMASAAS-GGGPTLYFPEPMAY   52 (340)
T ss_pred             ccEEEEEEeCCCcCCHHHHHHHHHHhcc-CCCceEEecCcHHH
Confidence            4567999999999999999966666544 44448888887653

>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=94.49  E-value=0.031  Score=49.38  Aligned_cols=23  Identities=26%  Similarity=0.216  Sum_probs=20.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      .++.++.|.|+.||||||+|.-+
T Consensus        19 ~~G~~~~l~G~nG~GKSTLl~~i   41 (176)
T cd03238          19 PLNVLVVVTGVSGSGKSTLVNEG   41 (176)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHH
Confidence            56889999999999999999754

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.46  E-value=0.058  Score=53.45  Aligned_cols=36  Identities=28%  Similarity=0.237  Sum_probs=30.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|+.||||||+++.+.+++..+|.=|..|
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lI  240 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFI  240 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            466788999999999999999999998888655555

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=94.44  E-value=0.05  Score=47.81  Aligned_cols=34  Identities=15%  Similarity=0.183  Sum_probs=26.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHH-HHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ-YAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~-~A~~~gwiVl~vP  102 (342)
                      -++|+|--|||||++|.+++. ......|.||--.
T Consensus         2 v~ii~GfLGsGKTTli~~ll~~~~~~~~~~vI~ne   36 (178)
T PF02492_consen    2 VIIITGFLGSGKTTLINHLLKRNRQGERVAVIVNE   36 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTTS-EEEEECS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhcCCceeEEEEcc
Confidence            579999999999999999995 4445567776543

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>PRK08118 topology modulation protein; Reviewed

Probab=94.42  E-value=0.039  Score=48.20  Aligned_cols=31  Identities=26%  Similarity=0.283  Sum_probs=22.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .|++|.|++||||||+..++...   .|.-++++
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~---l~~~~~~l   32 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEK---LNIPVHHL   32 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH---hCCCceec
Confidence            48999999999999877666543   34444444

>KOG0736|consensus

Probab=94.39  E-value=1.6  Score=46.75  Aligned_cols=114  Identities=14%  Similarity=0.140  Sum_probs=68.3

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-C---CCeEEEEEeCCCCCCCCCccCcchhHHh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-W---NNGAIVLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~---~~G~vv~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                      ..|.++.+-+++-+- -     |.++    +.++.+.+.|...++++ +   ..+.+|.++..+.       ..+|....
T Consensus       489 ~~pavifl~~~dvl~-i-----d~dg----ged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~-------~~lp~~i~  551 (953)
T KOG0736|consen  489 CSPAVLFLRNLDVLG-I-----DQDG----GEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSI-------EDLPADIQ  551 (953)
T ss_pred             cCceEEEEeccceee-e-----cCCC----chhHHHHHHHHHHHhcccccCCCCceEEEEecccc-------ccCCHHHH
Confidence            356666666664443 1     1122    56677778888777743 2   3444444444332       11443333


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcc-hHHHHHHhhCCCHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSE-GREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~-~~~el~~lSgGNP~~l~~lc~  340 (342)
                      +.--|       -|.|+-+|++|=-.++++|...-.+..+. -+.-...++|-.+++|..+.+
T Consensus       552 ~~f~~-------ei~~~~lse~qRl~iLq~y~~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~~  607 (953)
T KOG0736|consen  552 SLFLH-------EIEVPALSEEQRLEILQWYLNHLPLNQDVNLKQLARKTSGFSFGDLEALVA  607 (953)
T ss_pred             Hhhhh-------hccCCCCCHHHHHHHHHHHHhccccchHHHHHHHHHhcCCCCHHHHHHHhc
Confidence            22112       17899999999999999999988875222 223355688888888877654

>PRK14738 gmk guanylate kinase; Provisional

Probab=94.32  E-value=0.039  Score=49.79  Aligned_cols=26  Identities=27%  Similarity=0.309  Sum_probs=21.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .....++|.|+.|||||+++.++...
T Consensus        11 ~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         11 AKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            45678889999999999998887544

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

Probab=94.32  E-value=0.04  Score=48.04  Aligned_cols=23  Identities=30%  Similarity=0.374  Sum_probs=19.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..++|.|+.|||||+++.++...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35899999999999999987664

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.

>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=94.30  E-value=0.043  Score=45.42  Aligned_cols=35  Identities=23%  Similarity=0.375  Sum_probs=26.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.|||||++|.-+.-... ..|-|.+
T Consensus         9 ~~g~~~~i~G~nGsGKStLl~~l~g~~~~~~G~i~~   44 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKSTLLKALAGLLPPDSGSILI   44 (137)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHTTSSHESEEEEEE
T ss_pred             cCCCEEEEEccCCCccccceeeeccccccccccccc
Confidence            4578899999999999999986665544 4466543

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 ....

>KOG0727|consensus

Probab=94.28  E-value=0.034  Score=51.93  Aligned_cols=27  Identities=30%  Similarity=0.421  Sum_probs=22.0

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      -.+...++||||+|||||++..-+.++
T Consensus       186 idpprgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  186 IDPPRGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             CCCCcceEEeCCCCCcHHHHHHHHhhc
Confidence            357889999999999999987655443

>PRK05480 uridine/cytidine kinase; Provisional

Probab=94.28  E-value=0.07  Score=47.88  Aligned_cols=37  Identities=11%  Similarity=0.126  Sum_probs=26.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...+.|.|+.||||||+...+...-....+.+++.
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~   40 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQ   40 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhCCCceEEEeC
Confidence            4567899999999999999877776532223444444

>PRK10536 hypothetical protein; Provisional

Probab=94.27  E-value=0.15  Score=47.81  Aligned_cols=38  Identities=16%  Similarity=0.088  Sum_probs=29.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~vP~~  104 (342)
                      ..-++++|+.|||||++...+...+. ....-.++|.++
T Consensus        74 ~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP  112 (262)
T PRK10536         74 KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRP  112 (262)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCC
Confidence            34889999999999999999888766 444555666544

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=94.25  E-value=0.039  Score=53.69  Aligned_cols=35  Identities=26%  Similarity=0.327  Sum_probs=26.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      ..+--++|-||.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~Gef~vllGPSGcGKSTlLr~IAGLe~~~~G~I~i   62 (338)
T COG3839          27 EDGEFVVLLGPSGCGKSTLLRMIAGLEEPTSGEILI   62 (338)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            3467899999999999999987765433 4565554

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=94.23  E-value=0.071  Score=47.04  Aligned_cols=36  Identities=22%  Similarity=0.272  Sum_probs=29.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +.-++|.|..||||||....+.......|+-|+.++
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~~l~~~g~~v~~~~   38 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKKLLQENGYDVLFTR   38 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            345899999999999999999888777787776553

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.21  E-value=0.095  Score=52.23  Aligned_cols=36  Identities=25%  Similarity=0.268  Sum_probs=30.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+.|.|+.||||||+++.+..+...+|.=|..|
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI  275 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFI  275 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEE
Confidence            346889999999999999999999888888766555

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=94.20  E-value=0.19  Score=52.47  Aligned_cols=78  Identities=10%  Similarity=-0.018  Sum_probs=53.5

Q ss_pred             eEEEeCHHHHHHhhhcCCCChhhHHhhhhcCCceEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          10 KFYTLPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        10 ~~~~~~~~~~~~l~~~g~l~~~~~~~~~~~~~~~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....++...+..+...|..|            |..+.|++..+++...-.  ...++..-++|+|..||||||+...+..
T Consensus       349 ~~~~~sgt~ir~~l~~G~~p------------P~~f~rpeV~~iL~~~~~--~r~~~g~~Ivl~Gl~GSGKSTia~~La~  414 (568)
T PRK05537        349 TVLTISGTELRRRLREGLEI------------PEWFSFPEVVAELRRTYP--PRHKQGFTVFFTGLSGAGKSTIAKALMV  414 (568)
T ss_pred             ceeccCHHHHHHHHHCCCCC------------ChhhcHHHHHHHHHHHhc--cccCCCeEEEEECCCCChHHHHHHHHHH
Confidence            37788888888888885555            455778876655554422  2335566899999999999999888877


Q ss_pred             HHHh-CCeEEEEe
Q psy3261          90 YAHE-NNYLLVHI  101 (342)
Q Consensus        90 ~A~~-~gwiVl~v  101 (342)
                      .-.. .|--+.++
T Consensus       415 ~L~~~~g~~~~~l  427 (568)
T PRK05537        415 KLMEMRGRPVTLL  427 (568)
T ss_pred             HhhhccCceEEEe
Confidence            6544 45434444

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.20  E-value=0.056  Score=47.17  Aligned_cols=29  Identities=14%  Similarity=0.252  Sum_probs=22.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|++||||||+...+..   ..|+..+.+
T Consensus         2 i~i~G~pGsGKst~a~~la~---~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVE---NFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHH---HcCCeEEEC
Confidence            68999999999998777643   457766665

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.

>KOG0741|consensus

Probab=94.20  E-value=0.03  Score=57.04  Aligned_cols=57  Identities=21%  Similarity=0.354  Sum_probs=40.6

Q ss_pred             cCCCChhhHHhhhhcCCceEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          25 LGGITRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        25 ~g~l~~~~~~~~~~~~~~~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .|||.++|.+-|+    +++--|---=++++.|--     +-...++||||+|||||....|+=.+
T Consensus       223 IGGLd~EFs~IFR----RAFAsRvFpp~vie~lGi-----~HVKGiLLyGPPGTGKTLiARqIGkM  279 (744)
T KOG0741|consen  223 IGGLDKEFSDIFR----RAFASRVFPPEVIEQLGI-----KHVKGILLYGPPGTGKTLIARQIGKM  279 (744)
T ss_pred             cccchHHHHHHHH----HHHHhhcCCHHHHHHcCc-----cceeeEEEECCCCCChhHHHHHHHHH
Confidence            4888887776554    333444422356776633     56889999999999999999998543

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=94.19  E-value=0.052  Score=55.11  Aligned_cols=40  Identities=30%  Similarity=0.313  Sum_probs=31.0

Q ss_pred             EechhHHHHHHHHHhccCCC-CCCCeEEEEccCCCcHHHHHH
Q psy3261          45 LIRNCMLELVGYLKSMTNFD-RPSPRFVLYGEHGVGKSMALV   85 (342)
Q Consensus        45 lvR~~t~el~~~l~~~~~~~-~~~~r~vL~G~~GsGKS~~L~   85 (342)
                      +=|+.-.++...|+. .+.+ .++..+.|.|+.||||||+|.
T Consensus        10 i~r~Ie~~l~~vL~~-Vsl~i~~GEiv~L~G~SGsGKSTLLr   50 (504)
T TIGR03238        10 VKRKIQTDLERILVK-FNKELPSSSLLFLCGSSGDGKSEILA   50 (504)
T ss_pred             echHHHHHHHHHHhC-CceeecCCCEEEEECCCCCCHHHHHh
Confidence            345656677777776 3333 678899999999999999999

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=94.18  E-value=0.094  Score=45.65  Aligned_cols=37  Identities=11%  Similarity=0.016  Sum_probs=27.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|.|..|||||++...+.......+.-++++
T Consensus         5 ~~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~   41 (176)
T PRK05541          5 PNGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYL   41 (176)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            4567899999999999999988887776554333333

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=94.18  E-value=0.062  Score=46.88  Aligned_cols=30  Identities=13%  Similarity=0.195  Sum_probs=23.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ...++|.|++||||||++..+...   .|+..+
T Consensus         3 ~~ii~i~G~~GsGKsTl~~~l~~~---~g~~~~   32 (188)
T TIGR01360         3 CKIIFIVGGPGSGKGTQCEKIVEK---YGFTHL   32 (188)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH---hCCcEE
Confidence            457899999999999999888764   265444

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.

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=94.16  E-value=0.17  Score=43.02  Aligned_cols=38  Identities=16%  Similarity=0.244  Sum_probs=27.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCe--EEEEe-CCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNY--LLVHI-PWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gw--iVl~v-P~~  104 (342)
                      +..+++.|+.|+|||.+..-.+.....++.  .++++ |..
T Consensus        14 ~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~   54 (169)
T PF00270_consen   14 GKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTR   54 (169)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSH
T ss_pred             CCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecc
Confidence            456999999999999999977766554433  44444 655

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.15  E-value=0.15  Score=49.63  Aligned_cols=42  Identities=14%  Similarity=0.086  Sum_probs=31.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWF  108 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~  108 (342)
                      ....+++.|+.||||||+|.-++.+. -.++-|+.|-+..++.
T Consensus       159 ~~~nili~G~tgSGKTTll~aL~~~i-p~~~ri~tiEd~~El~  200 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTFTNAALREI-PAIERLITVEDAREIV  200 (332)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHhhC-CCCCeEEEecCCCccc
Confidence            35679999999999999998776654 4467777775555553

>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=94.14  E-value=0.045  Score=44.48  Aligned_cols=23  Identities=17%  Similarity=0.362  Sum_probs=20.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +...+.|.|+.|||||++|.-+.
T Consensus        14 ~ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          14 GKVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CCEEEEEEcCCCCCHHHHHHHhh
Confidence            45678999999999999999876

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

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=94.13  E-value=0.19  Score=49.12  Aligned_cols=27  Identities=15%  Similarity=0.027  Sum_probs=22.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ...-..|+|++|||||.+..|+...+.
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~q  151 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQ  151 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHh
Confidence            456677999999999999999977664

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.13  E-value=0.04  Score=51.19  Aligned_cols=28  Identities=21%  Similarity=0.261  Sum_probs=22.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .++--+.|-|+.||||||+|.=+.-.-.
T Consensus        27 ~~GEfvsilGpSGcGKSTLLriiAGL~~   54 (248)
T COG1116          27 EKGEFVAILGPSGCGKSTLLRLIAGLEK   54 (248)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            4678899999999999999987665443

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=94.08  E-value=0.11  Score=50.82  Aligned_cols=43  Identities=23%  Similarity=0.400  Sum_probs=31.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeCCccccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIPWVLRWF  108 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP~~~~~~  108 (342)
                      +..-++|.|+.||||||+|..++.+..+. +--|+.+-+..++.
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~  164 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYV  164 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhh
Confidence            35678999999999999999888765532 34566665555543

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.

>PRK00279 adk adenylate kinase; Reviewed

Probab=94.06  E-value=0.061  Score=48.65  Aligned_cols=31  Identities=23%  Similarity=0.379  Sum_probs=24.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      |++|.|++|||||++-..+   |...||..+.+.
T Consensus         2 ~I~v~G~pGsGKsT~a~~l---a~~~~~~~is~~   32 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFI---AEKYGIPHISTG   32 (215)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHhCCcEEECC
Confidence            7999999999999876554   555688888754

>KOG0741|consensus

Probab=94.05  E-value=0.41  Score=49.15  Aligned_cols=122  Identities=17%  Similarity=0.172  Sum_probs=76.0

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHH
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNID  129 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~  129 (342)
                      ..-+++++++  ...++-..++|.|++|||||.+.+++   |+.+++=-+-|=++++.+--+ |++             -
T Consensus       523 G~llv~qvk~--s~~s~lvSvLl~Gp~~sGKTaLAA~i---A~~S~FPFvKiiSpe~miG~s-Esa-------------K  583 (744)
T KOG0741|consen  523 GKLLVQQVKN--SERSPLVSVLLEGPPGSGKTALAAKI---ALSSDFPFVKIISPEDMIGLS-ESA-------------K  583 (744)
T ss_pred             HHHHHHHhhc--cccCcceEEEEecCCCCChHHHHHHH---HhhcCCCeEEEeChHHccCcc-HHH-------------H
Confidence            3344555554  23356788999999999999997765   678888777776666654332 211             2


Q ss_pred             HHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEE
Q psy3261         130 AAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFV  208 (342)
Q Consensus       130 a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLv  208 (342)
                      .+.+=+.|..+-+.-|.   +-+-.              .+..|+++.---|+++..++++|+=-|+++.+ ...+.||
T Consensus       584 c~~i~k~F~DAYkS~ls---iivvD--------------diErLiD~vpIGPRfSN~vlQaL~VllK~~pp-kg~kLli  644 (744)
T KOG0741|consen  584 CAHIKKIFEDAYKSPLS---IIVVD--------------DIERLLDYVPIGPRFSNLVLQALLVLLKKQPP-KGRKLLI  644 (744)
T ss_pred             HHHHHHHHHHhhcCcce---EEEEc--------------chhhhhcccccCchhhHHHHHHHHHHhccCCC-CCceEEE
Confidence            33344455555555454   22211              13344444444477999999999999999873 4445554

>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=94.04  E-value=0.064  Score=47.94  Aligned_cols=40  Identities=15%  Similarity=0.166  Sum_probs=26.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ....-++|-|++|||||+++.++.......|.++|.-..-
T Consensus        13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~   52 (199)
T PF06414_consen   13 EKPTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEF   52 (199)
T ss_dssp             SS-EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGG
T ss_pred             cCCEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHH
Confidence            3455677779999999999999977544678888875433

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.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=94.03  E-value=0.048  Score=50.15  Aligned_cols=28  Identities=21%  Similarity=0.198  Sum_probs=23.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .++--+.|.||.||||||+|.-+-....
T Consensus        29 ~~Ge~vaI~GpSGSGKSTLLniig~ld~   56 (226)
T COG1136          29 EAGEFVAIVGPSGSGKSTLLNLLGGLDK   56 (226)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcccC
Confidence            4677899999999999999987765444

>KOG2749|consensus

Probab=94.03  E-value=0.073  Score=51.81  Aligned_cols=38  Identities=26%  Similarity=0.353  Sum_probs=35.8

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++..+|+++.|+.-||||++..-+..||.++||=.+||
T Consensus       100 ~~~GPrv~vVGp~d~GKsTl~r~L~nyavk~gr~Plfv  137 (415)
T KOG2749|consen  100 SSYGPRVMVVGPTDVGKSTLCRILLNYAVKQGRRPLFV  137 (415)
T ss_pred             hccCCEEEEECCCccchHHHHHHHHHHHHHcCCcceEE
Confidence            46789999999999999999999999999999999888

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=94.02  E-value=0.016  Score=51.25  Aligned_cols=36  Identities=33%  Similarity=0.313  Sum_probs=24.7

Q ss_pred             EEEccCCCcHHHHHHHHHHHHHhCCe--EEEEeCCccc
Q psy3261          71 VLYGEHGVGKSMALVYALQYAHENNY--LLVHIPWVLR  106 (342)
Q Consensus        71 vL~G~~GsGKS~~L~q~~~~A~~~gw--iVl~vP~~~~  106 (342)
                      ||+++||.|||++|-.+++.+...|-  |+|.-|+..+
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~~~~I~vtAP~~~~   38 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKGKIRILVTAPSPEN   38 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-----EEEE-SS--S
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhcCceEEEecCCHHH
Confidence            68999999999999999999988876  6666676643

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.02  E-value=0.11  Score=49.75  Aligned_cols=42  Identities=19%  Similarity=0.128  Sum_probs=32.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLRW  107 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~~  107 (342)
                      ....+++.|+.||||||+|..++.+..++  +.-|+.|=+..++
T Consensus       131 ~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhh
Confidence            35679999999999999999998877654  6677777555443

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=94.02  E-value=0.2  Score=48.34  Aligned_cols=37  Identities=19%  Similarity=0.082  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh------CCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE------NNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~------~gwiVl~v  101 (342)
                      .+..-..|+|++|||||++..|+...+..      .|--|+||
T Consensus        94 ~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYI  136 (313)
T TIGR02238        94 ESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYI  136 (313)
T ss_pred             cCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEE
Confidence            45667779999999999999998865542      23466777

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.

>PRK10436 hypothetical protein; Provisional

Probab=94.01  E-value=0.12  Score=52.58  Aligned_cols=43  Identities=21%  Similarity=0.285  Sum_probs=33.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRW  107 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~  107 (342)
                      .+..-++++|+.||||||+|..++.+....+--|+.|=++.++
T Consensus       216 ~~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~  258 (462)
T PRK10436        216 QPQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEI  258 (462)
T ss_pred             hcCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCccc
Confidence            3566799999999999999988888865555567777555554

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

Probab=94.00  E-value=0.16  Score=48.47  Aligned_cols=84  Identities=14%  Similarity=0.044  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE--EEe-CCccccccCC-----cceeccCCCC
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLL--VHI-PWVLRWFAYP-----KEVSHSLTKE  121 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV--l~v-P~~~~~~~~~-----~~~~~s~~~~  121 (342)
                      +.+|+..+.-   .+..+.++=|||.+|+||||++--+....++.|--|  |-| |+. -++-|+     .-...-..++
T Consensus        37 a~~ll~~l~p---~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSS-p~TGGsiLGDRiRM~~~~~~~  112 (323)
T COG1703          37 ARELLRALYP---RTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSS-PFTGGSILGDRIRMQRLAVDP  112 (323)
T ss_pred             HHHHHHHHhh---cCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCC-CCCCccccccHhhHHhhccCC
Confidence            5567776644   335677999999999999999999999999998744  666 443 333331     0001111256


Q ss_pred             CccccHHHHHHHHHHH
Q psy3261         122 GMVDLNIDAAMWLRHF  137 (342)
Q Consensus       122 ~~~~qP~~a~~~L~~~  137 (342)
                      +.|.-|+.+.--|--+
T Consensus       113 ~vFiRs~~srG~lGGl  128 (323)
T COG1703         113 GVFIRSSPSRGTLGGL  128 (323)
T ss_pred             CeEEeecCCCccchhh
Confidence            6776666555544444

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=94.00  E-value=0.094  Score=50.04  Aligned_cols=23  Identities=13%  Similarity=0.083  Sum_probs=17.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..-++|+|++|+|||+++..+..
T Consensus        43 ~~~lll~G~~G~GKT~la~~l~~   65 (316)
T PHA02544         43 PNMLLHSPSPGTGKTTVAKALCN   65 (316)
T ss_pred             CeEEEeeCcCCCCHHHHHHHHHH
Confidence            45566699999999998766543

>PRK14530 adenylate kinase; Provisional

Probab=93.99  E-value=0.071  Score=48.21  Aligned_cols=31  Identities=29%  Similarity=0.352  Sum_probs=23.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ..+++|.|++||||||+...+.   ...|+..+.
T Consensus         3 ~~~I~i~G~pGsGKsT~~~~La---~~~~~~~i~   33 (215)
T PRK14530          3 QPRILLLGAPGAGKGTQSSNLA---EEFGVEHVT   33 (215)
T ss_pred             CCEEEEECCCCCCHHHHHHHHH---HHhCCeEEe
Confidence            4589999999999999888774   334655443

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.99  E-value=0.073  Score=50.93  Aligned_cols=37  Identities=19%  Similarity=0.151  Sum_probs=29.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-------CCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-------NNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-------~gwiVl~vP  102 (342)
                      ....-+.|+|++|||||+++.|+...+..       +| -|+||.
T Consensus        93 ~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~-~~~yi~  136 (310)
T TIGR02236        93 ETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGG-KAVYID  136 (310)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcc-eEEEEE
Confidence            34666789999999999999999877652       34 777774

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.

>TIGR00665 DnaB replicative DNA helicase

Probab=93.97  E-value=0.097  Score=52.54  Aligned_cols=38  Identities=16%  Similarity=0.207  Sum_probs=31.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH-HhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA-HENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A-~~~gwiVl~vP  102 (342)
                      .++.-++|.|.+|+|||+++.|++..+ ..+|+-|+++.
T Consensus       193 ~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~S  231 (434)
T TIGR00665       193 QPSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFS  231 (434)
T ss_pred             CCCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEe
Confidence            356678999999999999999998874 56798888883

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=93.97  E-value=0.077  Score=45.47  Aligned_cols=33  Identities=27%  Similarity=0.334  Sum_probs=25.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|+|++|||||++...+....   |+.++..
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l---~~~~~d~   35 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRL---GYDFIDT   35 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHh---CCCEEEC
Confidence            45689999999999999977765543   6655543

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=93.96  E-value=0.11  Score=47.58  Aligned_cols=32  Identities=22%  Similarity=0.545  Sum_probs=26.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      ...++|||++|+|||++..++     ....+++....
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~-----~~~~~~~~~d~   43 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYL-----PGKTLVLSFDM   43 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhc-----CCCCEEEeccc
Confidence            567999999999999998876     35688888754

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=93.95  E-value=0.049  Score=44.66  Aligned_cols=22  Identities=36%  Similarity=0.459  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|.|.+|+|||+++.++..
T Consensus         2 ~ki~~~G~~~~GKstl~~~l~~   23 (161)
T TIGR00231         2 IKIVIVGDPNVGKSTLLNRLLG   23 (161)
T ss_pred             eEEEEECCCCCCHHHHHHHHhC
Confidence            5899999999999999988864

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=93.94  E-value=0.084  Score=47.13  Aligned_cols=37  Identities=19%  Similarity=0.063  Sum_probs=29.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-+.|+|..|||||++...+.......|+-++++
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~l   58 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLL   58 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEE
Confidence            4567899999999999998888887777666655555

>PHA02244 ATPase-like protein

Probab=93.93  E-value=0.13  Score=50.82  Aligned_cols=32  Identities=19%  Similarity=0.259  Sum_probs=23.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ...++|.|++|||||++..++.+ +....|+.+
T Consensus       119 ~~PVLL~GppGtGKTtLA~aLA~-~lg~pfv~I  150 (383)
T PHA02244        119 NIPVFLKGGAGSGKNHIAEQIAE-ALDLDFYFM  150 (383)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHH-HhCCCEEEE
Confidence            66899999999999998766644 444444444

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=93.93  E-value=0.22  Score=51.89  Aligned_cols=122  Identities=21%  Similarity=0.255  Sum_probs=64.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccccc-CCcceeccCCCCCccccHHHHHHHHHHHHHhCccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFA-YPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKW  144 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~-~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~  144 (342)
                      +..-++++|+.||||||+|..++.+.-..+--|+.|=++.++.. +...+..+. +.| +    .-...|+.++..+-++
T Consensus       315 ~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~~~~~q~~v~~-~~g-~----~~~~~l~~~LR~dPDv  388 (564)
T TIGR02538       315 PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINLPGINQVNVNP-KIG-L----TFAAALRSFLRQDPDI  388 (564)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecCCCceEEEecc-ccC-C----CHHHHHHHHhccCCCE
Confidence            45678899999999999998888876544445666644444432 221111111 111 1    2355677776655544


Q ss_pred             cCCCCcc------------cccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHH
Q psy3261         145 LEDPRLT------------TSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTE  194 (342)
Q Consensus       145 L~~~~l~------------~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~E  194 (342)
                      +==+.|.            .+...+++--....+...+..|++.|+.....| .++..++.+
T Consensus       389 I~vGEiRd~eta~~a~~aa~tGHlv~tTlHa~~a~~~i~Rl~~lg~~~~~la-~~l~~vi~Q  449 (564)
T TIGR02538       389 IMVGEIRDLETAEIAIKAAQTGHLVLSTLHTNDAPETLARLVNMGIAPFNIA-SSVNLIMAQ  449 (564)
T ss_pred             EEeCCCCCHHHHHHHHHHHHcCCcEEEEeccCCHHHHHHHHHHcCCCHHHHH-HHHHHhhee
Confidence            3200111            122222322222344567788888887644443 334444444

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=93.90  E-value=0.042  Score=49.39  Aligned_cols=25  Identities=20%  Similarity=0.090  Sum_probs=21.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ..-++|+|+.||||||+|.++....
T Consensus        25 g~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHH
Confidence            4788999999999999999996543

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

>PRK06547 hypothetical protein; Provisional

Probab=93.84  E-value=0.11  Score=45.67  Aligned_cols=34  Identities=21%  Similarity=0.261  Sum_probs=26.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .....++|+|+.|||||++...+...   .|..+++.
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~---~~~~~~~~   46 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAAR---TGFQLVHL   46 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH---hCCCeecc
Confidence            45778999999999999998777654   45666654

>PF09820 AAA-ATPase_like: Predicted AAA-ATPase; InterPro: IPR018631 This entry is predicted to be an AAA-ATPase domain []

Probab=93.83  E-value=1  Score=42.79  Aligned_cols=146  Identities=14%  Similarity=0.063  Sum_probs=75.2

Q ss_pred             hhhhcCCc-eEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEE--EEeCCcc-cc--
Q psy3261          35 QTQIFNES-SILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLL--VHIPWVL-RW--  107 (342)
Q Consensus        35 ~~~~~~~~-~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiV--l~vP~~~-~~--  107 (342)
                      .|+..++. ..-|-| |.- |..|.+      ....++|.=||.=|||++|.-+-+|.. .+.-+.  +.|-... .|  
T Consensus         6 ~F~~i~~~~~~yVDK-T~~-I~~l~~------~~~~~~~~RPRRFGKSl~lsmL~~~f~~~~~~LF~~L~I~~~~~~~~~   77 (284)
T PF09820_consen    6 DFKKIREENYYYVDK-TMF-IKELLD------SGKYVFLSRPRRFGKSLNLSMLEAYFDDDSKELFKGLKISKHPTYWKH   77 (284)
T ss_pred             HHHHHHHCCeEEEEC-HHH-HHHHHh------cCCEEEEecccchhhhHHHHHHHHHHhhhhhhhcCCcccccccccccc
Confidence            34334333 445555 533 444433      144669999999999999999999877 222221  3332211 11  


Q ss_pred             ccCCcceeccCCCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHH
Q psy3261         108 FAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDV  187 (342)
Q Consensus       108 ~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~  187 (342)
                      .+. ..+..-.........+....+.|+......-..+.  ..             .+.            .+......+
T Consensus        78 ~~~-YpVI~ldfs~~~~~~~~~~~~~l~~~l~~~~~~~~--~~-------------~~~------------~~~~~~~~~  129 (284)
T PF09820_consen   78 MNK-YPVIFLDFSGVKGSSFEELEESLKEILSDIFKEHR--YL-------------YES------------VEEIDLADS  129 (284)
T ss_pred             ccc-ceEEEehhhhhccccHHHHHHHHHHHHHHHHHHHh--HH-------------hcc------------cccCCHHHH
Confidence            111 11111111111223333444444443221111111  00             000            013355677


Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAE  219 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~  219 (342)
                      +..+++-|..+.   ..||.|-||+|-..+..
T Consensus       130 l~~li~~l~~~~---~~kvvlLIDEYD~p~~~  158 (284)
T PF09820_consen  130 LKDLIEYLYEKY---GKKVVLLIDEYDKPIND  158 (284)
T ss_pred             HHHHHHHHHHHh---CCceEEEecCccHHHHH
Confidence            888888888775   89999999999777665

It is usually found together with IPR012547 from INTERPRO.

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=93.83  E-value=0.087  Score=49.78  Aligned_cols=35  Identities=23%  Similarity=0.156  Sum_probs=27.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ++|+|-+|||||+.-.++..+..+.+|=|..|.+.
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~   38 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDD   38 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEccc
Confidence            78999999999999999999999999999999744

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=93.81  E-value=0.078  Score=49.07  Aligned_cols=32  Identities=28%  Similarity=0.273  Sum_probs=26.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|.+|||||+...++..+....|+=|+++
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i   33 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIIL   33 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEE
Confidence            68999999999999999999887777655555

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.

>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=93.80  E-value=0.087  Score=48.94  Aligned_cols=36  Identities=25%  Similarity=0.439  Sum_probs=26.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~vP  102 (342)
                      .-|+++-|++|||||+++..++.+-.. -..|++--|
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITP   49 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEec
Confidence            459999999999999999999876443 244443334

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

>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=93.79  E-value=0.054  Score=48.49  Aligned_cols=26  Identities=19%  Similarity=0.045  Sum_probs=22.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      +..+++|+|+.|||||++|..+..-.
T Consensus        28 ~~~~~~l~G~Ng~GKStll~~i~~~~   53 (202)
T cd03243          28 SGRLLLITGPNMGGKSTYLRSIGLAV   53 (202)
T ss_pred             CCeEEEEECCCCCccHHHHHHHHHHH
Confidence            45799999999999999999998544

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

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=93.79  E-value=0.12  Score=45.70  Aligned_cols=27  Identities=22%  Similarity=0.365  Sum_probs=22.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ....++|.|+.||||||++..++..-.
T Consensus        24 ~g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          24 ARKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            367899999999999999988776543

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.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=93.76  E-value=0.083  Score=46.94  Aligned_cols=32  Identities=13%  Similarity=0.202  Sum_probs=23.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +.|.|+.||||||+...+...-...+..|++.
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l~~~~~~v~~~   33 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQ   33 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCCeEEEEe
Confidence            56899999999999988877652223444444

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.

>TIGR03263 guanyl_kin guanylate kinase

Probab=93.75  E-value=0.058  Score=46.97  Aligned_cols=23  Identities=35%  Similarity=0.387  Sum_probs=19.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..++|.|+.|||||+++..+...
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            46899999999999998887763

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.

>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=93.75  E-value=0.06  Score=43.34  Aligned_cols=21  Identities=29%  Similarity=0.347  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |++|.|.+|+|||+++..+..
T Consensus         1 ~V~iiG~~~~GKSTlin~l~~   21 (116)
T PF01926_consen    1 RVAIIGRPNVGKSTLINALTG   21 (116)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHhc
Confidence            689999999999999999983

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 ....

>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

Probab=93.73  E-value=0.055  Score=47.78  Aligned_cols=31  Identities=29%  Similarity=0.281  Sum_probs=25.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      +++.|..||||||++..+..+   .|+.++.-|.
T Consensus         2 I~ieG~~GsGKSTl~~~L~~~---~~~~~~~Ep~   32 (193)
T cd01673           2 IVVEGNIGAGKSTLAKELAEH---LGYEVVPEPV   32 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHHH---hCCccccccc
Confidence            689999999999999988876   4777766664

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.

>TIGR00376 DNA helicase, putative

Probab=93.71  E-value=0.075  Score=56.20  Aligned_cols=34  Identities=21%  Similarity=0.314  Sum_probs=29.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|.|++|||||+++..++..+.++|--|+..
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~  207 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVT  207 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            5688999999999999999999988877766555

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=93.71  E-value=0.17  Score=43.25  Aligned_cols=28  Identities=21%  Similarity=0.280  Sum_probs=24.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ..+++.|+.|||||+++...+.++..++
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~~~   52 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALKRG   52 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhccc
Confidence            7899999999999999888888877654

>PRK06762 hypothetical protein; Provisional

Probab=93.68  E-value=0.092  Score=45.15  Aligned_cols=32  Identities=22%  Similarity=0.276  Sum_probs=23.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .-++|+|.+||||||+...+.... ..+++++.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l-~~~~~~i~   34 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERL-GRGTLLVS   34 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh-CCCeEEec
Confidence            457899999999999887776553 23555553

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.66  E-value=0.096  Score=52.66  Aligned_cols=36  Identities=14%  Similarity=0.230  Sum_probs=30.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|+.||||||+.+.+.+++.++|+=|+-|
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV  134 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLV  134 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            346788999999999999999999999888755555

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=93.66  E-value=0.055  Score=49.44  Aligned_cols=35  Identities=23%  Similarity=0.275  Sum_probs=25.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++-.++|.||.||||||+|.-+-..=. ..|-|.+
T Consensus        26 ~~Gevv~iiGpSGSGKSTlLRclN~LE~~~~G~I~i   61 (240)
T COG1126          26 EKGEVVVIIGPSGSGKSTLLRCLNGLEEPDSGSITV   61 (240)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHCCcCCCCceEEE
Confidence            4678999999999999999986654322 3454443

>PRK00698 tmk thymidylate kinase; Validated

Probab=93.65  E-value=0.1  Score=46.21  Aligned_cols=33  Identities=18%  Similarity=0.192  Sum_probs=26.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      +.-++|.|+.||||||++..+..+....|.-++
T Consensus         3 ~~~I~ieG~~gsGKsT~~~~L~~~l~~~~~~~~   35 (205)
T PRK00698          3 GMFITIEGIDGAGKSTQIELLKELLEQQGRDVV   35 (205)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCcee
Confidence            467899999999999999999887766654333

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=93.63  E-value=0.096  Score=51.76  Aligned_cols=42  Identities=21%  Similarity=0.209  Sum_probs=31.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCccccc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLRWF  108 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~~~  108 (342)
                      ..-+++.|+.||||||+|..++.+..++  +.-|+.|=++.++.
T Consensus       149 ~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~  192 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYI  192 (372)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhc
Confidence            4568999999999999999988887643  45667775555543

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=93.60  E-value=0.12  Score=45.46  Aligned_cols=37  Identities=19%  Similarity=0.129  Sum_probs=29.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...++|.|.+|||||++...+...-...|+-++++
T Consensus        16 ~~~~~i~i~G~~GsGKstla~~l~~~l~~~~~~~~~l   52 (184)
T TIGR00455        16 HRGVVIWLTGLSGSGKSTIANALEKKLESKGYRVYVL   52 (184)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            4577999999999999999988888777777544444

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.60  E-value=0.17  Score=48.52  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=22.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ....+++.|+.||||||+|..++.+.
T Consensus       143 ~~~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHccC
Confidence            46799999999999999998877654

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.

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=93.59  E-value=0.089  Score=46.96  Aligned_cols=40  Identities=18%  Similarity=0.121  Sum_probs=30.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeE-----EEEeCCc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYL-----LVHIPWV  104 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwi-----Vl~vP~~  104 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|.|     |-|+|..
T Consensus        29 ~~G~~~~i~G~nG~GKSTLl~~i~G~~~~~~G~i~~~g~i~~~~q~   74 (204)
T cd03250          29 PKGELVAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGSIAYVSQE   74 (204)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCcCCCCCCeEEEcCEEEEEecC
Confidence            5788999999999999999988766543 56877     4455444

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK00300 gmk guanylate kinase; Provisional

Probab=93.57  E-value=0.074  Score=47.35  Aligned_cols=25  Identities=32%  Similarity=0.333  Sum_probs=22.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ++.-++|.|+.|||||+++..+...
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            5678999999999999998888775

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=93.56  E-value=0.064  Score=47.36  Aligned_cols=22  Identities=32%  Similarity=0.302  Sum_probs=19.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..++|.|+.||||||++..+..
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~   24 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQ   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4689999999999999999844

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

Probab=93.55  E-value=0.074  Score=50.49  Aligned_cols=121  Identities=13%  Similarity=0.040  Sum_probs=72.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCccccC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLE  146 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~  146 (342)
                      ..-.=++|+.|||||++..|++..|...|=.++||.--                 +.+ -|.++.++...+       +.
T Consensus        60 g~ItEiyG~~gsGKT~lal~~~~~aq~~g~~a~fIDtE-----------------~~l-~p~r~~~l~~~~-------~d  114 (279)
T COG0468          60 GRITEIYGPESSGKTTLALQLVANAQKPGGKAAFIDTE-----------------HAL-DPERAKQLGVDL-------LD  114 (279)
T ss_pred             ceEEEEecCCCcchhhHHHHHHHHhhcCCCeEEEEeCC-----------------CCC-CHHHHHHHHHhh-------hc
Confidence            34445899999999999999999999998888777321                 112 356777777766       66


Q ss_pred             CCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCC
Q psy3261         147 DPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPE  226 (342)
Q Consensus       147 ~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~  226 (342)
                        ++.+++.+...         .-.++++.-                 +...   .+..=||.||.+.++|...  |-+ 
T Consensus       115 --~l~v~~~~~~e---------~q~~i~~~~-----------------~~~~---~~~i~LvVVDSvaa~~r~~--~~~-  160 (279)
T COG0468         115 --NLLVSQPDTGE---------QQLEIAEKL-----------------ARSG---AEKIDLLVVDSVAALVRAE--EIE-  160 (279)
T ss_pred             --ceeEecCCCHH---------HHHHHHHHH-----------------HHhc---cCCCCEEEEecCcccchhh--hcC-
Confidence              67766654321         112222211                 1111   1224499999999888863  222 


Q ss_pred             CCCcccCCccchHHHHHHhhc
Q psy3261         227 DKSKVLPSRVTLTRSVINLVQ  247 (342)
Q Consensus       227 ~~~~I~~~~l~l~~~~~~~~~  247 (342)
                       ...+....--|-+++..+.+
T Consensus       161 -d~~~~~~~r~ls~~l~~L~~  180 (279)
T COG0468         161 -DGHLGLRARLLSKALRKLTR  180 (279)
T ss_pred             -cchHHHHHHHHHHHHHHHHH
Confidence             13333333445555555554

>PRK02496 adk adenylate kinase; Provisional

Probab=93.54  E-value=0.068  Score=46.89  Aligned_cols=31  Identities=19%  Similarity=0.290  Sum_probs=22.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .|++|.|++|||||++...+...   .|+.++.+
T Consensus         2 ~~i~i~G~pGsGKst~a~~la~~---~~~~~i~~   32 (184)
T PRK02496          2 TRLIFLGPPGAGKGTQAVVLAEH---LHIPHIST   32 (184)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH---hCCcEEEh
Confidence            47999999999999988877543   25544443

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=93.45  E-value=0.12  Score=45.70  Aligned_cols=35  Identities=17%  Similarity=0.094  Sum_probs=29.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..-+.+.|+.||||||++..++..-...|+-|-.|
T Consensus         6 ~~ii~ivG~sgsGKTTLi~~li~~l~~~g~~vg~I   40 (173)
T PRK10751          6 IPLLAIAAWSGTGKTTLLKKLIPALCARGIRPGLI   40 (173)
T ss_pred             ceEEEEECCCCChHHHHHHHHHHHHhhcCCeEEEE
Confidence            44678999999999999999999988878766544

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=93.44  E-value=0.16  Score=42.81  Aligned_cols=39  Identities=21%  Similarity=0.095  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .|.++.+.|-+   .-.+...++|.|+-|+|||++...++..
T Consensus         7 ~t~~l~~~l~~---~l~~~~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150         7 AMDKFGKAFAK---PLDFGTVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             HHHHHHHHHHH---hCCCCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            56667776654   1145678999999999999988776664

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.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=93.44  E-value=0.082  Score=46.58  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=21.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +..++|.|+.||||||++..+...
T Consensus         3 ge~i~l~G~sGsGKSTl~~~la~~   26 (176)
T PRK09825          3 GESYILMGVSGSGKSLIGSKIAAL   26 (176)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh
Confidence            457899999999999999988775

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

Probab=93.44  E-value=0.19  Score=50.13  Aligned_cols=38  Identities=24%  Similarity=0.224  Sum_probs=32.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCe--EEEEeCC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNY--LLVHIPW  103 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gw--iVl~vP~  103 (342)
                      ..+.++|+|+.|+|||-+|.-+-+++.+.+-  .|+|+..
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~s  151 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTS  151 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccH
Confidence            6899999999999999999999999988765  6777743

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=93.43  E-value=0.082  Score=51.62  Aligned_cols=33  Identities=15%  Similarity=0.245  Sum_probs=27.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHH--HhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYA--HENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A--~~~gwiVl~v  101 (342)
                      -++|.|.+|||||+++.+++...  ...+.-++++
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l   37 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYL   37 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEE
Confidence            47999999999999999999988  5555555555

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG3911 Predicted ATPase [General function prediction only]

Probab=93.41  E-value=0.064  Score=46.26  Aligned_cols=31  Identities=29%  Similarity=0.444  Sum_probs=24.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++||+|-+|+|||++|+-+.    ..|+.++..+
T Consensus        10 ~~fIltGgpGaGKTtLL~aLa----~~Gfatvee~   40 (183)
T COG3911          10 KRFILTGGPGAGKTTLLAALA----RAGFATVEEA   40 (183)
T ss_pred             eEEEEeCCCCCcHHHHHHHHH----HcCceeeccc
Confidence            589999999999999998653    4477666554

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=93.40  E-value=0.066  Score=45.11  Aligned_cols=32  Identities=34%  Similarity=0.422  Sum_probs=22.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAH-ENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~v  101 (342)
                      ++|.|+.|||||+++..++..-. ..++++-+.
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~~~~~~v~~t   34 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHT   34 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCccceeccccc
Confidence            68899999999998888876532 224544443

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.

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=93.40  E-value=0.071  Score=49.38  Aligned_cols=28  Identities=29%  Similarity=0.349  Sum_probs=23.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+..+++|.|+.||||||++.++--...
T Consensus        28 ~~Ge~~~i~G~nGsGKSTL~~~l~GLl~   55 (235)
T COG1122          28 EKGERVLLIGPNGSGKSTLLKLLNGLLK   55 (235)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHcCcCc
Confidence            4678999999999999999998765443

>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=93.36  E-value=0.092  Score=46.47  Aligned_cols=35  Identities=31%  Similarity=0.401  Sum_probs=27.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH-HHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ-YAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~-~A~~~gwiVl   99 (342)
                      +.+-.++|+|+.|+|||++|..+-. |+-..|-|.+
T Consensus        35 ~aGECvvL~G~SG~GKStllr~LYaNY~~d~G~I~v   70 (235)
T COG4778          35 NAGECVVLHGPSGSGKSTLLRSLYANYLPDEGQILV   70 (235)
T ss_pred             cCccEEEeeCCCCCcHHHHHHHHHhccCCCCceEEE
Confidence            4578999999999999999998876 4445565543

>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=93.36  E-value=0.13  Score=44.61  Aligned_cols=35  Identities=14%  Similarity=0.014  Sum_probs=29.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .-+.|+|-+||||||+-..+....++.|+-|.++-
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LD   37 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLD   37 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEec
Confidence            45789999999999988888889999998888873

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 ....

>PRK14531 adenylate kinase; Provisional

Probab=93.34  E-value=0.079  Score=46.68  Aligned_cols=22  Identities=23%  Similarity=0.389  Sum_probs=18.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|+++.|++||||||+-..+..
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~   24 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCA   24 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999998666644

>TIGR01351 adk adenylate kinases

Probab=93.33  E-value=0.079  Score=47.70  Aligned_cols=30  Identities=23%  Similarity=0.292  Sum_probs=23.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      |++|.|++|||||++-.++.   ...|+.+|..
T Consensus         1 rI~i~G~pGsGKsT~a~~La---~~~g~~~is~   30 (210)
T TIGR01351         1 RLVLLGPPGSGKGTQAKRIA---EKYGLPHIST   30 (210)
T ss_pred             CEEEECCCCCCHHHHHHHHH---HHcCCCeeeh
Confidence            58999999999999876654   4457766664

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=93.32  E-value=0.14  Score=54.35  Aligned_cols=53  Identities=23%  Similarity=0.253  Sum_probs=40.6

Q ss_pred             HHHHHHHHhccCC-------------CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE-EEeCCc
Q psy3261          51 LELVGYLKSMTNF-------------DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLL-VHIPWV  104 (342)
Q Consensus        51 ~el~~~l~~~~~~-------------~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV-l~vP~~  104 (342)
                      .+|.+.|++ ...             +.....++|+|-.|||||++|.+++.++++.|.-+ ||=|.+
T Consensus       157 ~~l~k~lk~-~~~~s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i~~LL~~ir~RGdrAIIyD~~G  223 (732)
T PRK13700        157 KDVARMLKK-DGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYARQRGDMVVIYDRSG  223 (732)
T ss_pred             HHHHHHHHh-cCCCCCeeEccccCCcchhhcceEEeCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCC
Confidence            467777776 221             13567999999999999999999999999886655 444666

>PRK03839 putative kinase; Provisional

Probab=93.32  E-value=0.074  Score=46.49  Aligned_cols=30  Identities=23%  Similarity=0.351  Sum_probs=21.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|.|.+||||||+..++..   .-|+-++.+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~---~~~~~~id~   31 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAE---KLGYEYVDL   31 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCcEEeh
Confidence            689999999999997666533   335554443

>PRK05439 pantothenate kinase; Provisional

Probab=93.32  E-value=0.48  Score=45.71  Aligned_cols=88  Identities=15%  Similarity=0.115  Sum_probs=48.8

Q ss_pred             ccCcceEEEeCHHHHHHhhhcCCCCh--hhHHhhhhcCCceEE--ech---hHHHHHH-----------HHHhccC--CC
Q psy3261           5 KQDLYKFYTLPDEVRSAIFELGGITR--VFNEQTQIFNESSIL--IRN---CMLELVG-----------YLKSMTN--FD   64 (342)
Q Consensus         5 ~~~~g~~~~~~~~~~~~l~~~g~l~~--~~~~~~~~~~~~~~l--vR~---~t~el~~-----------~l~~~~~--~~   64 (342)
                      .....-++.|+.+.+.+|....-+|-  .-.++.+-++++..|  |++   |-..+|+           .++.+..  ..
T Consensus         4 ~~~~~~~~~~~r~~w~~l~~~~~~~l~~~~~~~l~~~~~~~~~~~v~~iy~plarli~~~~~~~~~~~~~~~~fl~~~~~   83 (311)
T PRK05439          4 SNEFSPYLEFSREQWAALRDSTPLTLTEEELERLRGLNDPISLEEVAEIYLPLSRLLNLYVAANQRLQAALEQFLGKNGQ   83 (311)
T ss_pred             CcCCCCceeECHHHHHHHHhcCCCCCCHHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhcccCC
Confidence            34566789999999999986433332  112233344444322  111   1222222           2222111  22


Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      +...-+-|.|++||||||+...+.....
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLS  111 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3344567899999999999987777554

>PRK13768 GTPase; Provisional

Probab=93.30  E-value=0.1  Score=48.65  Aligned_cols=33  Identities=21%  Similarity=0.383  Sum_probs=27.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCe--EEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNY--LLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gw--iVl~v  101 (342)
                      -+++.|+.|||||++..+++.++..+|-  +|+.+
T Consensus         4 ~i~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i~~   38 (253)
T PRK13768          4 IVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVNL   38 (253)
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHhcCCceEEEEC
Confidence            5788999999999999999999887654  44554

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

Probab=93.27  E-value=0.072  Score=52.00  Aligned_cols=119  Identities=16%  Similarity=0.213  Sum_probs=68.2

Q ss_pred             CCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc----CCC-CCeEEEEEeCCCCCCCCCccCcchhH
Q psy3261         202 GVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ----SDW-NNGAIVLALSPRANLPDRRESHLPLY  276 (342)
Q Consensus       202 ~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~----~~~-~~G~vv~AtS~~~~~~~~~~~~~p~~  276 (342)
                      .+-|-.|.||++.++-+.  ++.+...     .+=.+=|.++.++.    -|. .|-=||+||.+-..        |-..
T Consensus       242 ekaPsIIFiDEIDAIg~k--R~d~~t~-----gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~--------LDPA  306 (406)
T COG1222         242 EKAPSIIFIDEIDAIGAK--RFDSGTS-----GDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDI--------LDPA  306 (406)
T ss_pred             hcCCeEEEEechhhhhcc--cccCCCC-----chHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccc--------cChh
Confidence            378999999999887554  2333222     22345556666654    244 34456777765432        2235


Q ss_pred             HhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         277 MLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       277 llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      |++.-.|+.     .|++|.=+.+.=+.++.-+..+--+..+-...+|-. ..|-|+.++.-+|+
T Consensus       307 LLRPGR~DR-----kIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaict  366 (406)
T COG1222         307 LLRPGRFDR-----KIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICT  366 (406)
T ss_pred             hcCCCcccc-----eeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHH
Confidence            554433442     378885555555566676666555531223334443 66778999988885

>PHA03136 thymidine kinase; Provisional

Probab=93.27  E-value=0.081  Score=52.09  Aligned_cols=38  Identities=16%  Similarity=0.170  Sum_probs=30.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeE--EEEeCCccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYL--LVHIPWVLR  106 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi--Vl~vP~~~~  106 (342)
                      +..|+.|+|+-|+||||++..+...   .+|.  |++||++-.
T Consensus        35 ~~~rvyieG~~gvGKTT~~~~l~~~---~~~~~~vl~v~EPm~   74 (378)
T PHA03136         35 RLVLLYLDGPFGTGKTTTAKLLMEM---PDTLAARLYLAEPMA   74 (378)
T ss_pred             eeEEEEEECCCcCCHHHHHHHHHhc---cccCCCeeeecCchH
Confidence            4569999999999999999887762   4565  788887654

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.27  E-value=0.13  Score=51.65  Aligned_cols=35  Identities=11%  Similarity=0.060  Sum_probs=28.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH-HhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA-HENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A-~~~gwiVl~v  101 (342)
                      ...+++.|+.||||||++.++.+.+ ...|.-|..+
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Li  258 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLY  258 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEe
Confidence            3458899999999999999999754 6778766555

>cd00154 Rab Rab family

Probab=93.27  E-value=0.075  Score=43.90  Aligned_cols=21  Identities=38%  Similarity=0.602  Sum_probs=18.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .|+++.|++|+|||+++.++.
T Consensus         1 ~~i~~~G~~~~GKStl~~~l~   21 (159)
T cd00154           1 FKIVLIGDSGVGKTSLLLRFV   21 (159)
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            378999999999999999875

Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. 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 di

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=93.27  E-value=0.066  Score=47.88  Aligned_cols=22  Identities=23%  Similarity=0.223  Sum_probs=19.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|+|+.|+|||++|..+..
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~~   50 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLGL   50 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            4699999999999999999773

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

>PTZ00088 adenylate kinase 1; Provisional

Probab=93.25  E-value=0.093  Score=48.36  Aligned_cols=35  Identities=23%  Similarity=0.386  Sum_probs=27.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ..|++|.|++||||||.-..+   |...|+.++.+-+.
T Consensus         6 ~mrIvl~G~PGsGK~T~a~~L---a~~~g~~~is~gdl   40 (229)
T PTZ00088          6 PLKIVLFGAPGVGKGTFAEIL---SKKENLKHINMGNI   40 (229)
T ss_pred             CceEEEECCCCCCHHHHHHHH---HHHhCCcEEECChH
Confidence            467999999999999887766   44558877777544

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=93.24  E-value=0.12  Score=49.86  Aligned_cols=38  Identities=21%  Similarity=0.132  Sum_probs=29.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC------eEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN------YLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g------wiVl~vP  102 (342)
                      .+..-+.|+|++|||||++..|+...+...+      --|+||.
T Consensus       100 ~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~  143 (317)
T PRK04301        100 ETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID  143 (317)
T ss_pred             cCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe
Confidence            4567788999999999999999998775432      2566663

>cd04154 Arl2 Arl2 subfamily

Probab=93.24  E-value=0.079  Score=45.67  Aligned_cols=25  Identities=24%  Similarity=0.324  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....++++.|+.|||||+++.+++.
T Consensus        12 ~~~~kv~ivG~~~~GKTsL~~~l~~   36 (173)
T cd04154          12 EREMRILILGLDNAGKTTILKKLLG   36 (173)
T ss_pred             CCccEEEEECCCCCCHHHHHHHHcc
Confidence            3568999999999999999988764

Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.

>PRK10867 signal recognition particle protein; Provisional

Probab=93.23  E-value=0.12  Score=52.14  Aligned_cols=36  Identities=17%  Similarity=0.339  Sum_probs=30.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      +...+++.|+.||||||+.+.+..++.++ |.=|+-|
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV  135 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLV  135 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEE
Confidence            35678899999999999999999988877 8755555

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=93.23  E-value=0.14  Score=42.02  Aligned_cols=33  Identities=24%  Similarity=0.425  Sum_probs=26.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++++.|+.|+|||++...+..+..+.|.=|+-|
T Consensus         1 ~i~~~GkgG~GKTt~a~~la~~l~~~g~~V~~i   33 (116)
T cd02034           1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAI   33 (116)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            478999999999999999988777676544433

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=93.22  E-value=0.11  Score=46.41  Aligned_cols=31  Identities=23%  Similarity=0.268  Sum_probs=20.6

Q ss_pred             EEEEccCCCcHHHHHHHH-HHHHHhCCeEEEE
Q psy3261          70 FVLYGEHGVGKSMALVYA-LQYAHENNYLLVH  100 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~-~~~A~~~gwiVl~  100 (342)
                      ++++|.+|+|||....+. +..|.+.|..|+.
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t   34 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT   34 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE
Confidence            689999999999988777 7777788887654

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=93.19  E-value=0.077  Score=45.83  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|.|.+|+|||+++.++..
T Consensus         2 ~kv~l~G~~g~GKTtl~~~~~~   23 (180)
T cd04137           2 RKIAVLGSRSVGKSSLTVQFVE   23 (180)
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            6899999999999999998873

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>PRK08233 hypothetical protein; Provisional

Probab=93.19  E-value=0.087  Score=45.65  Aligned_cols=24  Identities=13%  Similarity=0.043  Sum_probs=20.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..-+.|.|.+||||||+..++...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            356788999999999999888875

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=93.14  E-value=0.12  Score=54.43  Aligned_cols=39  Identities=26%  Similarity=0.258  Sum_probs=30.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCC-eEEEEeCCccc
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENN-YLLVHIPWVLR  106 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~g-wiVl~vP~~~~  106 (342)
                      ..++|+|++|||||+++..+....-... ..++|+|++..
T Consensus        38 ~~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~n~~~   77 (608)
T TIGR00764        38 RNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPED   77 (608)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEeCCCC
Confidence            4889999999999999888776655544 55678888744

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>KOG0989|consensus

Probab=93.13  E-value=0.085  Score=50.49  Aligned_cols=32  Identities=31%  Similarity=0.606  Sum_probs=22.9

Q ss_pred             HHHHHHhccCCCCCCCeEEEEccCCCcHHHHHH
Q psy3261          53 LVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALV   85 (342)
Q Consensus        53 l~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~   85 (342)
                      +++.|.+ +-...-.+.|++|||+|+|||.+..
T Consensus        44 vV~~L~~-a~~~~~lp~~LFyGPpGTGKTStal   75 (346)
T KOG0989|consen   44 VVQVLKN-ALLRRILPHYLFYGPPGTGKTSTAL   75 (346)
T ss_pred             HHHHHHH-HHhhcCCceEEeeCCCCCcHhHHHH
Confidence            4555655 3222457899999999999998743

>cd00879 Sar1 Sar1 subfamily

Probab=93.13  E-value=0.16  Score=44.36  Aligned_cols=26  Identities=15%  Similarity=0.239  Sum_probs=22.4

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+..+++|.|+.|||||+++.++..
T Consensus        16 ~~~~~ki~ilG~~~~GKStLi~~l~~   41 (190)
T cd00879          16 YNKEAKILFLGLDNAGKTTLLHMLKD   41 (190)
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHhc
Confidence            35678999999999999999998754

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.

>cd01861 Rab6 Rab6 subfamily

Probab=93.13  E-value=0.08  Score=44.56  Aligned_cols=21  Identities=24%  Similarity=0.529  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +++|.|++|||||+++.+++.
T Consensus         2 ki~liG~~~~GKSsli~~l~~   22 (161)
T cd01861           2 KLVFLGDQSVGKTSIITRFMY   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            789999999999999998863

Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. 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

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=93.12  E-value=0.072  Score=45.21  Aligned_cols=21  Identities=19%  Similarity=0.235  Sum_probs=18.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +++|.|++|||||+++.++..
T Consensus         1 ~i~~vG~~~~GKstLi~~l~~   21 (167)
T cd04160           1 SVLILGLDNAGKTTFLEQLKT   21 (167)
T ss_pred             CEEEEecCCCCHHHHHHHHhh
Confidence            478999999999999999875

Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.

>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=93.09  E-value=0.11  Score=45.33  Aligned_cols=24  Identities=21%  Similarity=0.335  Sum_probs=22.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+..++++.|..|||||++|.++.
T Consensus        12 ~~~~~ililGl~~sGKTtll~~l~   35 (175)
T PF00025_consen   12 KKEIKILILGLDGSGKTTLLNRLK   35 (175)
T ss_dssp             TSEEEEEEEESTTSSHHHHHHHHH
T ss_pred             CcEEEEEEECCCccchHHHHHHhh
Confidence            678899999999999999999875

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.06  E-value=0.12  Score=52.85  Aligned_cols=37  Identities=16%  Similarity=0.127  Sum_probs=29.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      .++.-++|.|++|||||++..|.+..+..+ |==++||
T Consensus        19 p~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyv   56 (484)
T TIGR02655        19 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFV   56 (484)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEE
Confidence            568899999999999999999998765443 5555555

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=93.05  E-value=0.06  Score=53.71  Aligned_cols=48  Identities=17%  Similarity=0.106  Sum_probs=35.9

Q ss_pred             ceEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          42 SSILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        42 ~~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      -++.||+.-..-.++|-. .-..--..+++|.|..||||||+...+..+
T Consensus       195 SaT~IR~~p~~~w~~i~~-~vr~~~~~~IvI~G~~gsGKTTL~~~La~~  242 (399)
T PRK08099        195 SGTQIRENPFRYWEYIPT-EVRPFFVRTVAILGGESSGKSTLVNKLANI  242 (399)
T ss_pred             CHHHHhhCHHHHHHhcCH-HHhhCCCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            477888876666666654 222245789999999999999999777754

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=92.99  E-value=0.18  Score=46.86  Aligned_cols=38  Identities=26%  Similarity=0.309  Sum_probs=31.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP  102 (342)
                      .++.=++|-|.+|+|||+++.|++..+..+ |.=|+|+.
T Consensus        17 ~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~S   55 (259)
T PF03796_consen   17 RPGELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFS   55 (259)
T ss_dssp             -TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEE
T ss_pred             CcCcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEc
Confidence            567789999999999999999999988776 68888884

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK04040 adenylate kinase; Provisional

Probab=92.97  E-value=0.094  Score=46.74  Aligned_cols=24  Identities=38%  Similarity=0.414  Sum_probs=20.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ..++|+|.+|||||+++..+....
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l   26 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKL   26 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHh
Confidence            578999999999999998887653

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=92.94  E-value=0.16  Score=50.75  Aligned_cols=38  Identities=11%  Similarity=0.086  Sum_probs=32.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH-HHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY-AHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~-A~~~gwiVl~vP  102 (342)
                      .++.-++|.|.+|+|||+++.+++.. |..+|+=|+++.
T Consensus       192 ~~g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fS  230 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFS  230 (421)
T ss_pred             CCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            35678899999999999999999954 558899888884

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=92.90  E-value=0.12  Score=48.37  Aligned_cols=30  Identities=17%  Similarity=0.293  Sum_probs=24.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ....++|.|.+|||||++|.+-+.|....+
T Consensus        12 ~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~   41 (315)
T PF00580_consen   12 TEGPLLVNAGAGSGKTTTLLERIAYLLYEG   41 (315)
T ss_dssp             -SSEEEEEE-TTSSHHHHHHHHHHHHHHTS
T ss_pred             CCCCEEEEeCCCCCchHHHHHHHHHhhccc
Confidence            456788889999999999999999887654

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.89  E-value=0.16  Score=51.14  Aligned_cols=35  Identities=23%  Similarity=0.191  Sum_probs=27.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH--hCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH--ENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~--~~gwiVl~v  101 (342)
                      ...++|.|+.|+||||+++.+.+++.  ..|.=|..|
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li  257 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALI  257 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEE
Confidence            45789999999999999999988775  455555555

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

Probab=92.88  E-value=0.088  Score=44.11  Aligned_cols=40  Identities=30%  Similarity=0.401  Sum_probs=26.8

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ...++.+.++..+   .....++|+|++||||+.+. +++|...
T Consensus         6 ~~~~l~~~l~~~a---~~~~pvli~GE~GtGK~~~A-~~lh~~~   45 (138)
T PF14532_consen    6 AMRRLRRQLERLA---KSSSPVLITGEPGTGKSLLA-RALHRYS   45 (138)
T ss_dssp             HHHHHHHHHHHHH---CSSS-EEEECCTTSSHHHHH-HCCHHTT
T ss_pred             HHHHHHHHHHHHh---CCCCcEEEEcCCCCCHHHHH-HHHHhhc
Confidence            3456667776622   45678999999999999964 4554433

>cd00157 Rho Rho (Ras homology) family

Probab=92.88  E-value=0.093  Score=44.56  Aligned_cols=22  Identities=27%  Similarity=0.403  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ++++.|++|||||+++.++...
T Consensus         2 ki~i~G~~~~GKSsli~~l~~~   23 (171)
T cd00157           2 KIVVVGDGAVGKTCLLISYTTG   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            7899999999999999988764

Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho 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 most Rho protein

>PHA02774 E1; Provisional

Probab=92.87  E-value=0.23  Score=51.62  Aligned_cols=49  Identities=18%  Similarity=0.281  Sum_probs=36.1

Q ss_pred             HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        52 el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++..|+.+....++.+.++|+||+|+|||.+...++.+.  +|-++.+|.
T Consensus       419 ~fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L--~G~vi~fvN  467 (613)
T PHA02774        419 SFLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFL--KGKVISFVN  467 (613)
T ss_pred             HHHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHh--CCCEEEEEE
Confidence            4555566644444556899999999999999988888875  466666664

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=92.84  E-value=0.097  Score=43.77  Aligned_cols=22  Identities=36%  Similarity=0.537  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|+++.|.+|||||+++.+.+.
T Consensus         2 ~ki~iiG~~~vGKTsl~~~~~~   23 (162)
T cd04138           2 YKLVVVGAGGVGKSALTIQLIQ   23 (162)
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4789999999999999988874

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>KOG0781|consensus

Probab=92.73  E-value=0.16  Score=51.28  Aligned_cols=51  Identities=20%  Similarity=0.264  Sum_probs=41.5

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++|..-+.. +.......-+++.|-.|+||||-|+-+..|-.+|++=|+-.
T Consensus       362 sVDlLRdI~s-ar~~krPYVi~fvGVNGVGKSTNLAKIayWLlqNkfrVLIA  412 (587)
T KOG0781|consen  362 SVDLLRDIMS-ARRRKRPYVISFVGVNGVGKSTNLAKIAYWLLQNKFRVLIA  412 (587)
T ss_pred             hhhHHHHHHH-HHhcCCCeEEEEEeecCccccchHHHHHHHHHhCCceEEEE
Confidence            5566666666 44445677888999999999999999999999999987654

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=92.72  E-value=0.17  Score=49.73  Aligned_cols=42  Identities=17%  Similarity=0.210  Sum_probs=29.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh---CCeEEEEeCCcccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE---NNYLLVHIPWVLRW  107 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~---~gwiVl~vP~~~~~  107 (342)
                      +.--+++.|+.||||||+|.-++.+-..   .+=.|+.+=++.++
T Consensus       133 ~~glilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE~  177 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIEF  177 (358)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCceE
Confidence            5678999999999999999887776532   23345555444444

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=92.68  E-value=0.1  Score=44.05  Aligned_cols=21  Identities=38%  Similarity=0.599  Sum_probs=19.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++++.|++|+|||+++.+++.
T Consensus         2 ki~v~G~~~~GKTsli~~~~~   22 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQ   22 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            789999999999999999874

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=92.67  E-value=0.15  Score=49.84  Aligned_cols=38  Identities=21%  Similarity=0.114  Sum_probs=30.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEeCCcccc
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAH-ENNYLLVHIPWVLRW  107 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~vP~~~~~  107 (342)
                      .+|.|..||||||+...+..+.. ..||-|..+.--..+
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~~g~~v~~~~~Dd~i   40 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRERGWAVAVITYDDII   40 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhccCCeEEEEcccccc
Confidence            47999999999999999998876 689988777544333

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily

Probab=92.66  E-value=0.11  Score=43.70  Aligned_cols=24  Identities=33%  Similarity=0.461  Sum_probs=20.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..++++.|++|+|||+++...+..
T Consensus         2 ~~ki~i~G~~~~GKtsl~~~~~~~   25 (164)
T cd04145           2 TYKLVVVGGGGVGKSALTIQFIQS   25 (164)
T ss_pred             ceEEEEECCCCCcHHHHHHHHHhC
Confidence            468999999999999999987653

This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali

>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts)

Probab=92.66  E-value=0.16  Score=47.31  Aligned_cols=37  Identities=30%  Similarity=0.239  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..|+...++.   ......+++|.|+.|+|||++...+..
T Consensus        17 ~~~~~~~~~~---~~~~~~~IllvG~tGvGKSSliNaLlg   53 (249)
T cd01853          17 ALELEAKGKE---ELDFSLTILVLGKTGVGKSSTINSIFG   53 (249)
T ss_pred             HHHHHHHhhh---hccCCeEEEEECCCCCcHHHHHHHHhC
Confidence            3444444433   345688999999999999999888764

This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=92.64  E-value=0.23  Score=52.28  Aligned_cols=36  Identities=33%  Similarity=0.474  Sum_probs=26.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH---------hCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH---------ENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~---------~~gwiVl~v  101 (342)
                      ....++|+|++|||||+++.-+...+.         ...|+.+.-
T Consensus       174 ~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~  218 (615)
T TIGR02903       174 FPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDG  218 (615)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEec
Confidence            345799999999999998877766553         245777653

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.

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=92.62  E-value=0.11  Score=47.23  Aligned_cols=35  Identities=17%  Similarity=0.243  Sum_probs=28.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH----hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH----ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~----~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-...    ..|-|.+
T Consensus        31 ~~Ge~~~l~G~nGsGKSTLlk~l~G~~~~~~~~~G~i~~   69 (226)
T cd03234          31 ESGQVMAILGSSGSGKTTLLDAISGRVEGGGTTSGQILF   69 (226)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHhCccCCCCCCceEEEE
Confidence            5678999999999999999988776644    4676654

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=92.62  E-value=0.13  Score=45.16  Aligned_cols=28  Identities=21%  Similarity=0.179  Sum_probs=23.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +.|+|..|||||++...+..    .|..|+..
T Consensus         2 i~itG~~gsGKst~~~~l~~----~g~~~i~~   29 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE----LGIPVIDA   29 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH----CCCCEEec
Confidence            68999999999999988776    47777665

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>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=92.59  E-value=0.16  Score=47.12  Aligned_cols=39  Identities=18%  Similarity=0.286  Sum_probs=26.6

Q ss_pred             EEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCccccccC
Q psy3261          72 LYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLRWFAY  110 (342)
Q Consensus        72 L~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~~~~~  110 (342)
                      +.|+.||||||...-...|...+  .-.+|+..-|.+.+.+
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~vNLDPa~~~~~y   41 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNGRDVYIVNLDPAVENLPY   41 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT-S-EEEEE--TT-S--SS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCceEEEcchHhccccc
Confidence            46999999999999999999877  6777888444444443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=92.57  E-value=0.15  Score=54.99  Aligned_cols=38  Identities=24%  Similarity=0.166  Sum_probs=32.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~~  104 (342)
                      ..-++|+|..|||||++|..++..+...|+-|+.+ |.+
T Consensus       368 ~~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg  406 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSG  406 (744)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcH
Confidence            35789999999999999999999888889888777 654

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK06217 hypothetical protein; Validated

Probab=92.56  E-value=0.12  Score=45.58  Aligned_cols=33  Identities=12%  Similarity=0.037  Sum_probs=24.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .+++|.|..||||||+-.++....   |+-+++...
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~l---~~~~~~~D~   34 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAERL---DIPHLDTDD   34 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc---CCcEEEcCc
Confidence            379999999999999988877543   655555443

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=92.54  E-value=0.097  Score=44.06  Aligned_cols=21  Identities=29%  Similarity=0.335  Sum_probs=18.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |++|.|++|||||+++..+..
T Consensus         1 ~i~i~G~~~~GKTsl~~~~~~   21 (160)
T cd04156           1 QVLLLGLDSAGKSTLLYKLKH   21 (160)
T ss_pred             CEEEEcCCCCCHHHHHHHHhc
Confidence            588999999999999998864

ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in h

>PLN02200 adenylate kinase family protein

Probab=92.52  E-value=0.16  Score=46.87  Aligned_cols=31  Identities=13%  Similarity=0.106  Sum_probs=23.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ....++|.|++||||||....+.   ...|+..|
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La---~~~g~~hi   72 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIV---ETFGFKHL   72 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH---HHhCCeEE
Confidence            34578999999999999877764   34466533

>PRK14528 adenylate kinase; Provisional

Probab=92.52  E-value=0.13  Score=45.59  Aligned_cols=31  Identities=13%  Similarity=0.196  Sum_probs=22.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+++|.|++|||||++...+..   ..|+.++.+
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~---~~~~~~is~   32 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCE---RLSIPQIST   32 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH---HhCCCeeeC
Confidence            4789999999999998766633   335544443

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=92.52  E-value=0.12  Score=45.56  Aligned_cols=35  Identities=23%  Similarity=0.341  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        16 ~~Ge~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~   51 (190)
T TIGR01166        16 ERGEVLALLGANGAGKSTLLLHLNGLLRPQSGAVLI   51 (190)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCceeEEE
Confidence            4678999999999999999987665432 4566544

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.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=92.49  E-value=0.085  Score=47.69  Aligned_cols=22  Identities=32%  Similarity=0.354  Sum_probs=19.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++++|.+|||||+.+..++...
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4799999999999999998875

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=92.47  E-value=0.12  Score=46.17  Aligned_cols=35  Identities=17%  Similarity=0.244  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   59 (205)
T cd03226          24 YAGEIIALTGKNGAGKTTLAKILAGLIKESSGSILL   59 (205)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            4678999999999999999987765433 4566543

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=92.46  E-value=0.11  Score=44.14  Aligned_cols=22  Identities=36%  Similarity=0.552  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++++.|++|||||+++.+++.
T Consensus         3 ~ki~i~G~~~vGKSsli~~~~~   24 (166)
T cd01869           3 FKLLLIGDSGVGKSCLLLRFAD   24 (166)
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            5789999999999999988863

Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t

>cd00876 Ras Ras family

Probab=92.44  E-value=0.11  Score=43.45  Aligned_cols=20  Identities=35%  Similarity=0.556  Sum_probs=18.2

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++++.|++|||||+++..+.
T Consensus         1 ki~i~G~~~~GKTsli~~l~   20 (160)
T cd00876           1 KVVVLGAGGVGKSAITIQFV   20 (160)
T ss_pred             CEEEECCCCCCHHHHHHHHH
Confidence            57899999999999998886

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

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=92.44  E-value=0.23  Score=48.75  Aligned_cols=31  Identities=19%  Similarity=0.285  Sum_probs=26.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ..-..++|.|++|||||++...+..++-..+
T Consensus        36 p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~   66 (350)
T CHL00081         36 PKIGGVMIMGDRGTGKSTTIRALVDLLPEIE   66 (350)
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHHHHhhcC
Confidence            4456899999999999999999999887655

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=92.41  E-value=0.12  Score=43.44  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++++.|++|+|||+++.++++
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~   22 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMY   22 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            789999999999999998884

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

>smart00175 RAB Rab subfamily of small GTPases

Probab=92.40  E-value=0.11  Score=43.58  Aligned_cols=21  Identities=38%  Similarity=0.515  Sum_probs=19.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .|+++.|++|||||+++..+.
T Consensus         1 ~kv~v~G~~~~GKTtli~~l~   21 (164)
T smart00175        1 FKIILIGDSGVGKSSLLSRFT   21 (164)
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            378999999999999999876

Rab GTPases are implicated in vesicle trafficking.

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 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=92.39  E-value=0.12  Score=45.85  Aligned_cols=25  Identities=24%  Similarity=0.386  Sum_probs=19.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +.+.++|.|+.|||||.++.++++-
T Consensus         2 k~~~vlL~Gps~SGKTaLf~~L~~~   26 (181)
T PF09439_consen    2 KRPTVLLVGPSGSGKTALFSQLVNG   26 (181)
T ss_dssp             ---EEEEE-STTSSHHHHHHHHHHS
T ss_pred             CCceEEEEcCCCCCHHHHHHHHhcC
Confidence            4678999999999999999999875

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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=92.39  E-value=0.13  Score=44.72  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=20.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+.--+-|.||.||||||+|.-+.-
T Consensus        26 a~GeivtlMGPSGcGKSTLls~~~G   50 (213)
T COG4136          26 AKGEIVTLMGPSGCGKSTLLSWMIG   50 (213)
T ss_pred             cCCcEEEEECCCCccHHHHHHHHHh
Confidence            3566788999999999999976553

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=92.39  E-value=0.2  Score=45.47  Aligned_cols=38  Identities=18%  Similarity=0.307  Sum_probs=30.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEe-CCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHI-PWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~v-P~~  104 (342)
                      ..++.+.|.+|||||.++..++.... ..|--|+=+ |.+
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~ll~~l~~~~~~~~ii~D~~G   62 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKVLLEELLKKKGAKVIIFDPHG   62 (229)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEcCCC
Confidence            56889999999999999999999888 555544444 555

It contains several conserved aspartates and histidines that could be metal ligands.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=92.36  E-value=0.14  Score=44.68  Aligned_cols=30  Identities=20%  Similarity=0.196  Sum_probs=23.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYL   97 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi   97 (342)
                      +.-++|.|.+||||||+...+.... ...|+
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~-~~~~~   31 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVL-AEPWL   31 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh-CCCcc
Confidence            4568999999999999998886653 23354

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

>cd04163 Era Era subfamily

Probab=92.36  E-value=0.12  Score=43.06  Aligned_cols=22  Identities=32%  Similarity=0.295  Sum_probs=19.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..++++.|+.|+|||+++.++.
T Consensus         3 ~~~i~~~G~~g~GKttl~~~l~   24 (168)
T cd04163           3 SGFVAIVGRPNVGKSTLLNALV   24 (168)
T ss_pred             eeEEEEECCCCCCHHHHHHHHh
Confidence            4679999999999999999975

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.

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=92.34  E-value=0.11  Score=48.28  Aligned_cols=29  Identities=21%  Similarity=0.366  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      .+.-+++|+|+.|+|||++|.-+..+-..
T Consensus        55 ~~ge~W~I~G~NGsGKTTLL~ll~~~~~p   83 (257)
T COG1119          55 NPGEHWAIVGPNGAGKTTLLSLLTGEHPP   83 (257)
T ss_pred             cCCCcEEEECCCCCCHHHHHHHHhcccCC
Confidence            57899999999999999999998887554

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.33  E-value=0.41  Score=50.61  Aligned_cols=74  Identities=14%  Similarity=0.059  Sum_probs=51.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CCccc-c-------c--cCCc-cee-ccC--------CCC-Cc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PWVLR-W-------F--AYPK-EVS-HSL--------TKE-GM  123 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~~~~-~-------~--~~~~-~~~-~s~--------~~~-~~  123 (342)
                      .....++.|..|+|||+++..++..+...|.-|+.+ |.+.. +       +  .|.. +|. .+.        .++ ..
T Consensus       175 ~~~H~lv~G~TGsGKT~l~~~l~~q~i~~g~~viv~DpKgD~~l~~~~~~~~~~~G~~dd~~~f~~~~p~~S~~~NPl~~  254 (634)
T TIGR03743       175 RVGHTLVLGTTGVGKTRLAELLITQDIRRGDVVIVIDPKGDADLKRRMRAEAKRAGRPDRFYYFHPAFPEISVRYNPLGN  254 (634)
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCchHHHHHHHHHHHHhCCCceEEEEecCCCCcCcCcChhhh
Confidence            356889999999999999999999999888888888 77641 0       0  0111 111 111        133 34


Q ss_pred             cccHHHHHHHHHHHHH
Q psy3261         124 VDLNIDAAMWLRHFQK  139 (342)
Q Consensus       124 ~~qP~~a~~~L~~~~~  139 (342)
                      |+++...+.|+..+..
T Consensus       255 ~~~~~eva~~i~~ll~  270 (634)
T TIGR03743       255 FSRISEVASRIAQLLP  270 (634)
T ss_pred             cCChHHHHHHHHHhcc
Confidence            8899888899988865

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=92.33  E-value=0.13  Score=46.07  Aligned_cols=35  Identities=23%  Similarity=0.353  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|=|.+
T Consensus        24 ~~G~~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   59 (210)
T cd03269          24 EKGEIFGLLGPNGAGKTTTIRMILGIILPDSGEVLF   59 (210)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            4678899999999999999887775432 3454433

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=92.31  E-value=0.24  Score=47.95  Aligned_cols=51  Identities=14%  Similarity=0.270  Sum_probs=36.5

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH--hCCeEEEEeC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH--ENNYLLVHIP  102 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~--~~gwiVl~vP  102 (342)
                      ...++++.+++ +.  .....++|+|++||||+++...+.....  ...|++|+-.
T Consensus        14 ~~~~~~~~i~~-~a--~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~   66 (326)
T PRK11608         14 SFLEVLEQVSR-LA--PLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCA   66 (326)
T ss_pred             HHHHHHHHHHH-Hh--CCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCC
Confidence            56667777777 32  4467899999999999988765554443  3468888764

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=92.31  E-value=0.17  Score=45.86  Aligned_cols=35  Identities=23%  Similarity=0.256  Sum_probs=28.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH------HhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA------HENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A------~~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-      -..|-|.+
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl~~i~G~~~~~~~~~~~G~i~~   64 (227)
T cd03260          24 PKGEITALIGPSGCGKSTLLRLLNRLNDLIPGAPDEGEVLL   64 (227)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcccccCCCCCeEEEE
Confidence            467899999999999999999887664      35687765

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=92.30  E-value=0.19  Score=48.71  Aligned_cols=42  Identities=19%  Similarity=0.267  Sum_probs=30.3

Q ss_pred             ceEEechhHHH-HHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          42 SSILIRNCMLE-LVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        42 ~~~lvR~~t~e-l~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      |....+.++.. ++..|..       ..+++|.|++|||||++..++...
T Consensus        45 ~~y~f~~~~~~~vl~~l~~-------~~~ilL~G~pGtGKTtla~~lA~~   87 (327)
T TIGR01650        45 PAYLFDKATTKAICAGFAY-------DRRVMVQGYHGTGKSTHIEQIAAR   87 (327)
T ss_pred             CCccCCHHHHHHHHHHHhc-------CCcEEEEeCCCChHHHHHHHHHHH
Confidence            46778876644 4444422       568999999999999998876554

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=92.25  E-value=0.28  Score=41.03  Aligned_cols=39  Identities=15%  Similarity=0.151  Sum_probs=28.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh----CCeEEEEeCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE----NNYLLVHIPW  103 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~----~gwiVl~vP~  103 (342)
                      .++.-+-++|++|||||.+-..++..-+.    +..+-.+++.
T Consensus        51 ~KpLVlSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~   93 (127)
T PF06309_consen   51 RKPLVLSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIAT   93 (127)
T ss_pred             CCCEEEEeecCCCCcHHHHHHHHHHHHHhcccCCCceeeeccc
Confidence            44566669999999999988887777554    4555555553

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

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=92.25  E-value=0.12  Score=43.40  Aligned_cols=20  Identities=30%  Similarity=0.448  Sum_probs=18.3

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++++.|++|||||+++.++.
T Consensus         2 ki~~vG~~~vGKTsli~~l~   21 (168)
T cd04119           2 KVISMGNSGVGKSCIIKRYC   21 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            78999999999999998775

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.

>cd01863 Rab18 Rab18 subfamily

Probab=92.25  E-value=0.12  Score=43.46  Aligned_cols=20  Identities=40%  Similarity=0.629  Sum_probs=18.3

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++++.|++|||||+++.++.
T Consensus         2 ki~v~G~~~~GKSsli~~l~   21 (161)
T cd01863           2 KILLIGDSGVGKSSLLLRFT   21 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            78999999999999998875

Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos

>KOG0730|consensus

Probab=92.25  E-value=0.12  Score=53.96  Aligned_cols=27  Identities=30%  Similarity=0.461  Sum_probs=22.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++..++++|||+|||||++..-+...|
T Consensus       466 ~ppkGVLlyGPPGC~KT~lAkalAne~  492 (693)
T KOG0730|consen  466 SPPKGVLLYGPPGCGKTLLAKALANEA  492 (693)
T ss_pred             CCCceEEEECCCCcchHHHHHHHhhhh
Confidence            688999999999999998866554444

>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=92.24  E-value=0.15  Score=42.80  Aligned_cols=30  Identities=23%  Similarity=0.257  Sum_probs=23.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++|.|++|||||++...+...   .||..+..
T Consensus         1 ~i~l~G~~GsGKstla~~la~~---l~~~~~~~   30 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKA---LGLPFVDL   30 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH---hCCCEEEc
Confidence            3789999999999998887543   37766644

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.

>PRK14526 adenylate kinase; Provisional

Probab=92.23  E-value=0.13  Score=46.71  Aligned_cols=20  Identities=25%  Similarity=0.378  Sum_probs=17.4

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +++|.|++||||||+...+.
T Consensus         2 ~i~l~G~pGsGKsT~a~~La   21 (211)
T PRK14526          2 KLVFLGPPGSGKGTIAKILS   21 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            68999999999999976654

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=92.22  E-value=0.32  Score=47.22  Aligned_cols=41  Identities=17%  Similarity=0.084  Sum_probs=29.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh--CCeEEEEeCCcccc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE--NNYLLVHIPWVLRW  107 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~--~gwiVl~vP~~~~~  107 (342)
                      ...+++.|+.||||||+|..++.+..+  .+.-++-|=+..++
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCccc
Confidence            446899999999999999888876542  35566666444443

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=92.22  E-value=0.12  Score=44.10  Aligned_cols=23  Identities=35%  Similarity=0.496  Sum_probs=20.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..|+++.|++|+|||+++.++..
T Consensus         3 ~~ki~vvG~~~~GKSsl~~~~~~   25 (167)
T cd01867           3 LFKLLLIGDSGVGKSCLLLRFSE   25 (167)
T ss_pred             ceEEEEECCCCCCHHHHHHHHhh
Confidence            46899999999999999998864

Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. 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 inhi

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=92.18  E-value=0.26  Score=47.30  Aligned_cols=34  Identities=24%  Similarity=0.142  Sum_probs=25.8

Q ss_pred             CCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          63 FDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        63 ~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .-.+...++|+|.+|||||++...+.   ..-||-++
T Consensus       129 ~~~~~~~I~l~G~~GsGKStvg~~La---~~Lg~~~i  162 (309)
T PRK08154        129 RAARRRRIALIGLRGAGKSTLGRMLA---ARLGVPFV  162 (309)
T ss_pred             hccCCCEEEEECCCCCCHHHHHHHHH---HHcCCCEE
Confidence            34578899999999999999987763   33466555

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=92.18  E-value=0.14  Score=46.12  Aligned_cols=35  Identities=23%  Similarity=0.256  Sum_probs=27.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   62 (216)
T TIGR00960        27 TKGEMVFLVGHSGAGKSTFLKLILGIEKPTRGKIRF   62 (216)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            4678999999999999999888776533 4576655

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=92.17  E-value=0.18  Score=51.68  Aligned_cols=47  Identities=15%  Similarity=0.092  Sum_probs=34.4

Q ss_pred             HHHHhccC-CCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          55 GYLKSMTN-FDRPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        55 ~~l~~~~~-~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      .-|+.+.. .-.++.-++|.|++|+|||++..|.+..+..+ |==|+||
T Consensus        18 ~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyi   66 (509)
T PRK09302         18 EGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFV   66 (509)
T ss_pred             hhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEE
Confidence            34444332 33568889999999999999999998876665 6555555

>cd04136 Rap_like Rap-like subfamily

Probab=92.16  E-value=0.13  Score=43.23  Aligned_cols=21  Identities=38%  Similarity=0.482  Sum_probs=18.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++++.|.+|+|||+++.+.+
T Consensus         2 ~ki~i~G~~~vGKTsl~~~~~   22 (163)
T cd04136           2 YKVVVLGSGGVGKSALTVQFV   22 (163)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            478999999999999988776

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>PRK06761 hypothetical protein; Provisional

Probab=92.15  E-value=0.2  Score=47.59  Aligned_cols=32  Identities=19%  Similarity=0.175  Sum_probs=27.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .-++|.|++||||||++.++.......|.=|.
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~g~~v~   35 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQNGIEVE   35 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcCceEEE
Confidence            46899999999999999999998876665443

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=92.14  E-value=0.14  Score=46.33  Aligned_cols=34  Identities=9%  Similarity=0.085  Sum_probs=27.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH-HhCCeEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA-HENNYLL   98 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A-~~~gwiV   98 (342)
                      .++..+.|.|+.||||||+|.-+.-.. -..|-|.
T Consensus        11 ~~Ge~~~l~G~NGsGKSTLlk~i~Gl~~~~sG~i~   45 (213)
T PRK15177         11 GYHEHIGILAAPGSGKTTLTRLLCGLDAPDEGDFI   45 (213)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCccCCCCCEE
Confidence            457889999999999999998877653 3567764

>TIGR00959 ffh signal recognition particle protein

Probab=92.14  E-value=0.22  Score=50.11  Aligned_cols=35  Identities=14%  Similarity=0.230  Sum_probs=29.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~v  101 (342)
                      ..-+++.|+.|+||||+.+.+..++. +.|.=|+.|
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV  134 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLV  134 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEE
Confidence            45788999999999999999999876 567766555

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.

>PRK14527 adenylate kinase; Provisional

Probab=92.13  E-value=0.16  Score=44.91  Aligned_cols=32  Identities=16%  Similarity=0.172  Sum_probs=23.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ++...+++.|++||||||+..++.   .+.|+..+
T Consensus         4 ~~~~~i~i~G~pGsGKsT~a~~La---~~~~~~~i   35 (191)
T PRK14527          4 TKNKVVIFLGPPGAGKGTQAERLA---QELGLKKL   35 (191)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHH---HHhCCCCC
Confidence            356789999999999999887763   33455443

>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=92.11  E-value=0.15  Score=44.19  Aligned_cols=35  Identities=20%  Similarity=0.284  Sum_probs=27.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.|||||++|.-+.-... ..|-|.+
T Consensus        25 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   60 (166)
T cd03223          25 KPGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGM   60 (166)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEE
Confidence            5688999999999999999988776533 4566543

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

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.11  E-value=0.23  Score=49.09  Aligned_cols=31  Identities=23%  Similarity=0.247  Sum_probs=26.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENN   95 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~g   95 (342)
                      ....-++|.|+.|+||||+++.+.+++. ..|
T Consensus       135 ~~g~ii~lvGptGvGKTTtiakLA~~~~~~~G  166 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTAKLAARCVMRFG  166 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC
Confidence            3467899999999999999999999864 444

>PTZ00132 GTP-binding nuclear protein Ran; Provisional

Probab=92.11  E-value=0.16  Score=45.51  Aligned_cols=25  Identities=32%  Similarity=0.541  Sum_probs=21.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|+.|||||+++.+.+.
T Consensus         7 ~~~~kv~liG~~g~GKTtLi~~~~~   31 (215)
T PTZ00132          7 VPEFKLILVGDGGVGKTTFVKRHLT   31 (215)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHh
Confidence            4568999999999999999976553

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=92.10  E-value=0.19  Score=45.90  Aligned_cols=37  Identities=16%  Similarity=0.367  Sum_probs=27.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccc
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWF  108 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~  108 (342)
                      -++|.||.|+|||.   .++..|.+.||=||...+.+-+-
T Consensus         3 v~~i~GpT~tGKt~---~ai~lA~~~g~pvI~~Driq~y~   39 (233)
T PF01745_consen    3 VYLIVGPTGTGKTA---LAIALAQKTGAPVISLDRIQCYP   39 (233)
T ss_dssp             EEEEE-STTSSHHH---HHHHHHHHH--EEEEE-SGGG-G
T ss_pred             EEEEECCCCCChhH---HHHHHHHHhCCCEEEecceeccc
Confidence            37899999999995   57889999999999998776643

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>KOG0090|consensus

Probab=92.08  E-value=0.48  Score=43.17  Aligned_cols=69  Identities=16%  Similarity=0.100  Sum_probs=45.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccH--HHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLN--IDAAMWLRHFQKQN  141 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP--~~a~~~L~~~~~~N  141 (342)
                      +..++++|.|+.+||||+++.|+.+- .-.+-++=-.|+.-.|.-+...       .-+.|-|  ...+.+|......|
T Consensus        36 s~~~~Vll~Gl~dSGKT~LF~qL~~g-s~~~TvtSiepn~a~~r~gs~~-------~~LVD~PGH~rlR~kl~e~~~~~  106 (238)
T KOG0090|consen   36 SKQNAVLLVGLSDSGKTSLFTQLITG-SHRGTVTSIEPNEATYRLGSEN-------VTLVDLPGHSRLRRKLLEYLKHN  106 (238)
T ss_pred             ccCCcEEEEecCCCCceeeeeehhcC-CccCeeeeeccceeeEeecCcc-------eEEEeCCCcHHHHHHHHHHcccc
Confidence            44589999999999999999999876 4445555555777777666543       1223333  25566666664544

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=92.07  E-value=0.33  Score=43.34  Aligned_cols=31  Identities=16%  Similarity=0.154  Sum_probs=24.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +.|.|.+|||||++..++....  .+..+++..
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~--~~~~~i~~D   32 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRIL--PNCCVIHQD   32 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc--CCCeEEccc
Confidence            5788999999999998888764  356666543

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.

>PRK08506 replicative DNA helicase; Provisional

Probab=92.06  E-value=0.28  Score=50.00  Aligned_cols=37  Identities=8%  Similarity=0.066  Sum_probs=32.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++.-++|-|.+|.|||+++.+++..|..+|+-|+++
T Consensus       190 ~~G~LivIaarpg~GKT~fal~ia~~~~~~g~~V~~f  226 (472)
T PRK08506        190 NKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFF  226 (472)
T ss_pred             CCCceEEEEcCCCCChHHHHHHHHHHHHhcCCcEEEE
Confidence            4677889999999999999999999988888888777

>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional

Probab=92.06  E-value=0.18  Score=48.13  Aligned_cols=32  Identities=28%  Similarity=0.270  Sum_probs=25.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ...++|+|..|||||+++..+-    ..||.++.-+
T Consensus         6 ~~~i~i~G~~GsGKtt~~~~l~----~~g~~~~d~~   37 (288)
T PRK05416          6 MRLVIVTGLSGAGKSVALRALE----DLGYYCVDNL   37 (288)
T ss_pred             ceEEEEECCCCCcHHHHHHHHH----HcCCeEECCc
Confidence            4579999999999999998884    5588776543

>PRK13973 thymidylate kinase; Provisional

Probab=92.06  E-value=0.24  Score=44.86  Aligned_cols=38  Identities=16%  Similarity=0.145  Sum_probs=32.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      +.=++|-|..||||||....+..+....|.-|++.+.+
T Consensus         3 g~~IviEG~dGsGKtTq~~~l~~~l~~~g~~~~~~~~p   40 (213)
T PRK13973          3 GRFITFEGGEGAGKSTQIRLLAERLRAAGYDVLVTREP   40 (213)
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            34578999999999999999999998888888777444

>cd04159 Arl10_like Arl10-like subfamily

Probab=92.05  E-value=0.12  Score=42.79  Aligned_cols=20  Identities=20%  Similarity=0.223  Sum_probs=17.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++|.|+.|||||+++.++..
T Consensus         2 i~i~G~~~~GKssl~~~l~~   21 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAG   21 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHcc
Confidence            67899999999999998854

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.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=92.03  E-value=0.16  Score=49.79  Aligned_cols=39  Identities=13%  Similarity=0.205  Sum_probs=31.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVL  105 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~  105 (342)
                      .+.-|..|.|+.|||||+++.|++.++...  +|||+--++
T Consensus       155 ~kGqr~~I~G~~G~GKT~L~~~Iak~~~~d--vvVyv~iGE  193 (369)
T cd01134         155 VKGGTAAIPGPFGCGKTVIQQSLSKYSNSD--IVIYVGCGE  193 (369)
T ss_pred             cCCCEEEEECCCCCChHHHHHHHHhCCCCC--EEEEEEeCC
Confidence            467899999999999999999988886543  677775553

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.

>PHA02624 large T antigen; Provisional

Probab=92.00  E-value=0.23  Score=51.88  Aligned_cols=41  Identities=15%  Similarity=0.104  Sum_probs=31.6

Q ss_pred             HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          51 LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        51 ~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .++.+.++.+....++.+-++|+||.|||||++...++...
T Consensus       415 ~~~~~~lk~~l~giPKk~~il~~GPpnTGKTtf~~sLl~~L  455 (647)
T PHA02624        415 DVIYDILKLIVENVPKRRYWLFKGPVNSGKTTLAAALLDLC  455 (647)
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            55566666645555778899999999999999988877664

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=92.00  E-value=0.15  Score=45.70  Aligned_cols=35  Identities=20%  Similarity=0.252  Sum_probs=27.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   61 (207)
T PRK13539         26 AAGEALVLTGPNGSGKTTLLRLIAGLLPPAAGTIKL   61 (207)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            5688999999999999999888776533 4576654

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=91.98  E-value=0.12  Score=48.57  Aligned_cols=35  Identities=23%  Similarity=0.343  Sum_probs=25.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .+..-++|-|+.||||||+|.-+--.-. ..|-|.+
T Consensus        25 ~~gef~vliGpSGsGKTTtLkMINrLiept~G~I~i   60 (309)
T COG1125          25 EEGEFLVLIGPSGSGKTTTLKMINRLIEPTSGEILI   60 (309)
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHhcccCCCCceEEE
Confidence            3567789999999999999998765432 3454443

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=91.97  E-value=0.16  Score=44.41  Aligned_cols=26  Identities=27%  Similarity=0.373  Sum_probs=22.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.|||||++|.-+.-.
T Consensus        26 ~~Ge~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          26 KQGEKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            46789999999999999998877643

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.

>cd01878 HflX HflX subfamily

Probab=91.96  E-value=0.15  Score=45.16  Aligned_cols=25  Identities=24%  Similarity=0.206  Sum_probs=21.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++..+++|.|+.|||||+++..++.
T Consensus        39 ~~~~~I~iiG~~g~GKStLl~~l~~   63 (204)
T cd01878          39 SGIPTVALVGYTNAGKSTLFNALTG   63 (204)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHhc
Confidence            3458999999999999999988765

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.

>cd01862 Rab7 Rab7 subfamily

Probab=91.96  E-value=0.13  Score=43.73  Aligned_cols=22  Identities=23%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ++++.|++|||||+++..+...
T Consensus         2 ki~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           2 KVIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            7899999999999999887653

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-

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=91.92  E-value=0.14  Score=46.72  Aligned_cols=35  Identities=23%  Similarity=0.371  Sum_probs=27.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   59 (236)
T cd03219          24 RPGEIHGLIGPNGAGKTTLFNLISGFLRPTSGSVLF   59 (236)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHcCCCCCCCceEEE
Confidence            4678999999999999999987765432 4576654

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).

>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=91.91  E-value=0.17  Score=44.09  Aligned_cols=27  Identities=26%  Similarity=0.389  Sum_probs=22.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .++..+.|.|+.|||||++|.-+.-..
T Consensus        26 ~~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          26 EPGESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            467899999999999999998776543

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

>PRK07429 phosphoribulokinase; Provisional

Probab=91.91  E-value=0.26  Score=47.91  Aligned_cols=39  Identities=15%  Similarity=0.068  Sum_probs=30.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .+...+-|+|+.||||||++..+.......++.|+...+
T Consensus         6 ~~~~IIgI~G~SGSGKSTla~~L~~ll~~~~~~vi~~Dd   44 (327)
T PRK07429          6 DRPVLLGVAGDSGCGKTTFLRGLADLLGEELVTVICTDD   44 (327)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHhHhccCceEEEEecc
Confidence            455678899999999999998888766666777877743

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=91.90  E-value=0.21  Score=44.71  Aligned_cols=37  Identities=22%  Similarity=0.073  Sum_probs=27.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAY  110 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~  110 (342)
                      .++.|+|+.|||||++..++...   -|+.|+   ++..+.+.
T Consensus         2 ~~i~itG~~gsGKst~~~~l~~~---~g~~~i---~~D~~~~~   38 (195)
T PRK14730          2 RRIGLTGGIASGKSTVGNYLAQQ---KGIPIL---DADIYARE   38 (195)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh---hCCeEe---eCcHHHHH
Confidence            36899999999999998887643   288777   35555444

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=91.89  E-value=0.35  Score=46.14  Aligned_cols=35  Identities=20%  Similarity=0.193  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .....+-|.|.+|||||++|..++.... ..+..|+
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~l~~~~~~~VI  137 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMRLKDSVPCAVI  137 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHhccCCCEEEE
Confidence            4577888999999999999999998754 3455555

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=91.89  E-value=0.16  Score=45.88  Aligned_cols=35  Identities=23%  Similarity=0.310  Sum_probs=27.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|.|.+
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~   59 (220)
T cd03265          24 RRGEIFGLLGPNGAGKTTTIKMLTTLLKPTSGRATV   59 (220)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            4678999999999999999987765432 4577655

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=91.87  E-value=0.14  Score=46.10  Aligned_cols=35  Identities=17%  Similarity=0.233  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|=|.+
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   59 (222)
T cd03224          24 PEGEIVALLGRNGAGKTTLLKTIMGLLPPRSGSIRF   59 (222)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            4688999999999999999976554332 3465544

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=91.86  E-value=0.21  Score=43.84  Aligned_cols=24  Identities=21%  Similarity=0.306  Sum_probs=21.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++..+++|.|+.|||||+++.++.
T Consensus        15 ~~~~kv~lvG~~~vGKTsli~~~~   38 (182)
T PTZ00133         15 KKEVRILMVGLDAAGKTTILYKLK   38 (182)
T ss_pred             CCccEEEEEcCCCCCHHHHHHHHh
Confidence            556899999999999999998874

>TIGR00602 rad24 checkpoint protein rad24

Probab=91.86  E-value=0.24  Score=52.23  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ...+|...++.......+...++|+|++|||||+++.-+...
T Consensus        92 ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        92 KIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             HHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            444566677662222344556999999999999998877643

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

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=91.86  E-value=0.14  Score=45.87  Aligned_cols=35  Identities=26%  Similarity=0.382  Sum_probs=26.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        23 ~~Ge~~~l~G~nGsGKSTLl~~l~G~~~p~~G~i~~   58 (213)
T cd03235          23 KPGEFLAIVGPNGAGKSTLLKAILGLLKPTSGSIRV   58 (213)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHcCCCCCCCCEEEE
Confidence            4678999999999999999987755432 3465543

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=91.86  E-value=0.16  Score=45.52  Aligned_cols=35  Identities=23%  Similarity=0.234  Sum_probs=26.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|=|.+
T Consensus        25 ~~G~~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   60 (214)
T cd03292          25 SAGEFVFLVGPSGAGKSTLLKLIYKEELPTSGTIRV   60 (214)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            4678999999999999998887766543 3454443

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>KOG0086|consensus

Probab=91.85  E-value=0.14  Score=44.22  Aligned_cols=42  Identities=19%  Similarity=0.290  Sum_probs=28.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeCCcccccc
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIPWVLRWFA  109 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP~~~~~~~  109 (342)
                      .++++.|+.|+|||.+|.|.+.--+.. --..+-|--+.+.++
T Consensus        10 fKfl~iG~aGtGKSCLLh~Fie~kfkDdssHTiGveFgSrIin   52 (214)
T KOG0086|consen   10 FKFLVIGSAGTGKSCLLHQFIENKFKDDSSHTIGVEFGSRIVN   52 (214)
T ss_pred             heeEEeccCCCChhHHHHHHHHhhhcccccceeeeeecceeee
Confidence            478999999999999999999865532 223334444444444

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=91.84  E-value=0.16  Score=45.17  Aligned_cols=35  Identities=23%  Similarity=0.291  Sum_probs=27.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        25 ~~Ge~~~l~G~nGsGKSTLl~~i~G~~~~~~G~v~~   60 (200)
T PRK13540         25 PAGGLLHLKGSNGAGKTTLLKLIAGLLNPEKGEILF   60 (200)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCCCCCeeEEE
Confidence            4788999999999999999997665432 4566544

>cd04113 Rab4 Rab4 subfamily

Probab=91.84  E-value=0.15  Score=43.07  Aligned_cols=21  Identities=33%  Similarity=0.626  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++++.|+.|+|||+++.+++.
T Consensus         2 ki~v~G~~~vGKTsli~~l~~   22 (161)
T cd04113           2 KFIIIGSSGTGKSCLLHRFVE   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            789999999999999999863

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

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=91.83  E-value=0.15  Score=45.72  Aligned_cols=33  Identities=18%  Similarity=0.366  Sum_probs=24.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      ++ .+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        25 ~g-~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   58 (211)
T cd03264          25 PG-MYGLLGPNGAGKTTLMRILATLTPPSSGTIRI   58 (211)
T ss_pred             CC-cEEEECCCCCCHHHHHHHHhCCCCCCccEEEE
Confidence            46 999999999999998877764322 4576654

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=91.82  E-value=0.16  Score=46.14  Aligned_cols=35  Identities=26%  Similarity=0.296  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|=|.+
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   66 (225)
T PRK10247         31 RAGEFKLITGPSGCGKSTLLKIVASLISPTSGTLLF   66 (225)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcccCCCCCeEEE
Confidence            4688999999999999999987765432 4565544

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=91.81  E-value=0.16  Score=45.77  Aligned_cols=35  Identities=20%  Similarity=0.201  Sum_probs=27.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        29 ~~G~~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~   64 (221)
T TIGR02211        29 GKGEIVAIVGSSGSGKSTLLHLLGGLDNPTSGEVLF   64 (221)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEE
Confidence            4678999999999999999988765433 4566554

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>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=91.80  E-value=0.16  Score=46.36  Aligned_cols=35  Identities=23%  Similarity=0.371  Sum_probs=27.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~l~G~~~p~~G~i~~   59 (235)
T cd03261          24 RRGEILAIIGPSGSGKSTLLRLIVGLLRPDSGEVLI   59 (235)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            4688999999999999999888875543 4566554

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.80  E-value=0.25  Score=49.10  Aligned_cols=26  Identities=27%  Similarity=0.401  Sum_probs=23.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ...+++.|+.|+||||+++.+.++..
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            46789999999999999999998776

>cd04124 RabL2 RabL2 subfamily

Probab=91.80  E-value=0.15  Score=43.36  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=19.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++++.|.+|||||+++.+.+.
T Consensus         2 ki~vvG~~~vGKTsli~~~~~   22 (161)
T cd04124           2 KIILLGDSAVGKSKLVERFLM   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            689999999999999988874

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

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=91.78  E-value=0.16  Score=46.16  Aligned_cols=35  Identities=17%  Similarity=0.363  Sum_probs=27.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   59 (232)
T cd03218          24 KQGEIVGLLGPNGAGKTTTFYMIVGLVKPDSGKILL   59 (232)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEE
Confidence            4678999999999999999888875543 4566544

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=91.76  E-value=0.16  Score=48.00  Aligned_cols=32  Identities=19%  Similarity=0.013  Sum_probs=24.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      -++|.|++||||||+-.++...-  .+|+.+..-
T Consensus         4 liil~G~pGSGKSTla~~L~~~~--~~~~~l~~D   35 (300)
T PHA02530          4 IILTVGVPGSGKSTWAREFAAKN--PKAVNVNRD   35 (300)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHC--CCCEEEecc
Confidence            57889999999999988865432  288877653

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=91.75  E-value=0.17  Score=45.38  Aligned_cols=35  Identities=20%  Similarity=0.299  Sum_probs=26.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|=|.+
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~l~G~~~~~~G~v~~   59 (213)
T cd03301          24 ADGEFVVLLGPSGCGKTTTLRMIAGLEEPTSGRIYI   59 (213)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            4678999999999999999977776533 4455443

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>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=91.75  E-value=0.22  Score=45.52  Aligned_cols=23  Identities=22%  Similarity=0.151  Sum_probs=19.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      +-|.|+.||||||+...+.....
T Consensus         2 igI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           2 IGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHh
Confidence            45789999999999988887654

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

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=91.74  E-value=0.21  Score=47.25  Aligned_cols=33  Identities=18%  Similarity=0.194  Sum_probs=27.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +-|.|+.||||||++..+...-...+..|+...
T Consensus         2 igI~G~sGsGKSTl~~~L~~ll~~~~~~vi~~D   34 (273)
T cd02026           2 IGVAGDSGCGKSTFLRRLTSLFGSDLVTVICLD   34 (273)
T ss_pred             EEEECCCCCCHHHHHHHHHHhhCCCceEEEECc
Confidence            568999999999999988877666677777764

This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=91.73  E-value=0.22  Score=47.11  Aligned_cols=32  Identities=9%  Similarity=0.113  Sum_probs=28.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -+-+.|.+||||||++.+++....+.| -|..|
T Consensus         3 ~i~i~G~~gSGKTTLi~~Li~~L~~~G-~V~~I   34 (274)
T PRK14493          3 VLSIVGYKATGKTTLVERLVDRLSGRG-RVGTV   34 (274)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCC-CEEEE
Confidence            367899999999999999999999999 67777

>cd04129 Rho2 Rho2 subfamily

Probab=91.73  E-value=0.15  Score=44.77  Aligned_cols=21  Identities=24%  Similarity=0.387  Sum_probs=19.2

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+++|.|+.|+|||+++.++.
T Consensus         2 ~Ki~ivG~~g~GKStLl~~l~   22 (187)
T cd04129           2 RKLVIVGDGACGKTSLLSVFT   22 (187)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            478999999999999999886

Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho 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 proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=91.73  E-value=0.17  Score=45.27  Aligned_cols=34  Identities=15%  Similarity=0.334  Sum_probs=25.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLL   98 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiV   98 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|=|.
T Consensus        24 ~~G~~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~   58 (208)
T cd03268          24 KKGEIYGFLGPNGAGKTTTMKIILGLIKPDSGEIT   58 (208)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCcCCCceEEE
Confidence            4688999999999999999988764322 345443

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>TIGR00767 rho transcription termination factor Rho

Probab=91.72  E-value=0.23  Score=49.53  Aligned_cols=86  Identities=15%  Similarity=0.103  Sum_probs=46.9

Q ss_pred             CceEEEEEeCccccccCCCc-----CCCCCCCcccCCccchHHHHHHhhcCCCCCeEE--E-EEeCCCCCCCC-C-----
Q psy3261         203 VCRTFVCVDGYNSFFAEKTN-----CKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAI--V-LALSPRANLPD-R-----  268 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~-----y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~v--v-~AtS~~~~~~~-~-----  268 (342)
                      ...|+|.||++..|-.---.     =+.+. +=++|.-|..++-|....++--.+|.+  + ++.-.+++.-+ +     
T Consensus       254 GkdVVLlIDEitR~arAqrei~~~~G~~~s-~G~~~~~~~~~~~~~~~a~~~~~~GSiT~~~TvLvetg~~mdd~i~~e~  332 (415)
T TIGR00767       254 KKDVVILLDSITRLARAYNTVTPASGKVLS-GGVDANALHRPKRFFGAARNIEEGGSLTIIATALIDTGSRMDEVIFEEF  332 (415)
T ss_pred             CCCeEEEEEChhHHHHHHHHhHhhcCCCCC-CCcChhhhcccHHHHhhcCCCCCCcchhheEEEEeccCCCCCcchHHHh
Confidence            67999999999666332100     12333 556777787777777666542245532  2 22223222212 1     


Q ss_pred             -----ccCcchhHHhhhcCCCCCCCc
Q psy3261         269 -----RESHLPLYMLKKAGFESIDPF  289 (342)
Q Consensus       269 -----~~~~~p~~llg~~g~~~~dP~  289 (342)
                           -...|.+.+..+.-|+.+|+.
T Consensus       333 kg~~~~~ivL~r~la~~~~fPAidi~  358 (415)
T TIGR00767       333 KGTGNMELHLDRKLADRRIFPAIDIK  358 (415)
T ss_pred             ccccCCeEEECHHHHhCCCCCCcCcc
Confidence                 114566667766667776764

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

>cd01866 Rab2 Rab2 subfamily

Probab=91.70  E-value=0.15  Score=43.59  Aligned_cols=21  Identities=33%  Similarity=0.613  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++++.|.+|+|||+++.++.
T Consensus         5 ~ki~vvG~~~vGKSsLl~~l~   25 (168)
T cd01866           5 FKYIIIGDTGVGKSCLLLQFT   25 (168)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            689999999999999999875

Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur

>cd01868 Rab11_like Rab11-like

Probab=91.69  E-value=0.15  Score=43.11  Aligned_cols=22  Identities=41%  Similarity=0.507  Sum_probs=19.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++++.|++|||||+++.++..
T Consensus         4 ~ki~vvG~~~~GKSsli~~l~~   25 (165)
T cd01868           4 FKIVLIGDSGVGKSNLLSRFTR   25 (165)
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            5899999999999999999863

Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP

>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=91.69  E-value=0.27  Score=42.69  Aligned_cols=33  Identities=18%  Similarity=0.160  Sum_probs=28.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -+.+.|..|||||+++..++......|+-|-.|
T Consensus         3 vi~i~G~~gsGKTTli~~L~~~l~~~g~~V~~i   35 (159)
T cd03116           3 VIGFVGYSGSGKTTLLEKLIPALSARGLRVAVI   35 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            467899999999999999999988888866555

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.

>TIGR00991 3a0901s02IAP34 GTP-binding protein (Chloroplast Envelope Protein Translocase)

Probab=91.69  E-value=0.24  Score=47.70  Aligned_cols=38  Identities=37%  Similarity=0.482  Sum_probs=29.1

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .-+|++..|++   .+....+++|.|..|+|||++.+.++-
T Consensus        23 ~l~~~l~~l~~---~~~~~~rIllvGktGVGKSSliNsIlG   60 (313)
T TIGR00991        23 KLLELLGKLKE---EDVSSLTILVMGKGGVGKSSTVNSIIG   60 (313)
T ss_pred             HHHHHHHhccc---ccccceEEEEECCCCCCHHHHHHHHhC
Confidence            34455555555   335678999999999999999999874

>cd01860 Rab5_related Rab5-related subfamily

Probab=91.68  E-value=0.16  Score=42.85  Aligned_cols=22  Identities=32%  Similarity=0.507  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++++.|+.|||||+++.++..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~   23 (163)
T cd01860           2 FKLVLLGDSSVGKSSLVLRFVK   23 (163)
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4789999999999999988864

This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo

>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=91.68  E-value=0.17  Score=45.52  Aligned_cols=35  Identities=20%  Similarity=0.158  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        28 ~~G~~~~l~G~nGsGKSTLl~~i~Gl~~~~~G~i~~   63 (218)
T cd03255          28 EKGEFVAIVGPSGSGKSTLLNILGGLDRPTSGEVRV   63 (218)
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHhCCcCCCceeEEE
Confidence            4678999999999999998887765432 4576654

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.

>cd04114 Rab30 Rab30 subfamily

Probab=91.66  E-value=0.16  Score=43.16  Aligned_cols=25  Identities=32%  Similarity=0.313  Sum_probs=21.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +...++++.|+.|||||+++.++..
T Consensus         5 ~~~~~v~v~G~~~~GKSsli~~l~~   29 (169)
T cd04114           5 DFLFKIVLIGNAGVGKTCLVRRFTQ   29 (169)
T ss_pred             CceeEEEEECCCCCCHHHHHHHHHh
Confidence            3457899999999999999999864

Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=91.65  E-value=0.17  Score=46.33  Aligned_cols=24  Identities=29%  Similarity=0.252  Sum_probs=19.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++.-.-|.||.||||||+|.-+=
T Consensus        31 ~~~~VTAlIGPSGcGKST~LR~lN   54 (253)
T COG1117          31 PKNKVTALIGPSGCGKSTLLRCLN   54 (253)
T ss_pred             cCCceEEEECCCCcCHHHHHHHHH
Confidence            455666788999999999997653

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=91.64  E-value=0.29  Score=53.13  Aligned_cols=46  Identities=20%  Similarity=0.209  Sum_probs=31.8

Q ss_pred             HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh--CCeEEEEeCC
Q psy3261          51 LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE--NNYLLVHIPW  103 (342)
Q Consensus        51 ~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~--~gwiVl~vP~  103 (342)
                      -+|++.+++       +..+||.|++||||||-+-|.+.-+--  .|-|++.=|+
T Consensus        56 ~~i~~ai~~-------~~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPR  103 (845)
T COG1643          56 DEILKAIEQ-------NQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPR  103 (845)
T ss_pred             HHHHHHHHh-------CCEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCch
Confidence            366777766       889999999999999977766554431  2344444453

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=91.64  E-value=0.18  Score=43.61  Aligned_cols=25  Identities=32%  Similarity=0.402  Sum_probs=21.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++..+.|.|+.|||||++|.-+.-
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~i~G   48 (163)
T cd03216          24 RRGEVHALLGENGAGKSTLMKILSG   48 (163)
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHhC
Confidence            4688999999999999999986653

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=91.63  E-value=0.17  Score=45.78  Aligned_cols=35  Identities=23%  Similarity=0.291  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   64 (228)
T cd03257          29 KKGETLGLVGESGSGKSTLARAILGLLKPTSGSIIF   64 (228)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            4688999999999999998887765432 4566544

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>PLN02674 adenylate kinase

Probab=91.63  E-value=0.28  Score=45.69  Aligned_cols=32  Identities=25%  Similarity=0.385  Sum_probs=23.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ++..+++|.|++||||+|.-..   .|...||..|
T Consensus        29 ~~~~~i~l~G~PGsGKgT~a~~---La~~~~~~hi   60 (244)
T PLN02674         29 KPDKRLILIGPPGSGKGTQSPI---IKDEYCLCHL   60 (244)
T ss_pred             ccCceEEEECCCCCCHHHHHHH---HHHHcCCcEE
Confidence            5578999999999999976443   3455565443

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=91.61  E-value=0.24  Score=47.51  Aligned_cols=63  Identities=19%  Similarity=0.208  Sum_probs=41.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHhCcc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTK  143 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~  143 (342)
                      ...=-++|||.|||||-+|..++.-     =++-.+|+.--++.-.         -+ -.-|..-..|=-++.+.|=+
T Consensus        86 qP~I~~VYGPTG~GKSqLlRNLis~-----~lI~P~PETVfFItP~---------~~-mIpp~E~~aW~~Ql~EgNY~  148 (369)
T PF02456_consen   86 QPFIGVVYGPTGSGKSQLLRNLISC-----QLIQPPPETVFFITPQ---------KD-MIPPQEITAWETQLCEGNYD  148 (369)
T ss_pred             CceEEEEECCCCCCHHHHHHHhhhc-----CcccCCCCceEEECCC---------CC-CCCHHHHHHHHHHHHhcCCC
Confidence            3445678999999999999987753     3444445443332221         12 34677888888888777743

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=91.60  E-value=0.32  Score=49.90  Aligned_cols=37  Identities=14%  Similarity=0.103  Sum_probs=32.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|.|++|||||+++.|++..+..+|==|+||
T Consensus       271 ~~g~~~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yi  307 (509)
T PRK09302        271 FRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLF  307 (509)
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEE
Confidence            5677889999999999999999999887777777776

>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=91.57  E-value=0.18  Score=43.87  Aligned_cols=25  Identities=24%  Similarity=0.390  Sum_probs=21.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++..+.|.|+.|||||++|.-+.-
T Consensus        24 ~~Ge~~~i~G~nGsGKStLl~~l~G   48 (173)
T cd03230          24 EKGEIYGLLGPNGAGKTTLIKIILG   48 (173)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhC
Confidence            4678999999999999999886643

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.

>cd01864 Rab19 Rab19 subfamily

Probab=91.57  E-value=0.16  Score=43.12  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..++++.|+.|+|||+++.+...
T Consensus         3 ~~kv~vvG~~~~GKTsli~~l~~   25 (165)
T cd01864           3 LFKIILIGDSNVGKTCVVQRFKS   25 (165)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhh
Confidence            46899999999999999998754

Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=91.56  E-value=0.16  Score=49.66  Aligned_cols=35  Identities=20%  Similarity=0.357  Sum_probs=25.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++.-+.|-||.||||||+|.-+.-.-. ..|-|.+
T Consensus        29 ~~Gef~~lLGPSGcGKTTlLR~IAGfe~p~~G~I~l   64 (352)
T COG3842          29 KKGEFVTLLGPSGCGKTTLLRMIAGFEQPSSGEILL   64 (352)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            3456677999999999999998876543 3454443

>KOG0733|consensus

Probab=91.56  E-value=0.14  Score=53.29  Aligned_cols=20  Identities=35%  Similarity=0.561  Sum_probs=17.7

Q ss_pred             CCCCeEEEEccCCCcHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMAL   84 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L   84 (342)
                      .|...++|+||+|||||++.
T Consensus       221 ~PprGvLlHGPPGCGKT~lA  240 (802)
T KOG0733|consen  221 RPPRGVLLHGPPGCGKTSLA  240 (802)
T ss_pred             CCCCceeeeCCCCccHHHHH
Confidence            58899999999999999763

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=91.55  E-value=0.18  Score=46.07  Aligned_cols=35  Identities=17%  Similarity=0.196  Sum_probs=27.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        33 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   68 (233)
T PRK11629         33 GEGEMMAIVGSSGSGKSTLLHLLGGLDTPTSGDVIF   68 (233)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            4678999999999999999888876543 4566544

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=91.55  E-value=0.23  Score=46.43  Aligned_cols=35  Identities=17%  Similarity=0.159  Sum_probs=28.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH------hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH------ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~------~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-...      ..|-|.+
T Consensus        43 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~~~~~~~~~G~I~~   83 (267)
T PRK14235         43 PEKTVTAFIGPSGCGKSTFLRCLNRMNDTIDGCRVTGKITL   83 (267)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcccccCCCCceEEEE
Confidence            5788999999999999999998887653      4687765

>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=91.55  E-value=0.3  Score=44.31  Aligned_cols=39  Identities=18%  Similarity=0.247  Sum_probs=25.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC---CeEEEEeCCcc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN---NYLLVHIPWVL  105 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~---gwiVl~vP~~~  105 (342)
                      ...+++.|+.|||||++...+......+   .=||+.-|...
T Consensus        19 ~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~   60 (205)
T PF02562_consen   19 NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVE   60 (205)
T ss_dssp             -SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCC
Confidence            6699999999999999988888777665   34555556553

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

>PRK14731 coaE dephospho-CoA kinase; Provisional

Probab=91.55  E-value=0.22  Score=44.91  Aligned_cols=30  Identities=20%  Similarity=0.123  Sum_probs=24.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..+.|+|..|||||+++..+..    .|+-|+.-
T Consensus         6 ~~igitG~igsGKSt~~~~l~~----~g~~v~d~   35 (208)
T PRK14731          6 FLVGVTGGIGSGKSTVCRFLAE----MGCELFEA   35 (208)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH----CCCeEEec
Confidence            4567999999999999888764    58888773

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=91.54  E-value=0.18  Score=46.09  Aligned_cols=35  Identities=26%  Similarity=0.343  Sum_probs=27.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        25 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   60 (241)
T cd03256          25 NPGEFVALIGPSGAGKSTLLRCLNGLVEPTSGSVLI   60 (241)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCcCCCCceEEE
Confidence            4688999999999999999888775432 4576654

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=91.53  E-value=0.18  Score=45.36  Aligned_cols=35  Identities=23%  Similarity=0.367  Sum_probs=25.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|=|.+
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   64 (218)
T cd03266          29 KPGEVTGLLGPNGAGKTTTLRMLAGLLEPDAGFATV   64 (218)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCcCCCCceEEE
Confidence            4678899999999999999977765432 4565544

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>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=91.52  E-value=0.17  Score=42.88  Aligned_cols=25  Identities=36%  Similarity=0.498  Sum_probs=20.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++..+.|.|+.|||||+++.-+.-
T Consensus        24 ~~Ge~~~i~G~nGsGKStLl~~l~G   48 (144)
T cd03221          24 NPGDRIGLVGRNGAGKSTLLKLIAG   48 (144)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHcC
Confidence            5678999999999999998876543

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.

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=91.52  E-value=0.18  Score=44.67  Aligned_cols=34  Identities=24%  Similarity=0.278  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLL   98 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiV   98 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|=+.
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~l~G~~~~~~G~i~   58 (195)
T PRK13541         24 LPSAITYIKGANGCGKSSLLRMIAGIMQPSSGNIY   58 (195)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCCCCCCcEEE
Confidence            4678999999999999999887765432 345544

>PRK13949 shikimate kinase; Provisional

Probab=91.52  E-value=0.18  Score=44.04  Aligned_cols=31  Identities=19%  Similarity=0.211  Sum_probs=22.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+++|.|++|||||++...+...   -||-++..
T Consensus         2 ~~I~liG~~GsGKstl~~~La~~---l~~~~id~   32 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALARE---LGLSFIDL   32 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH---cCCCeecc
Confidence            37999999999999998865543   35544443

>PRK05595 replicative DNA helicase; Provisional

Probab=91.51  E-value=0.37  Score=48.65  Aligned_cols=37  Identities=11%  Similarity=0.163  Sum_probs=31.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH-HHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY-AHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~-A~~~gwiVl~v  101 (342)
                      .++.-++|-|.+|+|||++..|++.. |..+|+=|+++
T Consensus       199 ~~g~liviaarpg~GKT~~al~ia~~~a~~~g~~vl~f  236 (444)
T PRK05595        199 QKGDMILIAARPSMGKTTFALNIAEYAALREGKSVAIF  236 (444)
T ss_pred             CCCcEEEEEecCCCChHHHHHHHHHHHHHHcCCcEEEE
Confidence            35677889999999999999999975 67788888777

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

Probab=91.51  E-value=0.19  Score=44.49  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=20.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .|++|-|++|+||||.-..+...
T Consensus         1 ~riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           1 MRILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999998887766

>PRK05748 replicative DNA helicase; Provisional

Probab=91.50  E-value=0.37  Score=48.71  Aligned_cols=37  Identities=14%  Similarity=0.187  Sum_probs=31.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH-HhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA-HENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A-~~~gwiVl~v  101 (342)
                      .++.-++|-|.+|+|||++..|++..+ .+.|+-|+++
T Consensus       201 ~~G~livIaarpg~GKT~~al~ia~~~a~~~g~~v~~f  238 (448)
T PRK05748        201 QPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIF  238 (448)
T ss_pred             CCCceEEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEE
Confidence            466789999999999999999999875 4668888777

>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP

Probab=91.50  E-value=0.18  Score=45.10  Aligned_cols=35  Identities=20%  Similarity=0.303  Sum_probs=27.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|.|.+
T Consensus        22 ~~Ge~~~l~G~nGsGKSTLl~~l~gl~~~~~G~i~~   57 (211)
T cd03298          22 AQGEITAIVGPSGSGKSTLLNLIAGFETPQSGRVLI   57 (211)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            5688999999999999999977765543 4577655

Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=91.50  E-value=0.18  Score=45.09  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        25 ~~G~~~~l~G~nGsGKSTLl~~l~G~~~~~~G~i~~   60 (211)
T cd03225          25 KKGEFVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLV   60 (211)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCCCCCCceEEE
Confidence            4678899999999999999887665432 4677665

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.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=91.49  E-value=0.18  Score=44.26  Aligned_cols=26  Identities=15%  Similarity=0.092  Sum_probs=22.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        24 ~~G~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          24 RAGEIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            46789999999999999988876644

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

---

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	342
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-14

>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 = 74.5 bits (182), Expect = 1e-14
 Identities = 62/368 (16%), Positives = 121/368 (32%), Gaps = 94/368 (25%)

Query: 6   QDLYKFYTLPDEVRSAIFELGGITRVFNEQ-TQIFNESSIL-------------IRNCML 51
           +  YKF  L   +++   +   +TR++ EQ  +++N++ +              +R  +L
Sbjct: 88  RINYKF--LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145

Query: 52  ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFAYP 111
           EL           RP+   ++ G  G GK+     AL     +  +   + + + W    
Sbjct: 146 EL-----------RPAKNVLIDGVLGSGKT---WVALD-VCLSYKVQCKMDFKIFWLNLK 190

Query: 112 KEVSHSLTKEGMVDL--NIDAAMWLRHFQKQNTK----WLEDP--RLTTSQEY------- 156
              S     E +  L   ID     R     N K     ++    RL  S+ Y       
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250

Query: 157 --VWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYN 214
             V + +  +  N+    L+    TR K  +D +    T    +S +    T    +   
Sbjct: 251 LNVQNAKAWNAFNLSCKILL---TTRFKQVTDFLSAATT--THISLDHHSMTLTPDEV-K 304

Query: 215 SFFAEKTNCKPEDKSKVLPSRVT----LTRSVINLVQSD----WNN-------------G 253
           S   +  +C+P+D    LP  V        S+I     D    W+N              
Sbjct: 305 SLLLKYLDCRPQD----LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE 360

Query: 254 AIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHV-----PELNDEEFHNLLNL 308
           + +  L P     + R+    L +            +P  +      ++   +   ++N 
Sbjct: 361 SSLNVLEP----AEYRKMFDRLSVFPP------SAHIPTILLSLIWFDVIKSDVMVVVNK 410

Query: 309 YESKKWLQ 316
                 ++
Sbjct: 411 LHKYSLVE 418

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	342
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.87
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.81
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.8
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.74
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.72
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.69
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.68
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.66
2fna_A	357	Conserved hypothetical protein; structural genomic	98.6
3bos_A	242	Putative DNA replication factor; P-loop containing	98.38
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.37
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.35
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.26
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.26
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.26
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.24
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.23
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.2
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.16
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.16
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.15
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.13
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.12
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.09
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.08
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.03
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.03
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.02
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.02
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.0
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.99
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.92
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.91
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.89
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.86
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.8
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.79
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.78
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.77
3pvs_A	447	Replication-associated recombination protein A; ma	97.75
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.68
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.67
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.63
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.63
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.62
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.55
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.54
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.5
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.5
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.49
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.47
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.41
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.3
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.28
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.27
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.18
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.12
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.98
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	96.98
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.98
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.87
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.8
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.72
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	96.69
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.54
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.44
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.3
2qgz_A	308	Helicase loader, putative primosome component; str	96.22
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.15
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.0
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.94
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.93
3io5_A	333	Recombination and repair protein; storage dimer, i	95.87
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.84
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.8
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.75
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.7
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.67
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.66
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.66
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.65
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.59
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.59
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.58
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.5
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	95.48
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	95.43
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.41
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.41
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.36
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.36
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.31
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.3
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	95.29
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.29
2cvh_A	220	DNA repair and recombination protein RADB; filamen	95.28
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	95.27
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.24
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.23
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.15
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.1
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.06
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	95.04
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.98
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.96
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.96
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.96
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.88
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	94.86
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	94.79
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	94.79
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.78
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.77
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.75
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.71
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.71
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.7
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.68
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.6
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.59
1xp8_A	366	RECA protein, recombinase A; recombination, radior	94.59
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.57
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.57
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.54
2z43_A	324	DNA repair and recombination protein RADA; archaea	94.51
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	94.5
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	94.48
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	94.48
3co5_A	143	Putative two-component system transcriptional RES	94.48
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.45
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.41
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.41
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	94.38
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	94.36
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	94.35
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	94.35
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.27
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	94.27
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	94.24
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.23
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.17
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.14
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.13
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	94.1
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.09
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.09
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.08
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.06
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.05
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.05
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.04
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	93.99
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.93
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	93.93
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	93.93
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	93.93
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	93.91
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.88
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	93.87
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	93.87
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	93.86
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.85
1via_A	175	Shikimate kinase; structural genomics, transferase	93.84
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	93.84
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	93.84
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.83
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	93.82
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.8
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.8
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.77
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	93.72
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.69
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	93.67
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	93.64
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	93.62
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	93.6
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	93.6
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.59
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.56
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.55
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	93.54
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	93.53
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.53
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	93.51
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	93.49
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	93.49
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.48
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	93.38
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	93.37
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.34
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	93.32
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	93.3
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	93.27
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	93.23
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	93.2
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.18
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	93.15
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.13
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	93.11
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	93.11
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	93.1
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.03
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.02
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.01
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	93.0
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	92.97
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	92.92
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.87
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	92.85
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	92.85
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	92.84
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	92.82
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	92.82
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	92.82
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	92.76
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	92.75
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	92.74
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	92.72
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	92.71
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	92.68
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	92.67
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.67
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	92.67
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	92.66
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	92.64
1p9r_A	418	General secretion pathway protein E; bacterial typ	92.63
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	92.61
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.58
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	92.58
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	92.57
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	92.55
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	92.53
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.52
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	92.52
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	92.52
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.51
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	92.5
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	92.5
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.48
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	92.42
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.41
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.38
2r44_A	331	Uncharacterized protein; putative ATPase, structur	92.36
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.36
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	92.34
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.33
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	92.31
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	92.29
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	92.27
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	92.24
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	92.23
2vli_A	183	Antibiotic resistance protein; transferase, tunica	92.23
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	92.23
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	92.22
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	92.21
3ice_A	422	Transcription termination factor RHO; transcriptio	92.2
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	92.19
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.18
1nrj_B	218	SR-beta, signal recognition particle receptor beta	92.17
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	92.16
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	92.15
2wji_A	165	Ferrous iron transport protein B homolog; membrane	92.14
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	92.14
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.1
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	92.1
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	92.09
1sgw_A	214	Putative ABC transporter; structural genomics, P p	92.08
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	92.04
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.04
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	92.01
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	92.01
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	92.0
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	92.0
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.98
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	91.98
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	91.97
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	91.95
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	91.94
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	91.93
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	91.93
2ghi_A	260	Transport protein; multidrug resistance protein, M	91.91
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	91.9
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	91.88
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.87
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	91.87
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	91.85
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	91.81
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	91.81
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.8
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	91.8
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	91.8
2og2_A	359	Putative signal recognition particle receptor; nuc	91.79
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	91.79
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	91.78
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	91.75
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	91.74
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	91.73
1g6h_A	257	High-affinity branched-chain amino acid transport	91.72
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.71
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.69
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	91.67
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	91.66
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	91.65
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	91.64
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.63
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	91.62
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	91.59
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	91.57
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	91.56
3kta_A	182	Chromosome segregation protein SMC; structural mai	91.55
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	91.55
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	91.53
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	91.53
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	91.52
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	91.5
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	91.49
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	91.49
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	91.45
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	91.44
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	91.44
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	91.43
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.41
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	91.4
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.4
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	91.39
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	91.38
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	91.34
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	91.32
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	91.31
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	91.29
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	91.28
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.26
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	91.24
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	91.21
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	91.17
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	91.14
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	91.13
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	91.13
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	91.13
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	91.12
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	91.11
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	91.11
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	91.1
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	91.08
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.07
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	91.06
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	91.03
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	91.02
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.01
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.0
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	90.98
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	90.91
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	90.91
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	90.91
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	90.88
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	90.87
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	90.86
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	90.85
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	90.83
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	90.83
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	90.79
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	90.79
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	90.78
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	90.78
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	90.76
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	90.75
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	90.74
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	90.74
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	90.71
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	90.7
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	90.68
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	90.67
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	90.66
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	90.66
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	90.65
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	90.64
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	90.64
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	90.62
2fh5_B	214	SR-beta, signal recognition particle receptor beta	90.62
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	90.61
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	90.58
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	90.58
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	90.57
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	90.56
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	90.56
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	90.55
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	90.53
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	90.52
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	90.51
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	90.51
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.46
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	90.41
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	90.4
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	90.35
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	90.35
1of1_A	376	Thymidine kinase; transferase, antiviral drug, enz	90.33
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	90.3
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	90.29
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	90.28
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	90.26
2xxa_A	433	Signal recognition particle protein; protein trans	90.26
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	90.25
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	90.2
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	90.2
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	90.19
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	90.18
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	90.18
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	90.17
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	90.15
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	90.14
1e2k_A	331	Thymidine kinase; transferase, antiviral drug, enz	90.12
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	90.11
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.07
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	90.05
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	90.05
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	90.04
3l0o_A	427	Transcription termination factor RHO; helicase, RH	90.02
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	89.98
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	89.96
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	89.95
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	89.9
3b6e_A	216	Interferon-induced helicase C domain-containing P;	89.9
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	89.89
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	89.88
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	89.83
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	89.82
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	89.81
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	89.78
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	89.75
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	89.73
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	89.73
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	89.72
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	89.71
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	89.68
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	89.64
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	89.64
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	89.63
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	89.63
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	89.6
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	89.5
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	89.49
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	89.46
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	89.43
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	89.39
3llu_A	196	RAS-related GTP-binding protein C; structural geno	89.39
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	89.38
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	89.35
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	89.28
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	89.26
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	89.24
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	89.22
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	89.2
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	89.19
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	89.1
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	89.09
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	89.05
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	89.01
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	88.99
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	88.98
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	88.97
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	88.92
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	88.88
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	88.87
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	88.8
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	88.8
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	88.76
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	88.75
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	88.68
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	88.67
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	88.66
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	88.6
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	88.57
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	88.55
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	88.53
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	88.52
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	88.52
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	88.46
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	88.39
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	88.33
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	88.3
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	88.28
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	88.28
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	88.27
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	88.14
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	88.1
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	88.08
1osn_A	341	Thymidine kinase, VZV-TK; chickenpox, BVDU-MP, tra	88.02
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	87.98
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	87.98
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	87.96
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	87.94
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	87.89
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	87.82
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	87.69
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	87.54
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	87.53
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	87.53
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	87.51
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	87.49

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.87  E-value=1.1e-07  Score=90.56  Aligned_cols=211  Identities=12%  Similarity=0.078  Sum_probs=116.1

Q ss_pred             ech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC------CeEEEEeCCccccccCCcceeccC
Q psy3261          46 IRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN------NYLLVHIPWVLRWFAYPKEVSHSL  118 (342)
Q Consensus        46 vR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~------gwiVl~vP~~~~~~~~~~~~~~s~  118 (342)
                      -|+ ...+|.+.++. .-.......++|+|++|||||+++..+.......      ++.++++.....            
T Consensus        23 gr~~~~~~l~~~l~~-~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~------------   89 (387)
T 2v1u_A           23 HREAELRRLAEVLAP-ALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHR------------   89 (387)
T ss_dssp             TCHHHHHHHHHTTGG-GTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTS------------
T ss_pred             CHHHHHHHHHHHHHH-HHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcC------------
Confidence            365 33444555555 3223456789999999999999999888876554      788887732211            


Q ss_pred             CCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhcc
Q psy3261         119 TKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKL  198 (342)
Q Consensus       119 ~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~  198 (342)
                           .........++..+        .   ...           ...|.+..              ..+..+.+.+.. 
T Consensus        90 -----~~~~~~~~~l~~~l--------~---~~~-----------~~~~~~~~--------------~~~~~l~~~l~~-  127 (387)
T 2v1u_A           90 -----ETPYRVASAIAEAV--------G---VRV-----------PFTGLSVG--------------EVYERLVKRLSR-  127 (387)
T ss_dssp             -----CSHHHHHHHHHHHH--------S---CCC-----------CSSCCCHH--------------HHHHHHHHHHTT-
T ss_pred             -----CCHHHHHHHHHHHh--------C---CCC-----------CCCCCCHH--------------HHHHHHHHHHhc-
Confidence                 00011223333333        1   100           01122222              234445555543 


Q ss_pred             ccCCCceEEEEEeCccccccCC-CcCCCCCCCcccCCccchHHHHHHhhcCC--CCCeEEEEEeCCCCCCCCCccCcchh
Q psy3261         199 STEGVCRTFVCVDGYNSFFAEK-TNCKPEDKSKVLPSRVTLTRSVINLVQSD--WNNGAIVLALSPRANLPDRRESHLPL  275 (342)
Q Consensus       199 ~~~~~~pVLvavD~~n~~~~~s-~~y~~~~~~~I~~~~l~l~~~~~~~~~~~--~~~G~vv~AtS~~~~~~~~~~~~~p~  275 (342)
                         ...|++|.|||+..+.... .              ..+...+++.....  -.+..+|++++... ...    .+..
T Consensus       128 ---~~~~~vlilDEi~~l~~~~~~--------------~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~-~~~----~l~~  185 (387)
T 2v1u_A          128 ---LRGIYIIVLDEIDFLPKRPGG--------------QDLLYRITRINQELGDRVWVSLVGITNSLG-FVE----NLEP  185 (387)
T ss_dssp             ---SCSEEEEEEETTTHHHHSTTH--------------HHHHHHHHHGGGCC-----CEEEEECSCST-TSS----SSCH
T ss_pred             ---cCCeEEEEEccHhhhcccCCC--------------ChHHHhHhhchhhcCCCceEEEEEEECCCc-hHh----hhCH
Confidence               2569999999998775431 1              23333334433321  22334555554331 111    1222


Q ss_pred             HHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCC----CccCcchHHHHHHhhC---CCHHHHhhhcc
Q psy3261         276 YMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKK----WLQTSEGREEIAFLTK---RVPQKMYEFCS  340 (342)
Q Consensus       276 ~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~----~l~~e~~~~el~~lSg---GNP~~l~~lc~  340 (342)
                      .+..+.+.      ..+.++.|+.+|...++......+    .+ +++....+.-.++   |||+.+.++|.
T Consensus       186 ~l~~r~~~------~~i~l~~l~~~~~~~il~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~G~~r~~~~~l~  250 (387)
T 2v1u_A          186 RVKSSLGE------VELVFPPYTAPQLRDILETRAEEAFNPGVL-DPDVVPLCAALAAREHGDARRALDLLR  250 (387)
T ss_dssp             HHHTTTTS------EECCBCCCCHHHHHHHHHHHHHHHBCTTTB-CSSHHHHHHHHHHSSSCCHHHHHHHHH
T ss_pred             HHHhcCCC------eEEeeCCCCHHHHHHHHHHHHHhhccCCCC-CHHHHHHHHHHHHHhccCHHHHHHHHH
Confidence            33332111      247899999999999998876542    22 4555556777888   99999888763

>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=98.81  E-value=1.1e-07  Score=83.56  Aligned_cols=104  Identities=11%  Similarity=0.126  Sum_probs=67.1

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..|.+|.|||+..+-.                  .....|++++.....+..+|++++....        ++..+..+  
T Consensus       125 ~~~~vlviDe~~~l~~------------------~~~~~l~~~l~~~~~~~~~i~~t~~~~~--------~~~~l~~r--  176 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSR------------------HSFNALLKTLEEPPEHVKFLLATTDPQK--------LPVTILSR--  176 (250)
T ss_dssp             SSSEEEEEETGGGSCH------------------HHHHHHHHHHHSCCTTEEEEEEESCGGG--------SCHHHHTT--
T ss_pred             CCceEEEEECcccccH------------------HHHHHHHHHHhcCCCceEEEEEeCChHh--------CCHHHHHH--
Confidence            4688999999966521                  2334566666544455666666654221        22233322  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                            +..++++.++.+|...++..+.. .+.-.+++...++...|+|||+.+..+|.
T Consensus       177 ------~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~~~~~~~~~  229 (250)
T 1njg_A          177 ------CLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD  229 (250)
T ss_dssp             ------SEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ------hhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence                  23589999999999999977654 34321454555677799999999988763

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.80  E-value=1e-07  Score=90.50  Aligned_cols=213  Identities=13%  Similarity=0.135  Sum_probs=117.0

Q ss_pred             EechhH-HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC---CeEEEEeCCccccccCCcceeccCCC
Q psy3261          45 LIRNCM-LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN---NYLLVHIPWVLRWFAYPKEVSHSLTK  120 (342)
Q Consensus        45 lvR~~t-~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~---gwiVl~vP~~~~~~~~~~~~~~s~~~  120 (342)
                      .-|+.. .+|.+.++. .........++|+|++|||||+++..+.......   ++-++++......             
T Consensus        23 ~gr~~e~~~l~~~l~~-~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~-------------   88 (386)
T 2qby_A           23 PHREDQIRKIASILAP-LYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQID-------------   88 (386)
T ss_dssp             TTCHHHHHHHHHSSGG-GGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHC-------------
T ss_pred             CChHHHHHHHHHHHHH-HHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCC-------------
Confidence            346633 334445544 2123556789999999999999999988776554   7777777432110             


Q ss_pred             CCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhcccc
Q psy3261         121 EGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLST  200 (342)
Q Consensus       121 ~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~  200 (342)
                              ....++..+       +.  .+...    .     ...+.+.              ...+..+.+.+..   
T Consensus        89 --------~~~~~~~~i-------~~--~l~~~----~-----~~~~~~~--------------~~~~~~l~~~l~~---  125 (386)
T 2qby_A           89 --------TPYRVLADL-------LE--SLDVK----V-----PFTGLSI--------------AELYRRLVKAVRD---  125 (386)
T ss_dssp             --------SHHHHHHHH-------TT--TTSCC----C-----CSSSCCH--------------HHHHHHHHHHHHT---
T ss_pred             --------CHHHHHHHH-------HH--HhCCC----C-----CCCCCCH--------------HHHHHHHHHHHhc---
Confidence                    012234444       44  33110    0     0112222              2334445555543   


Q ss_pred             CCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhh
Q psy3261         201 EGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLK  279 (342)
Q Consensus       201 ~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg  279 (342)
                       ...|++|.+|++..+.....              -.+...+++.+.. .-.+..+|++++.... ..    .+...+..
T Consensus       126 -~~~~~vlilDE~~~l~~~~~--------------~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~-~~----~~~~~~~~  185 (386)
T 2qby_A          126 -YGSQVVIVLDEIDAFVKKYN--------------DDILYKLSRINSEVNKSKISFIGITNDVKF-VD----LLDPRVKS  185 (386)
T ss_dssp             -CCSCEEEEEETHHHHHHSSC--------------STHHHHHHHHHHSCCC--EEEEEEESCGGG-GG----GCTTHHHH
T ss_pred             -cCCeEEEEEcChhhhhccCc--------------CHHHHHHhhchhhcCCCeEEEEEEECCCCh-Hh----hhCHHHhc
Confidence             25699999999988765432              2344455555532 2234455666554210 00    01112222


Q ss_pred             hcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCC--cc-CcchHHHHHHhhC---CCHHHHhhhcc
Q psy3261         280 KAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKW--LQ-TSEGREEIAFLTK---RVPQKMYEFCS  340 (342)
Q Consensus       280 ~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~--l~-~e~~~~el~~lSg---GNP~~l~~lc~  340 (342)
                      +  +.   + ..+.++.|+.+|...++......+.  .. +++....+...++   |||+.+.++|.
T Consensus       186 r--~~---~-~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~  246 (386)
T 2qby_A          186 S--LS---E-EEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLR  246 (386)
T ss_dssp             T--TT---T-EEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             c--CC---C-eeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            2  10   0 2589999999999999987655322  11 3444445666888   99999888763

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.74  E-value=6.6e-07  Score=85.42  Aligned_cols=208  Identities=10%  Similarity=0.095  Sum_probs=113.3

Q ss_pred             Eech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC--------CeEEEEeCCccccccCCccee
Q psy3261          45 LIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN--------NYLLVHIPWVLRWFAYPKEVS  115 (342)
Q Consensus        45 lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--------gwiVl~vP~~~~~~~~~~~~~  115 (342)
                      .-|+ ...+|.+.++. .........++|+|++|||||+++..+...+...        ++.++++......  +     
T Consensus        23 ~gr~~~~~~l~~~l~~-~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~--~-----   94 (384)
T 2qby_B           23 PFREDILRDAAIAIRY-FVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVG--G-----   94 (384)
T ss_dssp             TTCHHHHHHHHHHHHH-HHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHC--S-----
T ss_pred             CChHHHHHHHHHHHHH-HHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCC--C-----
Confidence            3466 34445556665 2223445689999999999999998888876554        7888777432110  0     


Q ss_pred             ccCCCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHH
Q psy3261         116 HSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEI  195 (342)
Q Consensus       116 ~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL  195 (342)
                       +        .-.....+++.+.       .   ...           ...+.+              ....+..+.+.+
T Consensus        95 -~--------~~~~~~~l~~~l~-------~---~~~-----------~~~~~~--------------~~~~~~~l~~~l  130 (384)
T 2qby_B           95 -T--------PQAVLSSLAGKLT-------G---FSV-----------PKHGIN--------------LGEYIDKIKNGT  130 (384)
T ss_dssp             -C--------HHHHHHHHHHHHH-------C---SCC-----------CSSSSC--------------THHHHHHHHHHH
T ss_pred             -C--------HHHHHHHHHHHhc-------C---CCC-----------CCCCCC--------------HHHHHHHHHHHh
Confidence             0        0011222233221       1   110           001111              123344445545


Q ss_pred             hccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccch-HHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcch
Q psy3261         196 KKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTL-TRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLP  274 (342)
Q Consensus       196 ~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l-~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p  274 (342)
                      ..     ..+ +|.|||+..+.....              ..+ ...+++..    .+..+|++++... ...    .+.
T Consensus       131 ~~-----~~~-vlilDEi~~l~~~~~--------------~~~~l~~l~~~~----~~~~iI~~t~~~~-~~~----~l~  181 (384)
T 2qby_B          131 RN-----IRA-IIYLDEVDTLVKRRG--------------GDIVLYQLLRSD----ANISVIMISNDIN-VRD----YME  181 (384)
T ss_dssp             SS-----SCE-EEEEETTHHHHHSTT--------------SHHHHHHHHTSS----SCEEEEEECSSTT-TTT----TSC
T ss_pred             cc-----CCC-EEEEECHHHhccCCC--------------CceeHHHHhcCC----cceEEEEEECCCc-hHh----hhC
Confidence            33     234 999999988754421              122 33333333    4445555554332 101    122


Q ss_pred             hHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCC--cc-CcchHHHHHHhhC---CCHHHHhhhcc
Q psy3261         275 LYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKW--LQ-TSEGREEIAFLTK---RVPQKMYEFCS  340 (342)
Q Consensus       275 ~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~--l~-~e~~~~el~~lSg---GNP~~l~~lc~  340 (342)
                      ..+..+  |   ..  .+.++.|+.+|...++......++  .. +++....+.-.++   |||+.+.++|.
T Consensus       182 ~~l~sr--~---~~--~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~  246 (384)
T 2qby_B          182 PRVLSS--L---GP--SVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLF  246 (384)
T ss_dssp             HHHHHT--C---CC--EEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHH
T ss_pred             HHHHhc--C---CC--eEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHH
Confidence            233332  2   11  489999999999999988765432  11 4544555666888   99999887763

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.72  E-value=4.1e-07  Score=86.80  Aligned_cols=208  Identities=14%  Similarity=0.094  Sum_probs=115.2

Q ss_pred             Eech-hHHHHHHHHHhccCCCCCCC--eEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeCCccccccCCcceeccCCC
Q psy3261          45 LIRN-CMLELVGYLKSMTNFDRPSP--RFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIPWVLRWFAYPKEVSHSLTK  120 (342)
Q Consensus        45 lvR~-~t~el~~~l~~~~~~~~~~~--r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP~~~~~~~~~~~~~~s~~~  120 (342)
                      .-|+ ...+|.+.++.... .....  .++|+|++|||||+++..+....... +|-++++.....              
T Consensus        20 ~gr~~~~~~l~~~l~~~~~-~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~--------------   84 (389)
T 1fnn_A           20 PHREQQLQQLDILLGNWLR-NPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIY--------------   84 (389)
T ss_dssp             TTCHHHHHHHHHHHHHHHH-STTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTC--------------
T ss_pred             CChHHHHHHHHHHHHHHHc-CCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccC--------------
Confidence            3466 44455566665222 22334  79999999999999999888877766 688877742211              


Q ss_pred             CCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhcccc
Q psy3261         121 EGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKLST  200 (342)
Q Consensus       121 ~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~~~  200 (342)
                         . .   ...+++.+       +.  .+...         ....+.+..              ..+..+.+.+...  
T Consensus        85 ---~-~---~~~~~~~l-------~~--~l~~~---------~~~~~~~~~--------------~~~~~l~~~l~~~--  123 (389)
T 1fnn_A           85 ---R-N---FTAIIGEI-------AR--SLNIP---------FPRRGLSRD--------------EFLALLVEHLRER--  123 (389)
T ss_dssp             ---C-S---HHHHHHHH-------HH--HTTCC---------CCSSCCCHH--------------HHHHHHHHHHHHT--
T ss_pred             ---C-C---HHHHHHHH-------HH--HhCcc---------CCCCCCCHH--------------HHHHHHHHHHhhc--
Confidence               0 0   11223333       11  11100         001122222              2333344444432  


Q ss_pred             CCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC----CCeEEEEEeCCCCCCCCCccCcchhH
Q psy3261         201 EGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW----NNGAIVLALSPRANLPDRRESHLPLY  276 (342)
Q Consensus       201 ~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~----~~G~vv~AtS~~~~~~~~~~~~~p~~  276 (342)
                        ..|++|.+|++..+    +              -.....|++++..-.    .+-.+|++++... ...   . +...
T Consensus       124 --~~~~vlilDE~~~l----~--------------~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~-~~~---~-l~~~  178 (389)
T 1fnn_A          124 --DLYMFLVLDDAFNL----A--------------PDILSTFIRLGQEADKLGAFRIALVIVGHNDA-VLN---N-LDPS  178 (389)
T ss_dssp             --TCCEEEEEETGGGS----C--------------HHHHHHHHHHTTCHHHHSSCCEEEEEEESSTH-HHH---T-SCHH
T ss_pred             --CCeEEEEEECcccc----c--------------hHHHHHHHHHHHhCCCCCcCCEEEEEEECCch-HHH---H-hCHH
Confidence              56899999999776    1              234555556654211    2445555544321 000   0 1112


Q ss_pred             HhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhC----CCccCcchHHHHHHhh---------CCCHHHHhhhcc
Q psy3261         277 MLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESK----KWLQTSEGREEIAFLT---------KRVPQKMYEFCS  340 (342)
Q Consensus       277 llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~----~~l~~e~~~~el~~lS---------gGNP~~l~~lc~  340 (342)
                      +..+.+.      ..+.++.|+.+|...++......    +.+ +++....+...+         +|||+.+..+|.
T Consensus       179 ~~~r~~~------~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~  248 (389)
T 1fnn_A          179 TRGIMGK------YVIRFSPYTKDQIFDILLDRAKAGLAEGSY-SEDILQMIADITGAQTPLDTNRGDARLAIDILY  248 (389)
T ss_dssp             HHHHHTT------CEEECCCCBHHHHHHHHHHHHHHHBCTTSS-CHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHH
T ss_pred             hhhcCCC------ceEEeCCCCHHHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHH
Confidence            2222211      13899999999999999877653    233 455555677788         899999988874

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=98.69  E-value=5.3e-07  Score=86.80  Aligned_cols=214  Identities=12%  Similarity=0.096  Sum_probs=112.7

Q ss_pred             EEech-hHHHHHHHH-HhccCC-CCCCCeEEE--EccCCCcHHHHHHHHHHHHHhC------CeEEEEeCCccccccCCc
Q psy3261          44 ILIRN-CMLELVGYL-KSMTNF-DRPSPRFVL--YGEHGVGKSMALVYALQYAHEN------NYLLVHIPWVLRWFAYPK  112 (342)
Q Consensus        44 ~lvR~-~t~el~~~l-~~~~~~-~~~~~r~vL--~G~~GsGKS~~L~q~~~~A~~~------gwiVl~vP~~~~~~~~~~  112 (342)
                      +.-|+ +..+|.+.+ +..... ......++|  +|++|+|||+++.++...+...      ++.++++.....      
T Consensus        24 l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------   97 (412)
T 1w5s_A           24 LRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNA------   97 (412)
T ss_dssp             CSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGC------
T ss_pred             CCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCC------
Confidence            44466 444555566 552221 034557888  9999999999999998876653      788888753211      


Q ss_pred             ceeccCCCCCccccHHHHHHHHHHHHHhCccccCCCCcccccceecCCCCCCCCCCCHHHHHHhhcccccchhHHHHHHH
Q psy3261         113 EVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAALIEHGITRVKYASDVVDVLF  192 (342)
Q Consensus       113 ~~~~s~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~~~l~~s~~~~~~~~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~  192 (342)
                              .    .   ...+++.+       +.  .+...         ....+.+.              ...+..+.
T Consensus        98 --------~----~---~~~~~~~l-------~~--~l~~~---------~~~~~~~~--------------~~~~~~l~  130 (412)
T 1w5s_A           98 --------P----N---LYTILSLI-------VR--QTGYP---------IQVRGAPA--------------LDILKALV  130 (412)
T ss_dssp             --------C----S---HHHHHHHH-------HH--HHTCC---------CCCTTCCH--------------HHHHHHHH
T ss_pred             --------C----C---HHHHHHHH-------HH--HhCCC---------CCCCCCCH--------------HHHHHHHH
Confidence                    0    0   11233333       11  11100         00012121              23344455


Q ss_pred             HHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-C--C--CCeEEEEEeCCCCCCCC
Q psy3261         193 TEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-D--W--NNGAIVLALSPRANLPD  267 (342)
Q Consensus       193 ~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~--~--~~G~vv~AtS~~~~~~~  267 (342)
                      +.|...    ..|++|.|||+..+.....            ..-.....+.+++.. .  -  .+..+|++++...    
T Consensus       131 ~~l~~~----~~~~llvlDe~~~l~~~~~------------~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~----  190 (412)
T 1w5s_A          131 DNLYVE----NHYLLVILDEFQSMLSSPR------------IAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVR----  190 (412)
T ss_dssp             HHHHHH----TCEEEEEEESTHHHHSCTT------------SCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETH----
T ss_pred             HHHHhc----CCeEEEEEeCHHHHhhccC------------cchHHHHHHHHHHHhcccCCCCceEEEEEEecccc----
Confidence            555432    5699999999977754210            002222223333321 1  1  2334555543221    


Q ss_pred             CccCcchhHHh---hhcCCCCCCCc-ceeecCCCCHHHHHHHHHHHHhC----CCccCcchHHHHHHhhC------CCHH
Q psy3261         268 RRESHLPLYML---KKAGFESIDPF-VPIHVPELNDEEFHNLLNLYESK----KWLQTSEGREEIAFLTK------RVPQ  333 (342)
Q Consensus       268 ~~~~~~p~~ll---g~~g~~~~dP~-~~i~v~~~s~~E~~~ll~yy~~~----~~l~~e~~~~el~~lSg------GNP~  333 (342)
                           +...+.   ...    ..++ ..+.++.|+.+|+..++......    +.+ +++....+.-.|+      |||+
T Consensus       191 -----~~~~l~~~~~~~----~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~~~~G~p~  260 (412)
T 1w5s_A          191 -----ALSYMREKIPQV----ESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVW-EPRHLELISDVYGEDKGGDGSAR  260 (412)
T ss_dssp             -----HHHHHHHHCHHH----HTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSC-CHHHHHHHHHHHCGGGTSCCCHH
T ss_pred             -----HHHHHhhhcchh----hhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCC-ChHHHHHHHHHHHHhccCCCcHH
Confidence                 111111   000    0111 12899999999999999766442    123 3444556777999      9999


Q ss_pred             HHhhhcc
Q psy3261         334 KMYEFCS  340 (342)
Q Consensus       334 ~l~~lc~  340 (342)
                      .+..+|.
T Consensus       261 ~~~~l~~  267 (412)
T 1w5s_A          261 RAIVALK  267 (412)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9888763

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.68  E-value=8.1e-07  Score=83.23  Aligned_cols=49  Identities=14%  Similarity=0.070  Sum_probs=36.7

Q ss_pred             eeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .++++.||.+|+..++.... ..|.-.+++...++...|||||..+..+|
T Consensus       197 ~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~P~~l~~~~  246 (350)
T 2qen_A          197 EVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDGIPGWLVVFG  246 (350)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence            58999999999999986543 33432144455678889999999888776

>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=98.66  E-value=6.8e-07  Score=77.59  Aligned_cols=103  Identities=9%  Similarity=0.044  Sum_probs=64.6

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.+|.|||++.+...                  ....|+.++.....+..+|++++....        +...+..+  
T Consensus       101 ~~~~vliiDe~~~l~~~------------------~~~~l~~~l~~~~~~~~~i~~~~~~~~--------~~~~l~~r--  152 (226)
T 2chg_A          101 APFKIIFLDEADALTAD------------------AQAALRRTMEMYSKSCRFILSCNYVSR--------IIEPIQSR--  152 (226)
T ss_dssp             CSCEEEEEETGGGSCHH------------------HHHHHHHHHHHTTTTEEEEEEESCGGG--------SCHHHHTT--
T ss_pred             cCceEEEEeChhhcCHH------------------HHHHHHHHHHhcCCCCeEEEEeCChhh--------cCHHHHHh--
Confidence            46889999999766331                  234455555544445666666543210        12233322  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            +..++++.++.+|...++..+.. .|.--+++....+...++|||+.+..++
T Consensus       153 ------~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l  204 (226)
T 2chg_A          153 ------CAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINAL  204 (226)
T ss_dssp             ------SEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ------CceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  22489999999999999976654 2432145555567779999999987764

>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=98.60  E-value=1.3e-06  Score=81.97  Aligned_cols=123  Identities=12%  Similarity=0.070  Sum_probs=69.3

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++.|....  . .|++|+|||++.+.....              ..+...+..+... ..+..+|++.+....   
T Consensus       124 ~~~l~~~l~~~~--~-~~~vlvlDe~~~~~~~~~--------------~~~~~~l~~~~~~-~~~~~~i~~g~~~~~---  182 (357)
T 2fna_A          124 FANLLESFEQAS--K-DNVIIVLDEAQELVKLRG--------------VNLLPALAYAYDN-LKRIKFIMSGSEMGL---  182 (357)
T ss_dssp             HHHHHHHHHHTC--S-SCEEEEEETGGGGGGCTT--------------CCCHHHHHHHHHH-CTTEEEEEEESSHHH---
T ss_pred             HHHHHHHHHhcC--C-CCeEEEEECHHHhhccCc--------------hhHHHHHHHHHHc-CCCeEEEEEcCchHH---
Confidence            556667776543  1 399999999977654212              2333444443332 135666776653210   


Q ss_pred             CccCcchhHHhhhcCC--CCCCC-cceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         268 RRESHLPLYMLKKAGF--ESIDP-FVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~--~~~dP-~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           + ..+++....  ..... ...+++++||.+|+..++..... .+.- .++ ..++...|||||..+..+|
T Consensus       183 -----l-~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~-~~~-~~~i~~~t~G~P~~l~~~~  250 (357)
T 2fna_A          183 -----L-YDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADID-FKD-YEVVYEKIGGIPGWLTYFG  250 (357)
T ss_dssp             -----H-HHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCC-CCC-HHHHHHHHCSCHHHHHHHH
T ss_pred             -----H-HHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCC-CCc-HHHHHHHhCCCHHHHHHHH
Confidence                 0 011100000  00111 13589999999999999975432 3332 122 2678889999999988776

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.38  E-value=3.2e-06  Score=74.74  Aligned_cols=49  Identities=8%  Similarity=0.049  Sum_probs=37.2

Q ss_pred             eeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .++++.++.+|...++..+.. .|+--+++....+...++||++++..++
T Consensus       168 ~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l  217 (242)
T 3bos_A          168 TYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVL  217 (242)
T ss_dssp             EEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             eEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence            488999999999999987754 3432245555567778999999998765

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.37  E-value=1.5e-05  Score=73.01  Aligned_cols=119  Identities=19%  Similarity=0.327  Sum_probs=68.5

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhh---cC-CCCCeEEEEEeCCCCCCCCCccCcchhHHh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLV---QS-DWNNGAIVLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~---~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                      ..|.+|.+|+++.+......-       .....-...+.+..++   .+ ....+++|.+++...       ..++..++
T Consensus       109 ~~~~vl~iDEid~l~~~~~~~-------~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~-------~~l~~~l~  174 (285)
T 3h4m_A          109 KAPSIIFIDEIDAIAAKRTDA-------LTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRP-------DILDPAIL  174 (285)
T ss_dssp             TCSEEEEEETTHHHHBCCSSS-------CCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCG-------GGBCHHHH
T ss_pred             cCCeEEEEECHHHhcccCccc-------cCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCc-------hhcCHHHc
Confidence            457889999999987653200       1111112223333333   22 334556666665432       11333444


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                      ....|+.     .+.++.++.+|...+++.+...--+..+....++...+.| +|+++..+|.
T Consensus       175 ~~~Rf~~-----~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~  232 (285)
T 3h4m_A          175 RPGRFDR-----IIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICT  232 (285)
T ss_dssp             STTSEEE-----EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             CCCcCCe-----EEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            3222321     4788999999999999988765444333345566666665 9999998874

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.35  E-value=2.2e-05  Score=74.57  Aligned_cols=109  Identities=6%  Similarity=0.117  Sum_probs=64.8

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC----CCCccCcchhHHhhh
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL----PDRRESHLPLYMLKK  280 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~----~~~~~~~~p~~llg~  280 (342)
                      |.+|.||+++.+-                  -.....|++++.... ..+++++++.....    .......++..+..+
T Consensus       190 ~~vl~IDEi~~l~------------------~~~~~~L~~~le~~~-~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR  250 (368)
T 3uk6_A          190 PGVLFIDEVHMLD------------------IESFSFLNRALESDM-APVLIMATNRGITRIRGTSYQSPHGIPIDLLDR  250 (368)
T ss_dssp             BCEEEEESGGGSB------------------HHHHHHHHHHTTCTT-CCEEEEEESCSEEECBTSSCEEETTCCHHHHTT
T ss_pred             CceEEEhhccccC------------------hHHHHHHHHHhhCcC-CCeeeeecccceeeeeccCCCCcccCCHHHHhh
Confidence            6788899997652                  234456666665432 33555555532100    000011233344433


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhC-CCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTK-RVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSg-GNP~~l~~lc~  340 (342)
                              +..+.++.++.+|...+++..... +.--+++....+...+. |||+++..+|.
T Consensus       251 --------~~~i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~  304 (368)
T 3uk6_A          251 --------LLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLIT  304 (368)
T ss_dssp             --------EEEEEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             --------ccEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHH
Confidence                    234799999999999999876554 33214544555666888 99999998874

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.26  E-value=7.5e-05  Score=72.91  Aligned_cols=122  Identities=11%  Similarity=0.132  Sum_probs=70.6

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.+|++-++++.-.  ...  ..-+...-.++..|+..+.| +-.++++|.|+|...   +    .+...+++.-
T Consensus       240 ~aP~IIFiDEiDai~~~R~--~~~--~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrp---d----~LDpAllRpG  308 (405)
T 4b4t_J          240 HAPSIIFMDEIDSIGSTRV--EGS--GGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRL---D----ILDPALLRPG  308 (405)
T ss_dssp             TCSEEEEEESSSCCTTSCS--CSS--SGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCS---S----SSCHHHHSTT
T ss_pred             hCCceEeeecchhhccCCC--CCC--CCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCCh---h----hCCHhHcCCC
Confidence            4689999999998876522  000  00011112344555555555 334556555544332   1    1334565433


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      .|+.     .|+|+.-+.++-..+++.|...--+..+....+|-- .-|-++.++..+|.
T Consensus       309 RfD~-----~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~  363 (405)
T 4b4t_J          309 RIDR-----KIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCT  363 (405)
T ss_dssp             SSCC-----EEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             cCce-----EEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHH
Confidence            3543     478888888999999998876544422223345544 44679999999984

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.26  E-value=2.1e-05  Score=74.54  Aligned_cols=55  Identities=7%  Similarity=0.012  Sum_probs=39.7

Q ss_pred             ch-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC-------CeEEEEeC
Q psy3261          47 RN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN-------NYLLVHIP  102 (342)
Q Consensus        47 R~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-------gwiVl~vP  102 (342)
                      |+ +..+|...|.. +-...+...++|+|++|||||++...++.-..+.       ++.+++|.
T Consensus        25 Re~E~~~i~~~L~~-~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~IN   87 (318)
T 3te6_A           25 QVEDFTRIFLPIYD-SLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHID   87 (318)
T ss_dssp             HHHHHHHHHHHHHH-HHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEE
T ss_pred             HHHHHHHHHHHHHH-HhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEe
Confidence            44 55566667766 3344678899999999999999999988766532       45556653

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.26  E-value=8.8e-05  Score=70.03  Aligned_cols=117  Identities=14%  Similarity=0.110  Sum_probs=67.7

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC--CCCeEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD--WNNGAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~--~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.||++.++..... -..      ....-.+...|+..+.+-  ...+++|.+++...   .    .+...++.+
T Consensus       104 ~~~~vl~iDEid~l~~~~~-~~~------~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~---~----~ld~al~rR  169 (322)
T 1xwi_A          104 NKPSIIFIDEIDSLCGSRS-ENE------SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIP---W----VLDSAIRRR  169 (322)
T ss_dssp             TSSEEEEEETTTGGGCCSS-SCC------TTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCT---T----TSCHHHHHT
T ss_pred             cCCcEEEeecHHHhccccc-ccc------chHHHHHHHHHHHHHhcccccCCCEEEEEecCCc---c----cCCHHHHhh
Confidence            3577888999999876532 100      011114555566666542  23455544444321   1    133345543


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                        |+.     .+.++..+.++-..++..+....-.. .+....++-..|.| +|+++..+|.
T Consensus       170 --f~~-----~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          170 --FEK-----RIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             --CCE-----EEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             --cCe-----EEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence              432     37888899999999998876544332 34444455556655 6999999884

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.24  E-value=1.7e-05  Score=75.18  Aligned_cols=103  Identities=11%  Similarity=0.125  Sum_probs=66.1

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.+|.||++..+-.                  .....|++++.....+..+|++++....        ++..+..+  
T Consensus       118 ~~~~vliiDe~~~l~~------------------~~~~~Ll~~le~~~~~~~~Il~~~~~~~--------l~~~l~sr--  169 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSR------------------HSFNALLKTLEEPPEHVKFLLATTDPQK--------LPVTILSR--  169 (373)
T ss_dssp             SSSEEEEEECGGGSCH------------------HHHHHHHHHHHSCCSSEEEEEEESCGGG--------SCHHHHTT--
T ss_pred             CCeEEEEEECcchhcH------------------HHHHHHHHHHhcCCCceEEEEEeCChHh--------CcHHHHhh--
Confidence            4567888999965521                  2345667777655556667777653221        22223222  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            ...++++.++.+|...++..+.. .|+-.+++....+...++|||+.+..+|
T Consensus       170 ------~~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G~~r~~~~~l  221 (373)
T 1jr3_A          170 ------CLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT  221 (373)
T ss_dssp             ------SEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             ------eeEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCCCHHHHHHHH
Confidence                  13489999999999999976654 3443244445557779999999998776

>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=98.23  E-value=1.2e-05  Score=74.52  Aligned_cols=103  Identities=15%  Similarity=0.094  Sum_probs=62.6

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.+|.||++..+...                  ....|++++.....+..+|++++...      .  ++..+..+  
T Consensus       106 ~~~~viiiDe~~~l~~~------------------~~~~L~~~le~~~~~~~~il~~~~~~------~--l~~~l~sr--  157 (323)
T 1sxj_B          106 GKHKIVILDEADSMTAG------------------AQQALRRTMELYSNSTRFAFACNQSN------K--IIEPLQSQ--  157 (323)
T ss_dssp             TCCEEEEEESGGGSCHH------------------HHHTTHHHHHHTTTTEEEEEEESCGG------G--SCHHHHTT--
T ss_pred             CCceEEEEECcccCCHH------------------HHHHHHHHHhccCCCceEEEEeCChh------h--chhHHHhh--
Confidence            34788999999665321                  12334555544445566676664321      1  12223222  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            ...++++.++.+|...++..... .|+--+++....+...++|||+.+..++
T Consensus       158 ------~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~a~~~l  209 (323)
T 1sxj_B          158 ------CAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNL  209 (323)
T ss_dssp             ------SEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ------ceEEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  12489999999999999976643 3432145545567779999999876654

>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=98.20  E-value=0.00012  Score=68.95  Aligned_cols=117  Identities=10%  Similarity=0.122  Sum_probs=68.5

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC--CCCeEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD--WNNGAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~--~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.||++.++......   ..    ....-.+...|+..+.+-  ...+++|.+++...   .    .++..+..+
T Consensus       109 ~~~~vl~iDEid~l~~~~~~---~~----~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~---~----~ld~al~~R  174 (322)
T 3eie_A          109 NKPSIIFIDQVDALTGTRGE---GE----SEASRRIKTELLVQMNGVGNDSQGVLVLGATNIP---W----QLDSAIRRR  174 (322)
T ss_dssp             TSSEEEEEECGGGGSCC-------------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCG---G----GSCHHHHHH
T ss_pred             cCCeEEEechhhhhhccCCC---Cc----chHHHHHHHHHHHHhccccccCCceEEEEecCCh---h----hCCHHHHcc
Confidence            45778889999988764220   00    001124455566666542  34556555554321   1    133445543


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                        |+.     .+.++..+.+|-..+++.+....-.. .+....++--.|.| +++++..+|.
T Consensus       175 --f~~-----~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          175 --FER-----RIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             --CCE-----EEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             --cCe-----EEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence              422     37888899999999999887654432 34444455556665 9999999884

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.16  E-value=0.00013  Score=72.41  Aligned_cols=122  Identities=11%  Similarity=0.099  Sum_probs=67.6

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.+|++-+++..-.  .  ....-+.........|+..+.| .-.++++|.++|...   +    .+...+++.-
T Consensus       301 ~aP~IIfiDEiDai~~~R~--~--~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrp---d----~LDpALlRpG  369 (467)
T 4b4t_H          301 KKACIIFFDEIDAVGGARF--D--DGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRP---N----TLDPALLRPG  369 (467)
T ss_dssp             TCSEEEEEECCTTTSBCCS--S--SSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCT---T----SBCHHHHSTT
T ss_pred             cCCceEeeccccccccccc--C--cCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCc---c----cCChhhhccc
Confidence            4699999999988876521  0  1111111111223334444434 334555555544322   1    1334565433


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHh-hCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFL-TKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~l-SgGNP~~l~~lc~  340 (342)
                      .|+.     .|+|+.-+.++-..+++.|...--+..+-...+|--+ .|-++.++..+|.
T Consensus       370 RFD~-----~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  424 (467)
T 4b4t_H          370 RIDR-----KVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCT  424 (467)
T ss_dssp             TCCE-----EECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             cccE-----EEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHH
Confidence            3543     3788878888989999988765444222223344444 4669999999984

>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=98.16  E-value=5.7e-05  Score=70.01  Aligned_cols=103  Identities=12%  Similarity=0.154  Sum_probs=64.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.+|.||+++.+..                  .....|++++.....+..+|++++....        ++..+..+  
T Consensus       109 ~~~~vliiDe~~~l~~------------------~~~~~L~~~le~~~~~~~~i~~~~~~~~--------l~~~l~sr--  160 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQ------------------DAQQALRRTMEMFSSNVRFILSCNYSSK--------IIEPIQSR--  160 (327)
T ss_dssp             CSCEEEEEETGGGSCH------------------HHHHHHHHHHHHTTTTEEEEEEESCGGG--------SCHHHHHT--
T ss_pred             CCCeEEEEeCCCcCCH------------------HHHHHHHHHHHhcCCCCeEEEEeCCccc--------cCHHHHhh--
Confidence            3467888999976632                  1234566666544445566666543211        22223322  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            +..+.++.++.+|+..++.......-+. +++....+...++|||+.+..++
T Consensus       161 ------~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~~~~~l  212 (327)
T 1iqp_A          161 ------CAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINIL  212 (327)
T ss_dssp             ------EEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ------CcEEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCCCHHHHHHHH
Confidence                  1237889999999999998775543222 55555667779999999887654

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.15  E-value=4.1e-05  Score=70.74  Aligned_cols=103  Identities=10%  Similarity=0.077  Sum_probs=63.9

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.+|.||++..+...                  ....|++++.....+..+|++++....        +...+..+  
T Consensus       101 ~~~~vliiDe~~~l~~~------------------~~~~L~~~le~~~~~~~~i~~~~~~~~--------l~~~l~sr--  152 (319)
T 2chq_A          101 APFKIIFLDEADALTAD------------------AQAALRRTMEMYSKSCRFILSCNYVSR--------IIEPIQSR--  152 (319)
T ss_dssp             CCCEEEEEETGGGSCHH------------------HHHTTGGGTSSSSSSEEEEEEESCGGG--------SCHHHHTT--
T ss_pred             CCceEEEEeCCCcCCHH------------------HHHHHHHHHHhcCCCCeEEEEeCChhh--------cchHHHhh--
Confidence            45788899999665321                  223355555544455566666543210        12223222  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            +..++++.++.+|...++.......-+. +++....+...++||++.+...+
T Consensus       153 ------~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l  204 (319)
T 2chq_A          153 ------CAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINAL  204 (319)
T ss_dssp             ------CEEEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             ------CeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  1248999999999999998776543232 55555567779999999987654

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.13  E-value=7e-05  Score=73.93  Aligned_cols=121  Identities=7%  Similarity=0.033  Sum_probs=68.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC-CCe-EEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW-NNG-AIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~-~~G-~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.+|++-+++..-.  .  ....-+..--.....|+..+.|-. .++ +||+||..-..        +...+++.
T Consensus       273 ~~P~IifiDEiDai~~~R~--~--~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~--------LDpAllRp  340 (437)
T 4b4t_L          273 HEPCIIFMDEVDAIGGRRF--S--EGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDT--------LDPALLRP  340 (437)
T ss_dssp             SCSEEEEEECCCSSSCCCS--S--SCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTS--------SCTTTTST
T ss_pred             cCCceeeeecccccccccc--c--CCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchh--------hCHHHhCC
Confidence            4699999999988876521  0  011111111234455666665533 334 45555544221        22334433


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhh-CCCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLT-KRVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lS-gGNP~~l~~lc~  340 (342)
                      -.|+.     .|+|+.-+.++-..++..|...--+..+....++--.| |-++.++..+|.
T Consensus       341 GRfD~-----~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~  396 (437)
T 4b4t_L          341 GRLDR-----KVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCAT  396 (437)
T ss_dssp             TSEEE-----EECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHH
T ss_pred             Cccce-----eeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHH
Confidence            22432     37788778888889998887654442232344555555 569999999884

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.12  E-value=2.7e-05  Score=76.85  Aligned_cols=121  Identities=15%  Similarity=0.159  Sum_probs=68.5

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCcc-chHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRV-TLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l-~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.+|++-++++.-..-.+.     ...+. .+...|+..+.|- -..+++|.|+|...   +.    +...+++.
T Consensus       273 ~aP~IifiDEiDal~~~R~~~~~~-----~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp---~~----LD~AllRp  340 (434)
T 4b4t_M          273 KAPTIIFIDELDAIGTKRFDSEKS-----GDREVQRTMLELLNQLDGFSSDDRVKVLAATNRV---DV----LDPALLRS  340 (434)
T ss_dssp             HCSEEEEEECTHHHHCCCSSGGGG-----TTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSC---CC----CCTTTCST
T ss_pred             cCCeEEeecchhhhhhccCCCCCC-----CchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCc---hh----cCHhHhcC
Confidence            358999999999887652200000     01111 3445566666553 34555555555432   11    22334332


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhh-CCCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLT-KRVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lS-gGNP~~l~~lc~  340 (342)
                      -.|+.     .|+++.-+.++-..+++.|...--+..+-...+|--.| |-++.++..+|.
T Consensus       341 GRfD~-----~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~  396 (434)
T 4b4t_M          341 GRLDR-----KIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTV  396 (434)
T ss_dssp             TSEEE-----EEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHH
T ss_pred             CceeE-----EEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            22432     37888788888899999887654442222334555554 569999999984

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.09  E-value=0.00012  Score=68.68  Aligned_cols=49  Identities=16%  Similarity=0.117  Sum_probs=37.1

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+.++.++.+|...++..+....-+. +++....+...++|||+++..++
T Consensus       178 ~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l  227 (338)
T 3pfi_A          178 QFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIALRLL  227 (338)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             EeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHH
Confidence            48999999999999998776543332 45445566668999999998765

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.08  E-value=5.3e-05  Score=70.52  Aligned_cols=49  Identities=14%  Similarity=-0.000  Sum_probs=37.5

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+.++.++.+|...+++.+....-+. +++....+...++|||+++..+|
T Consensus       162 ~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l  211 (324)
T 1hqc_A          162 VEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLF  211 (324)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHH
T ss_pred             EEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence            48899999999999998876543222 45555667778999999998875

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.03  E-value=0.00021  Score=70.33  Aligned_cols=121  Identities=10%  Similarity=0.146  Sum_probs=67.0

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeE-EEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGA-IVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~-vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.++.+|++.+++..-..-......    ..-.++..|+..+.|- -..++ ||+||..-.        .+...+++.
T Consensus       264 ~aP~IifiDEiD~i~~~R~~~~~~~~~----~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~--------~LD~AllRp  331 (428)
T 4b4t_K          264 NAPSIIFIDEVDSIATKRFDAQTGSDR----EVQRILIELLTQMDGFDQSTNVKVIMATNRAD--------TLDPALLRP  331 (428)
T ss_dssp             TCSEEEEEECTHHHHCSCSSSCSCCCC----HHHHHHHHHHHHHHHSCSSCSEEEEEEESCSS--------SCCHHHHSS
T ss_pred             cCCCeeechhhhhhhccccCCCCCCCh----HHHHHHHHHHHHhhCCCCCCCEEEEEecCChh--------hcChhhhcC
Confidence            469999999999988753211111110    0113455566666653 23444 455554322        134456543


Q ss_pred             cCCCCCCCcceeecCCCC-HHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELN-DEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s-~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      -.|+.     .|++++++ .++-+.++..+...--+..+....++-. .-|-++.++..+|.
T Consensus       332 GRfd~-----~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~  388 (428)
T 4b4t_K          332 GRLDR-----KIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ  388 (428)
T ss_dssp             SSEEE-----EEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CcceE-----EEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHH
Confidence            23432     37888775 5555667787766544422323345544 45679999999984

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=98.03  E-value=0.00029  Score=63.32  Aligned_cols=123  Identities=14%  Similarity=0.124  Sum_probs=57.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.||++..+..... -.....  -..........|+..+.+ ....+++|.+++...   .    .++..+....
T Consensus        97 ~~~~vl~iDeid~l~~~~~-~~~~~~--~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~---~----~ld~~l~~~~  166 (262)
T 2qz4_A           97 RAPCIVYIDEIDAVGKKRS-TTMSGF--SNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRA---D----ILDGALMRPG  166 (262)
T ss_dssp             TCSEEEEEECC----------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCG---G----GGGSGGGSTT
T ss_pred             cCCeEEEEeCcchhhcccc-ccccCc--cchhHHHHHHHHHHHhhCcCCCCCEEEEecCCCh---h----hcCHHHhcCC
Confidence            3588999999988865422 000000  011112333334443333 334455555555322   0    1222333221


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcch--HHHHHHhhCC-CHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEG--REEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~--~~el~~lSgG-NP~~l~~lc~  340 (342)
                      .|+     ..+.++..+.+|...+++.+...--+..+..  ...+...+.| +|+++..+|.
T Consensus       167 R~~-----~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~  223 (262)
T 2qz4_A          167 RLD-----RHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICN  223 (262)
T ss_dssp             SCC-----EEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             cCC-----eEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHH
Confidence            232     1367888899999999988765433321211  2345556665 5778888773

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.02  E-value=0.00018  Score=67.83  Aligned_cols=102  Identities=11%  Similarity=0.073  Sum_probs=64.3

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .|-++.+|+...+ ..                 .....|++++.....+..+|+++.....        ++..+..+   
T Consensus       134 ~~~vlilDE~~~L-~~-----------------~~~~~L~~~le~~~~~~~~Il~t~~~~~--------l~~~l~sR---  184 (354)
T 1sxj_E          134 RYKCVIINEANSL-TK-----------------DAQAALRRTMEKYSKNIRLIMVCDSMSP--------IIAPIKSQ---  184 (354)
T ss_dssp             CCEEEEEECTTSS-CH-----------------HHHHHHHHHHHHSTTTEEEEEEESCSCS--------SCHHHHTT---
T ss_pred             CCeEEEEeCcccc-CH-----------------HHHHHHHHHHHhhcCCCEEEEEeCCHHH--------HHHHHHhh---
Confidence            4667789998663 22                 2245566666544445666776654321        22223222   


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccC-cchHHHHHHhhCCCHHHHhhhc
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQT-SEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~-e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ...++++.++.+|....+...... |+--+ ++....+...++||+|.+..++
T Consensus       185 -----~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          185 -----CLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             -----SEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             -----ceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence                 134899999999999999876543 44224 5555667779999999988765

>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=98.02  E-value=0.00015  Score=69.28  Aligned_cols=117  Identities=10%  Similarity=0.124  Sum_probs=67.0

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC--CCCeEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD--WNNGAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~--~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.||++..+......-   ..    ...-.+...|+..+.+-  ...+++|.+++...   .    .++..++.+
T Consensus       142 ~~~~vl~iDEid~l~~~r~~~---~~----~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~---~----~ld~al~rR  207 (355)
T 2qp9_X          142 NKPSIIFIDQVDALTGTRGEG---ES----EASRRIKTELLVQMNGVGNDSQGVLVLGATNIP---W----QLDSAIRRR  207 (355)
T ss_dssp             TSSEEEEEECGGGGTC---------C----THHHHHHHHHHHHHHHCC---CCEEEEEEESCG---G----GSCHHHHHT
T ss_pred             cCCeEEEEechHhhcccCCCC---cc----hHHHHHHHHHHHHhhcccccCCCeEEEeecCCc---c----cCCHHHHcc
Confidence            458889999998886542100   00    00113455566665542  23445555444321   1    133445543


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                        |+.     .+.++..+.+|...+++.+....-+. .+.....|...|.| +|+++..+|.
T Consensus       208 --f~~-----~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~  262 (355)
T 2qp9_X          208 --FER-----RIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVK  262 (355)
T ss_dssp             --CCE-----EEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             --cCE-----EEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence              422     36788899999999998887654322 34444556667777 9999999984

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.00  E-value=0.00053  Score=61.87  Aligned_cols=121  Identities=12%  Similarity=0.079  Sum_probs=65.7

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeE-EEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGA-IVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~-vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.++.+|++..+..... -.   ...-....-.++..++..+.+ .-+.++ ||+||.....        +...+...
T Consensus       103 ~~~~il~iDeid~l~~~~~-~~---~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~--------l~~~l~r~  170 (257)
T 1lv7_A          103 AAPCIIFIDEIDAVGRQRG-AG---LGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDV--------LDPALLRP  170 (257)
T ss_dssp             TCSEEEEETTHHHHTCCCS-TT---SCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTT--------SCGGGGST
T ss_pred             cCCeeehhhhhhhhccCCC-CC---cCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCchh--------CCHHHcCC
Confidence            4588889999988765422 00   000011112344555555543 223444 4555443221        22233322


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                      ..|+.     ++.++..+.+|-..+++.+...--+..+.....+-..+.| |++++..+|.
T Consensus       171 ~rf~~-----~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~  226 (257)
T 1lv7_A          171 GRFDR-----QVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (257)
T ss_dssp             TSSCE-----EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CcCCe-----EEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHH
Confidence            22322     4777777888989999888765333222223455567788 9999998874

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.00  E-value=0.00017  Score=70.85  Aligned_cols=122  Identities=11%  Similarity=0.132  Sum_probs=66.3

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.+|++-+++..-..-.+..    +..--.....|+..+.| +-.++++|.|+|...   +.    +...+++.-
T Consensus       274 ~aP~IIfiDEiDai~~~R~~~~~~~----~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrp---d~----LDpALlRpG  342 (437)
T 4b4t_I          274 NAPSIVFIDEIDAIGTKRYDSNSGG----EREIQRTMLELLNQLDGFDDRGDVKVIMATNKI---ET----LDPALIRPG  342 (437)
T ss_dssp             TCSEEEEEEEESSSSCCCSCSSCSS----CCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCS---TT----CCTTSSCTT
T ss_pred             cCCcEEEEehhhhhcccCCCCCCCc----cHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCh---hh----cCHHHhcCC
Confidence            4699999999998877522011100    01111333344444444 344555554444322   11    222343322


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      .|+.     .|+|+.-+.++-+.+++.|...--+..+....+|-- .-|-++.++..+|.
T Consensus       343 RfD~-----~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  397 (437)
T 4b4t_I          343 RIDR-----KILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCT  397 (437)
T ss_dssp             TEEE-----EECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             ceeE-----EEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            2332     377887788888899998876544422223344444 44679999999884

>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=97.99  E-value=0.00019  Score=70.73  Aligned_cols=117  Identities=14%  Similarity=0.122  Sum_probs=68.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC--CCCeEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD--WNNGAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~--~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.||++.+++.... -.  .    ....-.+...|+..+.+-  ...+++|.+++...   .    .++..++.+
T Consensus       226 ~~~~vl~iDEid~l~~~~~-~~--~----~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~---~----~ld~al~rR  291 (444)
T 2zan_A          226 NKPSIIFIDEIDSLCGSRS-EN--E----SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIP---W----VLDSAIRRR  291 (444)
T ss_dssp             SCSEEEEESCTTTTCCCSS-CC--C----CGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCG---G----GSCHHHHTT
T ss_pred             cCCeEEEEechHhhccCCC-Cc--c----ccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCc---c----ccCHHHHhh
Confidence            3577888999998876422 00  0    011124556666666552  23445544444321   1    133345542


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                        |+.     .+.++..+.++...++..+....-+. .+....+|-..|.| +++++..+|.
T Consensus       292 --f~~-----~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          292 --FEK-----RIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             --CCE-----EEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             --cce-----EEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence              431     37788889999999998876543322 34444556667777 9999999884

>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=97.92  E-value=0.00011  Score=68.69  Aligned_cols=37  Identities=24%  Similarity=0.308  Sum_probs=30.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ....++|+|++|||||+++..+.......|+-+++++
T Consensus        36 ~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~   72 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSS   72 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            4678999999999999999988888877777666663

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.91  E-value=0.00037  Score=68.84  Aligned_cols=106  Identities=10%  Similarity=0.162  Sum_probs=66.4

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCC-------CCCCCCccCcchhHH
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPR-------ANLPDRRESHLPLYM  277 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~-------~~~~~~~~~~~p~~l  277 (342)
                      |-++.||+.+.+    +              -.....|++.+.....+ ++|+++...       .....+  ..+|..+
T Consensus       296 ~~VliIDEa~~l----~--------------~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~--~~l~~~i  354 (456)
T 2c9o_A          296 PGVLFVDEVHML----D--------------IECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSP--HGIPLDL  354 (456)
T ss_dssp             ECEEEEESGGGC----B--------------HHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEE--TTCCHHH
T ss_pred             ceEEEEechhhc----C--------------HHHHHHHHHHhhccCCC-EEEEecCCcccccccccccccc--ccCChhH
Confidence            348889999877    2              34667788888766555 677676221       000001  1233334


Q ss_pred             hhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhh-CCCHHHHhhhc
Q psy3261         278 LKKAGFESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLT-KRVPQKMYEFC  339 (342)
Q Consensus       278 lg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lS-gGNP~~l~~lc  339 (342)
                      ..+        +..+.++.|+.+|...++..-.. .++--+++....+..++ +|+|+....+|
T Consensus       355 ~sR--------~~~~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll  410 (456)
T 2c9o_A          355 LDR--------VMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLL  410 (456)
T ss_dssp             HTT--------EEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTH
T ss_pred             Hhh--------cceeeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHH
Confidence            333        23478999999999999976543 23321455455566688 99999988776

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.89  E-value=0.00045  Score=65.32  Aligned_cols=117  Identities=9%  Similarity=0.020  Sum_probs=73.2

Q ss_pred             hHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCC
Q psy3261         185 SDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRAN  264 (342)
Q Consensus       185 ~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~  264 (342)
                      .+.+..+++++......+ .+-++.||+...+-.                  .-...|++++.....+..+|++++....
T Consensus        90 i~~ir~l~~~~~~~~~~~-~~kvviIdead~l~~------------------~a~naLLk~lEep~~~~~~Il~t~~~~~  150 (334)
T 1a5t_A           90 VDAVREVTEKLNEHARLG-GAKVVWVTDAALLTD------------------AAANALLKTLEEPPAETWFFLATREPER  150 (334)
T ss_dssp             HHHHHHHHHHTTSCCTTS-SCEEEEESCGGGBCH------------------HHHHHHHHHHTSCCTTEEEEEEESCGGG
T ss_pred             HHHHHHHHHHHhhccccC-CcEEEEECchhhcCH------------------HHHHHHHHHhcCCCCCeEEEEEeCChHh
Confidence            344555666655432122 355667999965521                  2346788888776677777887764321


Q ss_pred             CCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhcc
Q psy3261         265 LPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFCS  340 (342)
Q Consensus       265 ~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc~  340 (342)
                              ++..+..+        ...++++.++.+|....+....   .+ +++....+..+|+|+|+....++.
T Consensus       151 --------l~~ti~SR--------c~~~~~~~~~~~~~~~~L~~~~---~~-~~~~~~~l~~~s~G~~r~a~~~l~  206 (334)
T 1a5t_A          151 --------LLATLRSR--------CRLHYLAPPPEQYAVTWLSREV---TM-SQDALLAALRLSAGSPGAALALFQ  206 (334)
T ss_dssp             --------SCHHHHTT--------SEEEECCCCCHHHHHHHHHHHC---CC-CHHHHHHHHHHTTTCHHHHHHTTS
T ss_pred             --------CcHHHhhc--------ceeeeCCCCCHHHHHHHHHHhc---CC-CHHHHHHHHHHcCCCHHHHHHHhc
Confidence                    22223222        1248889999999998887653   33 454445677799999999988764

>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=97.86  E-value=0.00061  Score=65.05  Aligned_cols=116  Identities=11%  Similarity=0.122  Sum_probs=66.0

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC---CCCeEE-EEEeCCCCCCCCCccCcchhHHh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD---WNNGAI-VLALSPRANLPDRRESHLPLYML  278 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~---~~~G~v-v~AtS~~~~~~~~~~~~~p~~ll  278 (342)
                      ..|.+|.||++..+......       ..+.....+...|+..+.+.   ....++ |+||....        .+...+.
T Consensus       175 ~~~~vl~iDEid~l~~~~~~-------~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~--------~l~~~l~  239 (357)
T 3d8b_A          175 QQPAVIFIDEIDSLLSQRGD-------GEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQ--------EIDEAAR  239 (357)
T ss_dssp             TCSEEEEEETHHHHTBC-------------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGG--------GBCHHHH
T ss_pred             cCCeEEEEeCchhhhccCCC-------CcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChh--------hCCHHHH
Confidence            34778889999888764220       01111234555555555542   233444 55543311        1333444


Q ss_pred             hhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         279 KKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       279 g~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                      .+  |.     ..+.++..+.+|...++..+....-+. .++...++...|.| +|+++..+|.
T Consensus       240 ~R--f~-----~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          240 RR--LV-----KRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             TT--CC-----EEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             hh--Cc-----eEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            42  32     136788899999999998776543222 44444556667777 8999999885

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.80  E-value=0.00068  Score=65.35  Aligned_cols=115  Identities=15%  Similarity=0.111  Sum_probs=60.8

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC---CCCeE-EEEEeCCCCCCCCCccCcchhHHhh
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD---WNNGA-IVLALSPRANLPDRRESHLPLYMLK  279 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~---~~~G~-vv~AtS~~~~~~~~~~~~~p~~llg  279 (342)
                      .|.+|.||+++.++.... -      ..+.....+...|+..+.+.   ....+ ||+||....        .++..++.
T Consensus       207 ~~~il~iDEid~l~~~~~-~------~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~--------~l~~~l~~  271 (389)
T 3vfd_A          207 QPSIIFIDQVDSLLCERR-E------GEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQ--------ELDEAVLR  271 (389)
T ss_dssp             SSEEEEEETGGGGC---------------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGG--------GCCHHHHT
T ss_pred             CCeEEEEECchhhcccCC-C------ccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCch--------hcCHHHHc
Confidence            466778999999876532 0      00111123444455544431   22334 455553211        13334443


Q ss_pred             hcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         280 KAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       280 ~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                      +  |.     ..+.++..+.+|...++..+....-.. .++...++...+.| +++++..+|.
T Consensus       272 R--~~-----~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          272 R--FI-----KRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             T--CC-----EEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             C--cc-----eEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            2  32     137888899999999998877654332 34444455556655 7778888774

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.79  E-value=0.00027  Score=65.26  Aligned_cols=115  Identities=10%  Similarity=0.098  Sum_probs=65.2

Q ss_pred             EEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCC
Q psy3261         206 TFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFES  285 (342)
Q Consensus       206 VLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~  285 (342)
                      -+|.||++..++....      .   ....-.+...|++++...-.+..+|+++....  .+.. ..+...+..+  |. 
T Consensus       132 ~vl~iDEid~l~~~~~------~---~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~--~~~~-~~~~~~l~~R--~~-  196 (309)
T 3syl_A          132 GVLFIDEAYYLYRPDN------E---RDYGQEAIEILLQVMENNRDDLVVILAGYADR--MENF-FQSNPGFRSR--IA-  196 (309)
T ss_dssp             SEEEEETGGGSCCCC------------CCTHHHHHHHHHHHHHCTTTCEEEEEECHHH--HHHH-HHHSTTHHHH--EE-
T ss_pred             CEEEEEChhhhccCCC------c---ccccHHHHHHHHHHHhcCCCCEEEEEeCChHH--HHHH-HhhCHHHHHh--CC-
Confidence            3788999988875422      0   11224566777777765545556666654321  0000 0000112222  21 


Q ss_pred             CCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHh--------hCCCHHHHhhhc
Q psy3261         286 IDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFL--------TKRVPQKMYEFC  339 (342)
Q Consensus       286 ~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~l--------SgGNP~~l~~lc  339 (342)
                          ..+.++.++.+|...+++.+....-+. +++....+.-.        ..||.+++.++|
T Consensus       197 ----~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l  255 (309)
T 3syl_A          197 ----HHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNAL  255 (309)
T ss_dssp             ----EEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHH
T ss_pred             ----eEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence                258999999999999998876643333 44333333333        349999998876

>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=97.78  E-value=0.001  Score=61.83  Aligned_cols=121  Identities=13%  Similarity=0.118  Sum_probs=65.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CC-CCeEEEEEeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DW-NNGAIVLALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~-~~G~vv~AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.++.+|++.++..... -...+..   ...-.+...|+..+.+ .- .+..||+||.....        +...++..
T Consensus       107 ~~p~il~iDEid~l~~~~~-~~~~~~~---~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~--------ld~al~r~  174 (301)
T 3cf0_A          107 AAPCVLFFDELDSIAKARG-GNIGDGG---GAADRVINQILTEMDGMSTKKNVFIIGATNRPDI--------IDPAILRP  174 (301)
T ss_dssp             TCSEEEEECSTTHHHHHHT-TTTCCSS---CSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGG--------SCGGGGST
T ss_pred             cCCeEEEEEChHHHhhccC-CCcCCcc---hHHHHHHHHHHHHhhcccCCCCEEEEEecCCccc--------cChHHhcC
Confidence            3588999999988875421 0000000   0112345556666654 22 34444555533211        22233332


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhC-CCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTK-RVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSg-GNP~~l~~lc~  340 (342)
                      ..|+.     .+.++..+.+|-..+++++....-+..+.....+-.++. -++.+|..+|.
T Consensus       175 gRf~~-----~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~  230 (301)
T 3cf0_A          175 GRLDQ-----LIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  230 (301)
T ss_dssp             TSSCE-----EEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHH
T ss_pred             Cccce-----EEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHH
Confidence            22431     478888999999999988876543322222334444454 46778888873

>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=97.77  E-value=0.00042  Score=64.98  Aligned_cols=102  Identities=8%  Similarity=-0.008  Sum_probs=64.3

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .+.+|.||+++.+...                  ....|++++.....+..+|++++...      .  +...+..+  +
T Consensus       133 ~~~vliiDE~~~l~~~------------------~~~~Ll~~le~~~~~~~~il~~~~~~------~--l~~~l~sR--~  184 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD------------------AQSALRRTMETYSGVTRFCLICNYVT------R--IIDPLASQ--C  184 (353)
T ss_dssp             SCEEEEETTGGGSCHH------------------HHHHHHHHHHHTTTTEEEEEEESCGG------G--SCHHHHHH--S
T ss_pred             CceEEEEECCCccCHH------------------HHHHHHHHHHhcCCCceEEEEeCchh------h--Ccchhhcc--C
Confidence            4578889999776332                  12456666665445666676664321      0  22233333  1


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            ..+.++.++.+|....+...... |+--+++....+...++||++.+..++
T Consensus       185 ------~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          185 ------SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             ------EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             ------ceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  13889999999999999876543 442145555567779999999976654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.75  E-value=0.00073  Score=66.81  Aligned_cols=103  Identities=16%  Similarity=0.146  Sum_probs=62.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.++.||++..+-.. .                 -..|+..+..  ....+|+||+....      ..+...++.+  
T Consensus       105 ~~~~iLfIDEI~~l~~~-~-----------------q~~LL~~le~--~~v~lI~att~n~~------~~l~~aL~sR--  156 (447)
T 3pvs_A          105 GRRTILFVDEVHRFNKS-Q-----------------QDAFLPHIED--GTITFIGATTENPS------FELNSALLSR--  156 (447)
T ss_dssp             TCCEEEEEETTTCC------------------------CCHHHHHT--TSCEEEEEESSCGG------GSSCHHHHTT--
T ss_pred             CCCcEEEEeChhhhCHH-H-----------------HHHHHHHHhc--CceEEEecCCCCcc------cccCHHHhCc--
Confidence            35778999999665321 1                 1123444433  23566777765321      1133344433  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHhC-------CCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYESK-------KWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-------~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            +..+.+..++.+|...+++.+...       .-+. +++....+...++||+|++..+|
T Consensus       157 ------~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~L  215 (447)
T 3pvs_A          157 ------ARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTL  215 (447)
T ss_dssp             ------EEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHH
T ss_pred             ------eeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHH
Confidence                  224788999999999999988765       1121 44445556668999999998776

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.68  E-value=0.0028  Score=58.09  Aligned_cols=116  Identities=16%  Similarity=0.196  Sum_probs=60.8

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC----CCeEEEEEeCCCCCCCCCccCcchhHHhh
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW----NNGAIVLALSPRANLPDRRESHLPLYMLK  279 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~----~~G~vv~AtS~~~~~~~~~~~~~p~~llg  279 (342)
                      .|.+|.+|++.++..... -..      +...-.+...|+..+.+-.    ..+++|.+++...   .    .++..++.
T Consensus       113 ~~~vl~iDEid~l~~~~~-~~~------~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~---~----~l~~~l~~  178 (297)
T 3b9p_A          113 QPSIIFIDEVDSLLSERS-SSE------HEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRP---Q----ELDEAALR  178 (297)
T ss_dssp             CSEEEEEETGGGTSBCC------------CCSHHHHHHHHHHHHHCC------CEEEEEEESCG---G----GBCHHHHH
T ss_pred             CCcEEEeccHHHhccccc-cCc------chHHHHHHHHHHHHHhcccccCCCCcEEEEeecCCh---h----hCCHHHHh
Confidence            467777999998876533 111      0111133334444444321    1345554444321   0    13334444


Q ss_pred             hcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCH-HHHhhhcc
Q psy3261         280 KAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVP-QKMYEFCS  340 (342)
Q Consensus       280 ~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP-~~l~~lc~  340 (342)
                      +  |..     .+.++..+.++-..++..+....-.. .++....+...|.|++ +++..+|.
T Consensus       179 R--~~~-----~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          179 R--FTK-----RVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             H--CCE-----EEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             h--CCe-----EEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3  321     36777788999899987776543221 3444445666777765 48877774

>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=97.67  E-value=0.00079  Score=61.76  Aligned_cols=120  Identities=14%  Similarity=0.189  Sum_probs=64.4

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC---------CCCeEEEEEeCCCCCCCCCccCcchh
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD---------WNNGAIVLALSPRANLPDRRESHLPL  275 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~---------~~~G~vv~AtS~~~~~~~~~~~~~p~  275 (342)
                      +.+|.+|++..+.....      ...-....-.+...|+.++.+.         ....+++.+++.... ..+  ..++.
T Consensus       117 ~~vl~iDEi~~l~~~~~------~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~--~~l~~  187 (310)
T 1ofh_A          117 NGIVFIDEIDKICKKGE------YSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQV-ARP--SDLIP  187 (310)
T ss_dssp             HCEEEEECGGGGSCCSS------CCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSS-SCG--GGSCH
T ss_pred             CCEEEEEChhhcCcccc------ccccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEcCCccc-CCc--ccCCH
Confidence            56788999988765421      0000111123456677777643         122344444432110 011  12334


Q ss_pred             HHhhhcCCCCCCCcceeecCCCCHHHHHHHHHH----H--------HhCCC-cc-CcchHHHHHHhh--------CCCHH
Q psy3261         276 YMLKKAGFESIDPFVPIHVPELNDEEFHNLLNL----Y--------ESKKW-LQ-TSEGREEIAFLT--------KRVPQ  333 (342)
Q Consensus       276 ~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~y----y--------~~~~~-l~-~e~~~~el~~lS--------gGNP~  333 (342)
                      .+..+  |.     ..+.++.++.+|...+++.    +        ...+. +. +++....+.-.+        +||+|
T Consensus       188 ~l~~R--~~-----~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R  260 (310)
T 1ofh_A          188 ELQGR--LP-----IRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGAR  260 (310)
T ss_dssp             HHHHT--CC-----EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHHHHHHHHHHHHHSCCCTTH
T ss_pred             HHHhh--CC-----ceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHHHHHHhhhhcccccccCcH
Confidence            55544  21     2489999999999998872    1        12343 11 444444444455        79999


Q ss_pred             HHhhhcc
Q psy3261         334 KMYEFCS  340 (342)
Q Consensus       334 ~l~~lc~  340 (342)
                      ++.++|.
T Consensus       261 ~l~~~l~  267 (310)
T 1ofh_A          261 RLHTVME  267 (310)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998763

>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=97.63  E-value=0.00045  Score=68.08  Aligned_cols=48  Identities=6%  Similarity=-0.094  Sum_probs=34.9

Q ss_pred             eecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         292 IHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +.++.++.+|...++..... .++--.++....+...++||+|++..++
T Consensus       258 i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~~L  306 (440)
T 2z4s_A          258 AKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAI  306 (440)
T ss_dssp             CBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            68888999999999977654 2332145444556668999999998765

>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=97.63  E-value=0.0005  Score=68.99  Aligned_cols=105  Identities=9%  Similarity=0.116  Sum_probs=61.8

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.+|.||++..+....               ......|+.++...  +.-+|++++... .+.     ++. + ... 
T Consensus       147 ~~~~vliIDEid~l~~~~---------------~~~l~~L~~~l~~~--~~~iIli~~~~~-~~~-----l~~-l-~~r-  200 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGD---------------RGGVGQLAQFCRKT--STPLILICNERN-LPK-----MRP-F-DRV-  200 (516)
T ss_dssp             TTSEEEEECSGGGCCTTS---------------TTHHHHHHHHHHHC--SSCEEEEESCTT-SST-----TGG-G-TTT-
T ss_pred             CCCeEEEEECCCccchhh---------------HHHHHHHHHHHHhc--CCCEEEEEcCCC-Ccc-----chh-h-Hhc-
Confidence            568899999997775431               12345566666532  222444433321 111     111 1 111 


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            ...+.++.++.+|...++..... .|+--.++....+...|+||++.+..++
T Consensus       201 ------~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          201 ------CLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             ------SEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHH
T ss_pred             ------eEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence                  12478899999999998866543 3442245555667778999999987764

>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=97.62  E-value=0.0015  Score=65.22  Aligned_cols=119  Identities=13%  Similarity=0.202  Sum_probs=68.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.+|++.++.....    ....   .....+...|+.++.+. -...++|.|++...   .    .++..+....
T Consensus       296 ~~p~iLfLDEId~l~~~~~----~~~~---~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~---~----~Ld~al~r~g  361 (489)
T 3hu3_A          296 NAPAIIFIDELDAIAPKRE----KTHG---EVERRIVSQLLTLMDGLKQRAHVIVMAATNRP---N----SIDPALRRFG  361 (489)
T ss_dssp             TCSEEEEEESHHHHCBCTT----SCCC---HHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG---G----GBCGGGGSTT
T ss_pred             cCCcEEEecchhhhccccc----cccc---hHHHHHHHHHHHHhhccccCCceEEEEecCCc---c----ccCHHHhCCC
Confidence            4588899999988876422    0000   11135666677777643 33445544444322   0    1223333322


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhh-CCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLT-KRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lS-gGNP~~l~~lc~  340 (342)
                      .|..     .+.++..+.+|-..+++.+...--+..+....++-..+ |.+++++..+|.
T Consensus       362 Rf~~-----~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~~  416 (489)
T 3hu3_A          362 RFDR-----EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (489)
T ss_dssp             SSCE-----EEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             cCce-----EEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHHH
Confidence            3422     37888899999999999887654443222334555444 558999998874

>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=97.55  E-value=0.00085  Score=62.55  Aligned_cols=103  Identities=8%  Similarity=0.024  Sum_probs=58.5

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .+-++.||++..+.+..                 ....|+.++.....+..+|+++.....        ++..+..+  +
T Consensus       105 ~~~vliiDEi~~l~~~~-----------------~~~~L~~~le~~~~~~~iI~~~n~~~~--------l~~~l~sR--~  157 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAE-----------------SQRHLRSFMEAYSSNCSIIITANNIDG--------IIKPLQSR--C  157 (324)
T ss_dssp             CEEEEEEESCCCGGGHH-----------------HHHHHHHHHHHHGGGCEEEEEESSGGG--------SCTTHHHH--S
T ss_pred             CCeEEEEECCcccCcHH-----------------HHHHHHHHHHhCCCCcEEEEEeCCccc--------cCHHHHhh--C
Confidence            57788999997664221                 234555555433345566776654321        22233333  1


Q ss_pred             CCCCCcceeecCCCCHHHHHH----HHHHH----HhCCCccCc-chHHHHHHhhCCCHHHHhhhc
Q psy3261         284 ESIDPFVPIHVPELNDEEFHN----LLNLY----ESKKWLQTS-EGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~----ll~yy----~~~~~l~~e-~~~~el~~lSgGNP~~l~~lc  339 (342)
                            ..++++.++.+|...    +++..    ...|+--++ +....+...++||.|++...+
T Consensus       158 ------~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L  216 (324)
T 3u61_B          158 ------RVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGEL  216 (324)
T ss_dssp             ------EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHH
T ss_pred             ------cEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHH
Confidence                  248999999998433    33332    233432145 545556678999999877654

>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=97.54  E-value=0.0016  Score=64.93  Aligned_cols=122  Identities=17%  Similarity=0.144  Sum_probs=65.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.||++.++.....    ....-.++....+...|+..+.+ .-+.+++|.+++....       .+...++...
T Consensus       107 ~~p~ILfIDEid~l~~~r~----~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~-------~Ld~allR~g  175 (476)
T 2ce7_A          107 HAPCIVFIDEIDAVGRHRG----AGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPD-------ILDPALLRPG  175 (476)
T ss_dssp             TCSEEEEEETGGGTCCC-------------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGG-------GSCGGGGSTT
T ss_pred             cCCCEEEEechhhhhhhcc----cccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChh-------hhchhhcccC
Confidence            3588999999988765421    00011122222333444443432 2234565555554321       1222344332


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCH-HHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVP-QKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP-~~l~~lc~  340 (342)
                      .|+.     .+.++..+.+|-..+++.+....-+..+.....+-..|.||. ++|..+|.
T Consensus       176 RFd~-----~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~  230 (476)
T 2ce7_A          176 RFDK-----KIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVN  230 (476)
T ss_dssp             SSCE-----EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             ccee-----EeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHH
Confidence            3432     377888888888899988876544422223445666787876 88988873

>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=97.50  E-value=0.0035  Score=56.27  Aligned_cols=122  Identities=13%  Similarity=0.122  Sum_probs=65.6

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|-++.+|++..+.....  .  ....-.......+..++..++| +-.+.+++.|++....       .++..++...
T Consensus       107 ~~~~i~~~Deid~l~~~~~--~--~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~-------~ld~~l~r~~  175 (254)
T 1ixz_A          107 HAPCIVFIDEIDAVGRKRG--S--GVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPD-------ILDPALLRPG  175 (254)
T ss_dssp             SSSEEEEEETHHHHHC-------------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGG-------GSCGGGGSTT
T ss_pred             cCCeEEEehhhhhhhcccC--c--cccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCch-------hCCHHHcCCC
Confidence            4678899999977654321  0  0000011112444555555554 4456666666665321       1223344332


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                      .|+.     .+.++..+.+|-..+++.+...--+..+.....+-..+.| +++++..+|.
T Consensus       176 rf~~-----~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~  230 (254)
T 1ixz_A          176 RFDR-----QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  230 (254)
T ss_dssp             SSCE-----EEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             cCCe-----EEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            3432     3778888899999999887653333222224445555655 5689988874

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.50  E-value=0.0061  Score=55.60  Aligned_cols=122  Identities=12%  Similarity=0.108  Sum_probs=66.0

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|-++.+|++..+.....  ..  ...-.......+..++..+++ .-.+.+++.|++....       .+...++...
T Consensus       131 ~~~~i~~iDeid~l~~~~~--~~--~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~-------~ld~~l~r~~  199 (278)
T 1iy2_A          131 HAPCIVFIDEIDAVGRKRG--SG--VGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPD-------ILDPALLRPG  199 (278)
T ss_dssp             SCSEEEEEETHHHHHCC------------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTT-------SSCHHHHSTT
T ss_pred             cCCcEEehhhhHhhhcccc--cc--cCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCch-------hCCHhHcCCC
Confidence            3578899999976654311  00  000011112344445555554 4455566666655321       1333444433


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCC-HHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRV-PQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGN-P~~l~~lc~  340 (342)
                      .|+.     .+.++..+.+|-..+++.+....-+..+.....+-..+.|| +++|..+|.
T Consensus       200 rf~~-----~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~  254 (278)
T 1iy2_A          200 RFDR-----QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  254 (278)
T ss_dssp             SSCC-----EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             cCCe-----EEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            3432     47888889999999999886543332222244455566665 488888774

>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=97.49  E-value=0.0037  Score=58.84  Aligned_cols=101  Identities=8%  Similarity=0.083  Sum_probs=61.8

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      +-++.||++..+-.                  ..-..|++++.....+..+|+++.....        +...+..+    
T Consensus       111 ~~viiiDe~~~l~~------------------~~~~~L~~~le~~~~~~~~il~~n~~~~--------i~~~i~sR----  160 (340)
T 1sxj_C          111 FKLIILDEADAMTN------------------AAQNALRRVIERYTKNTRFCVLANYAHK--------LTPALLSQ----  160 (340)
T ss_dssp             CEEEEETTGGGSCH------------------HHHHHHHHHHHHTTTTEEEEEEESCGGG--------SCHHHHTT----
T ss_pred             ceEEEEeCCCCCCH------------------HHHHHHHHHHhcCCCCeEEEEEecCccc--------cchhHHhh----
Confidence            56788999865421                  1234566666554456666766643210        11223222    


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                          ...+.+.+++.+|....+...... ++--+++....+..+|+|+++.+..++
T Consensus       161 ----~~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G~~r~~~~~l  212 (340)
T 1sxj_C          161 ----CTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVL  212 (340)
T ss_dssp             ----SEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHT
T ss_pred             ----ceeEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                124788999999999988777643 432145445557779999999876554

>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=97.47  E-value=0.005  Score=55.89  Aligned_cols=111  Identities=19%  Similarity=0.235  Sum_probs=61.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC--CCCeEEEEEeCCCCCCCCCccCcchh-HHhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD--WNNGAIVLALSPRANLPDRRESHLPL-YMLK  279 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~--~~~G~vv~AtS~~~~~~~~~~~~~p~-~llg  279 (342)
                      ..+.+|.+|++..+++... .. +      ...-.+.+.|..++.+.  ....++|.+++....       .++. .+.+
T Consensus       123 ~~~~vl~iDEid~l~~~~~-~~-~------~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~-------~l~~~~l~~  187 (272)
T 1d2n_A          123 SQLSCVVVDDIERLLDYVP-IG-P------RFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKD-------VLQEMEMLN  187 (272)
T ss_dssp             SSEEEEEECCHHHHTTCBT-TT-T------BCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHH-------HHHHTTCTT
T ss_pred             cCCcEEEEEChhhhhccCC-CC-h------hHHHHHHHHHHHHhcCccCCCCCEEEEEecCChh-------hcchhhhhc
Confidence            3578899999999876532 11 0      01124566777776642  234555555554220       0110 1111


Q ss_pred             hcCCCCCCCcceeecCCCCH-HHHHHHHHHHHhCCCccCcchHHHHHHhhCC-----CHHHHhhhc
Q psy3261         280 KAGFESIDPFVPIHVPELND-EEFHNLLNLYESKKWLQTSEGREEIAFLTKR-----VPQKMYEFC  339 (342)
Q Consensus       280 ~~g~~~~dP~~~i~v~~~s~-~E~~~ll~yy~~~~~l~~e~~~~el~~lSgG-----NP~~l~~lc  339 (342)
                        .|.     ..+.++.++. +++..++..   .+-+ +++....+...+.|     |.+++..++
T Consensus       188 --rf~-----~~i~~p~l~~r~~i~~i~~~---~~~~-~~~~~~~l~~~~~g~~~~g~ir~l~~~l  242 (272)
T 1d2n_A          188 --AFS-----TTIHVPNIATGEQLLEALEL---LGNF-KDKERTTIAQQVKGKKVWIGIKKLLMLI  242 (272)
T ss_dssp             --TSS-----EEEECCCEEEHHHHHHHHHH---HTCS-CHHHHHHHHHHHTTSEEEECHHHHHHHH
T ss_pred             --ccc-----eEEcCCCccHHHHHHHHHHh---cCCC-CHHHHHHHHHHhcCCCccccHHHHHHHH
Confidence              121     2478888887 676666654   2334 45545556667777     888877654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.41  E-value=0.002  Score=68.17  Aligned_cols=118  Identities=11%  Similarity=0.162  Sum_probs=69.3

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC-CCeEEEE-EeCCCCCCCCCccCcchhHHhhh
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW-NNGAIVL-ALSPRANLPDRRESHLPLYMLKK  280 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~-~~G~vv~-AtS~~~~~~~~~~~~~p~~llg~  280 (342)
                      ..|.+|.||++-+++....    ...   ...+-.++..|+..+.+-. +++++|. ||..-..        ++..+.+.
T Consensus       296 ~~PsIIfIDEiDal~~~r~----~~~---~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~--------LD~ALrR~  360 (806)
T 3cf2_A          296 NAPAIIFIDELDAIAPKRE----KTH---GEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNS--------IDPALRRF  360 (806)
T ss_dssp             SCSEEEEEESGGGTCCTTT----TCC---CTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTT--------SCTTTTST
T ss_pred             cCCeEEEEehhcccccccC----CCC---ChHHHHHHHHHHHHHhcccccCCEEEEEecCChhh--------cCHHHhCC
Confidence            4688999999988876522    011   1112356677777776532 3445544 4443322        22333332


Q ss_pred             cCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         281 AGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       281 ~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      ..|+.     .|+++.-+.++=..+++.+....-+..+....++-. ..|-.|.+|..+|.
T Consensus       361 GRFd~-----~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~  416 (806)
T 3cf2_A          361 GRFDR-----EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (806)
T ss_dssp             TSSCE-----EEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             cccce-----EEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHH
Confidence            23542     378888889999999998865443422223334444 55678999988884

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.30  E-value=0.017  Score=53.03  Aligned_cols=119  Identities=9%  Similarity=0.115  Sum_probs=65.4

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc-CCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ-SDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~-~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.++.+|++..+.....   ....   . ..-.+...++..++ ++-.+.+++.|++....       .+...+++..
T Consensus       102 ~~p~i~~~Deid~~~~~r~---~~~~---~-~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~-------~LD~al~r~g  167 (274)
T 2x8a_A          102 SAPCVIFFDEVDALCPRRS---DRET---G-ASVRVVNQLLTEMDGLEARQQVFIMAATNRPD-------IIDPAILRPG  167 (274)
T ss_dssp             TCSEEEEEETCTTTCC----------------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGG-------GSCHHHHSTT
T ss_pred             cCCCeEeeehhhhhhcccC---CCcc---h-HHHHHHHHHHHhhhcccccCCEEEEeecCChh-------hCCHhhcCcc
Confidence            4688999999987654311   1110   0 11244555555555 45566666666654321       1223444332


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCC---ccCcchHHHHHHh---hCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKW---LQTSEGREEIAFL---TKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~---l~~e~~~~el~~l---SgGNP~~l~~lc~  340 (342)
                      .|+.     .|.|+.-+.++-..+++.+...+-   +..+....++-..   .|-.+.+|..+|.
T Consensus       168 Rfd~-----~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~  227 (274)
T 2x8a_A          168 RLDK-----TLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVR  227 (274)
T ss_dssp             SSCE-----EEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHH
T ss_pred             cCCe-----EEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHH
Confidence            3542     377888889999999998875432   1112222334332   2788999998884

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.28  E-value=0.0053  Score=61.92  Aligned_cols=45  Identities=20%  Similarity=0.133  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         295 PELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       295 ~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+|+.+|+..++.-+.....-..++...++.-.++|+|..+.-++
T Consensus       284 ~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~a  328 (591)
T 1z6t_A          284 SSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIG  328 (591)
T ss_dssp             SSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCcHHHHHHH
Confidence            589999999999877654222124445678889999999887654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.27  E-value=0.007  Score=60.60  Aligned_cols=122  Identities=12%  Similarity=0.113  Sum_probs=65.9

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc-CCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ-SDWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~-~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|-++.+|++.++.....  ..  ...-+.........++..++ ++-..+++|.|++.....       +...++...
T Consensus       122 ~~p~il~IDEId~l~~~r~--~~--~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~-------LD~aLlr~g  190 (499)
T 2dhr_A          122 HAPCIVFIDEIDAVGRKRG--SG--VGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDI-------LDPALLRPG  190 (499)
T ss_dssp             SSSCEEEEECGGGTCCCSS--SS--TTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGG-------SCTTTSSTT
T ss_pred             cCCCEEEEehHHHHHHhhc--cC--cCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhh-------cCccccccc
Confidence            3577899999977754321  00  00001111234444554454 455566777776653211       222233222


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCH-HHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVP-QKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP-~~l~~lc~  340 (342)
                      .|+.     .+.|+..+.++-..++..+....-+..+.....+-..+.||- ++|..+|.
T Consensus       191 Rfdr-----~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~  245 (499)
T 2dhr_A          191 RFDR-----QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  245 (499)
T ss_dssp             SSCC-----EEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHH
T ss_pred             ccce-----EEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            2332     477888888999999988765332312222334555777765 89988873

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.18  E-value=0.00028  Score=60.12  Aligned_cols=35  Identities=20%  Similarity=0.197  Sum_probs=29.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVH  100 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~  100 (342)
                      +...++|+|++|||||+++..+...+. ..|..|++
T Consensus        37 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~   72 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYF   72 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEE
Confidence            467899999999999999999988876 67766555

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.12  E-value=0.0049  Score=65.55  Aligned_cols=95  Identities=13%  Similarity=0.106  Sum_probs=43.9

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++++...    ..|+++.||+++.+.+......          ...+...|+.++..  .+..+|+||+....   
T Consensus       251 l~~~~~~~~~~----~~~~iL~IDEi~~l~~~~~~~g----------~~~~~~~L~~~l~~--~~i~~I~at~~~~~---  311 (854)
T 1qvr_A          251 LKAVIQEVVQS----QGEVILFIDELHTVVGAGKAEG----------AVDAGNMLKPALAR--GELRLIGATTLDEY---  311 (854)
T ss_dssp             HHHHHHHHHTT----CSSEEEEECCC-----------------------------HHHHHT--TCCCEEEEECHHHH---
T ss_pred             HHHHHHHHHhc----CCCeEEEEecHHHHhccCCccc----------hHHHHHHHHHHHhC--CCeEEEEecCchHH---
Confidence            45566677652    4689999999988876533110          12233445555532  12346777654210   


Q ss_pred             CccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH
Q psy3261         268 RRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE  310 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~  310 (342)
                      +. ..+...+..        -|.++.|+.++.+|...+++.+.
T Consensus       312 ~~-~~~d~aL~r--------Rf~~i~l~~p~~~e~~~iL~~~~  345 (854)
T 1qvr_A          312 RE-IEKDPALER--------RFQPVYVDEPTVEETISILRGLK  345 (854)
T ss_dssp             HH-HTTCTTTCS--------CCCCEEECCCCHHHHHHHHHHHH
T ss_pred             hh-hccCHHHHh--------CCceEEeCCCCHHHHHHHHHhhh
Confidence            00 000011111        12348999999999999997544

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.98  E-value=0.0015  Score=54.67  Aligned_cols=44  Identities=27%  Similarity=0.277  Sum_probs=30.6

Q ss_pred             Eechh-HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          45 LIRNC-MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        45 lvR~~-t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      +-|+. ..++++.+..     .....++|+|++|||||+++.++......
T Consensus        25 ~g~~~~~~~l~~~l~~-----~~~~~~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           25 IGRDEEIRRTIQVLQR-----RTKNNPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             CSCHHHHHHHHHHHTS-----SSSCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHhc-----CCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            34553 3344444433     34567999999999999999888877655

>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=96.98  E-value=0.015  Score=58.58  Aligned_cols=49  Identities=18%  Similarity=0.184  Sum_probs=33.8

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc--CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ--TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~--~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +++|+.|+.+|+..++..+.-..-..  .++-..++.-.+||+|-.+.-+.
T Consensus       287 ~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g  337 (549)
T 2a5y_B          287 FIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFF  337 (549)
T ss_dssp             EEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             EEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHH
Confidence            48999999999999998774322210  11123457779999999887554

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.98  E-value=0.0013  Score=55.22  Aligned_cols=44  Identities=20%  Similarity=0.255  Sum_probs=30.6

Q ss_pred             Eechh-HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          45 LIRNC-MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        45 lvR~~-t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      +-|+. ..++++.+..     .....++|+|++|||||+++..+......
T Consensus        25 ~g~~~~~~~l~~~l~~-----~~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           25 IGRDTEIRRAIQILSR-----RTKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             CSCHHHHHHHHHHHTS-----SSSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             hcchHHHHHHHHHHhC-----CCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            34553 3344444433     44667899999999999999888777655

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.87  E-value=0.0018  Score=55.98  Aligned_cols=34  Identities=24%  Similarity=0.259  Sum_probs=27.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|+|++|||||+++..+...+..+|.-|+++
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~   88 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIV   88 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            7899999999999999888888777766555443

>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=96.80  E-value=0.0058  Score=64.61  Aligned_cols=132  Identities=11%  Similarity=0.148  Sum_probs=55.2

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLP  266 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~  266 (342)
                      +..++++-+.     ..|.+|.+|++-+++..-..-....    +...=.++..|+..+.|- -..+++|.|+|...   
T Consensus       559 vr~lF~~Ar~-----~~P~IifiDEiDsl~~~R~~~~~~~----~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p---  626 (806)
T 3cf2_A          559 VREIFDKARQ-----AAPCVLFFDELDSIAKARGGNIGDG----GGAADRVINQILTEMDGMSTKKNVFIIGATNRP---  626 (806)
T ss_dssp             HHHHHHHHHT-----TCSEEEECSCGGGCC------------------CHHHHHHHHHHHSSCSSSSEEEECC-CCS---
T ss_pred             HHHHHHHHHH-----cCCceeechhhhHHhhccCCCCCCC----chHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCc---
Confidence            3445555544     4689999999999986521010000    001114667777777653 34566666555432   


Q ss_pred             CCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         267 DRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       267 ~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      +    .+...+++.-.|+.     .|.|+.-+.++=..+++.+....-+..+....+|-- .-|-.+.++..+|.
T Consensus       627 ~----~lD~AllRpgRfd~-----~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~  692 (806)
T 3cf2_A          627 D----IIDPAILRPGRLDQ-----LIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  692 (806)
T ss_dssp             S----SSCHHHHSTTTSCC-----EEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHH
T ss_pred             h----hCCHhHcCCCcceE-----EEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHH
Confidence            1    13445665333543     356664455555566665554333321211222322 33456677777663

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.72  E-value=0.0018  Score=56.07  Aligned_cols=37  Identities=16%  Similarity=0.112  Sum_probs=30.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~  103 (342)
                      +.-++++|++|||||++|.+++..+...|.=|+.+ |.
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~   40 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPK   40 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeec
Confidence            44688999999999999999999888887766555 44

>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=96.69  E-value=0.048  Score=59.09  Aligned_cols=49  Identities=18%  Similarity=0.101  Sum_probs=35.3

Q ss_pred             eeecCC-CCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         291 PIHVPE-LNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       291 ~i~v~~-~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      .+.++. |+.+|+..++.-+....--..++...++--.++|.|-.+.-++
T Consensus       279 ~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~~~~  328 (1249)
T 3sfz_A          279 VVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIG  328 (1249)
T ss_dssp             CEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHHHHH
T ss_pred             EEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHHHHH
Confidence            378884 9999999999877643322133445678889999999887554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.54  E-value=0.0018  Score=54.02  Aligned_cols=48  Identities=29%  Similarity=0.223  Sum_probs=36.8

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ..+++..|+++     +...++|+|+.|||||+++.-+...+...|.-+++++
T Consensus        24 n~~~~~~l~~~-----~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~   71 (149)
T 2kjq_A           24 NAELVYVLRHK-----HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYID   71 (149)
T ss_dssp             THHHHHHCCCC-----CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             cHHHHHHHHhc-----CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEc
Confidence            33556666662     5778999999999999999999988877775555554

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.44  E-value=0.0026  Score=55.21  Aligned_cols=38  Identities=18%  Similarity=0.068  Sum_probs=31.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+...++|+|+.||||||++..+.......|++++++.
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d   60 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILD   60 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEec
Confidence            45678999999999999999998887777899876663

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.30  E-value=0.0032  Score=56.44  Aligned_cols=37  Identities=14%  Similarity=0.044  Sum_probs=32.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++.-++++|+.|+|||++|.|+++.+...|.-|+++
T Consensus        10 ~~G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~   46 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVF   46 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCcEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            3567889999999999999999999999888777766

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.22  E-value=0.0072  Score=56.51  Aligned_cols=36  Identities=22%  Similarity=0.325  Sum_probs=29.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~v  101 (342)
                      ....++|+|++|||||.++..+...+. ..|.-|+++
T Consensus       151 ~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~  187 (308)
T 2qgz_A          151 EQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLL  187 (308)
T ss_dssp             SCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEE
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEE
Confidence            367899999999999999988888887 777655554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.15  E-value=0.0037  Score=51.44  Aligned_cols=42  Identities=19%  Similarity=0.311  Sum_probs=28.2

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ...++.+.++. +.  .....++|+|++|||||++...+...+..
T Consensus         9 ~~~~~~~~~~~-~a--~~~~~vll~G~~GtGKt~lA~~i~~~~~~   50 (145)
T 3n70_A            9 WINQYRRRLQQ-LS--ETDIAVWLYGAPGTGRMTGARYLHQFGRN   50 (145)
T ss_dssp             HHHHHHHHHHH-HT--TCCSCEEEESSTTSSHHHHHHHHHHSSTT
T ss_pred             HHHHHHHHHHH-Hh--CCCCCEEEECCCCCCHHHHHHHHHHhCCc
Confidence            34456666665 22  34567999999999999877666554433

>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=96.00  E-value=0.0076  Score=50.64  Aligned_cols=34  Identities=21%  Similarity=0.196  Sum_probs=26.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...++|.|+.||||||++..+...-   |++++..
T Consensus         6 ~~g~~i~l~G~~GsGKSTl~~~l~~~~---g~~~i~~   39 (175)
T 1knq_A            6 HDHHIYVLMGVSGSGKSAVASEVAHQL---HAAFLDG   39 (175)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHH---TCEEEEG
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHhh---CcEEEeC
Confidence            345689999999999999988876532   8877653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.94  E-value=0.0069  Score=53.41  Aligned_cols=37  Identities=16%  Similarity=0.067  Sum_probs=31.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++.-++|.|++|||||+++.|++..+..+|.=|+|+
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~   57 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYV   57 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            4577899999999999999999988877777666666

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.93  E-value=0.008  Score=51.19  Aligned_cols=38  Identities=16%  Similarity=0.124  Sum_probs=30.3

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..+...++|.|..||||||+...+..+....|+-|.++
T Consensus        10 ~~~~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~   47 (186)
T 2yvu_A           10 IEKGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVL   47 (186)
T ss_dssp             CSCCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cCCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            34567899999999999999999988877777544444

>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=95.87  E-value=0.0061  Score=57.69  Aligned_cols=37  Identities=11%  Similarity=-0.001  Sum_probs=30.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP  102 (342)
                      .+. ++.|+|++|||||++++|+++.+.++  |-.|+||.
T Consensus        27 ~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId   65 (333)
T 3io5_A           27 QSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYD   65 (333)
T ss_dssp             CSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             cCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            445 79999999999999999999988765  66677773

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.84  E-value=0.0065  Score=52.88  Aligned_cols=37  Identities=16%  Similarity=0.159  Sum_probs=28.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++.-++|.|+.|||||+++.+++..+...+.=|+++
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~   57 (235)
T 2w0m_A           21 PQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYV   57 (235)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEE
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            4667899999999999999999997665444334443

>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=95.80  E-value=0.0069  Score=58.10  Aligned_cols=37  Identities=16%  Similarity=0.212  Sum_probs=32.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|+|++|||||+++.|++..+...|--|+||
T Consensus        59 ~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyI   95 (356)
T 3hr8_A           59 PRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFI   95 (356)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            4567889999999999999999999888777777777

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.75  E-value=0.0074  Score=53.26  Aligned_cols=37  Identities=22%  Similarity=0.179  Sum_probs=31.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH-HHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY-AHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~-A~~~gwiVl~v  101 (342)
                      .++.-++|.|++|+|||+++.|++.. |...|+-|+|+
T Consensus        28 ~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~   65 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFV   65 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceee
Confidence            46778999999999999999998765 55668878776

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=95.70  E-value=0.0088  Score=56.13  Aligned_cols=43  Identities=14%  Similarity=0.191  Sum_probs=35.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcccccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWFA  109 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~~  109 (342)
                      .++..+.|.|+.||||||+|.-+.-..  .|-|+.++|.-..+..
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~--~G~I~~~v~q~~~lf~  166 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL--GGSVLSFANHKSHFWL  166 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH--TCEEECGGGTTSGGGG
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc--CceEEEEecCcccccc
Confidence            678899999999999999999888776  8999998876544433

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.67  E-value=0.011  Score=51.00  Aligned_cols=33  Identities=18%  Similarity=0.253  Sum_probs=26.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .+...++|.|+.||||||++..+....   |++++.
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~---g~~~i~   59 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET---GLEFAE   59 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH---CCEEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh---CCeEEc
Confidence            456789999999999999998876543   887765

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.66  E-value=0.012  Score=55.06  Aligned_cols=38  Identities=8%  Similarity=0.090  Sum_probs=32.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-++|.|++|+|||+++.|+...+..+|.-|+|+.
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            46778999999999999999999988887887777763

>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=95.65  E-value=0.0084  Score=49.52  Aligned_cols=29  Identities=21%  Similarity=0.236  Sum_probs=23.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -++|.|++||||||+...+    ...||.++.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L----~~~g~~~i~~   31 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL----KERGAKVIVM   31 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH----HHTTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH----HHCCCcEEEH
Confidence            5889999999999988877    5668877764

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=95.59  E-value=0.011  Score=53.33  Aligned_cols=50  Identities=14%  Similarity=0.240  Sum_probs=30.8

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++++.++..+   .....++|+|++|||||+++..+.......+.-+++|
T Consensus        14 ~~~~~~~~~~~~~---~~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v   63 (265)
T 2bjv_A           14 SFLEVLEQVSHLA---PLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISL   63 (265)
T ss_dssp             HHHHHHHHHHHHT---TSCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEE
T ss_pred             HHHHHHHHHHHHh---CCCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEE
Confidence            3344555665522   2347899999999999977666655544444333444

>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=95.59  E-value=0.011  Score=56.52  Aligned_cols=38  Identities=18%  Similarity=0.245  Sum_probs=33.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|||||+++.|++..+...|--|+||.
T Consensus        59 ~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~   96 (349)
T 2zr9_A           59 PRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFID   96 (349)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            46778999999999999999999998888887777774

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.58  E-value=0.01  Score=52.78  Aligned_cols=40  Identities=23%  Similarity=0.301  Sum_probs=27.6

Q ss_pred             HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          51 LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        51 ~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+.+..|+.+....++.+.++++||+|||||++...++..
T Consensus        42 ~~f~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           42 ITFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             HHHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHH
Confidence            3445555554433445667999999999999987666554

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.50  E-value=0.011  Score=49.88  Aligned_cols=34  Identities=24%  Similarity=0.143  Sum_probs=27.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++|.|.+||||||+...+.......|.-+.++|
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~~   36 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEEE
Confidence            5899999999999999998887666676566664

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=95.48  E-value=0.32  Score=52.96  Aligned_cols=42  Identities=24%  Similarity=0.239  Sum_probs=29.8

Q ss_pred             Eech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          45 LIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        45 lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +-|+ ...+|.+.|.. .   ....-+.|+|+.|+|||++..++.+.
T Consensus       131 VGRe~eLeeL~elL~~-~---d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLE-L---RPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCHHHHHHHHHHHHH-C---CSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHhc-c---CCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            5676 44455556654 2   23567899999999999999888653

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=95.43  E-value=0.46  Score=48.19  Aligned_cols=68  Identities=24%  Similarity=0.169  Sum_probs=41.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC---CeEEEEe--CCccccccCCcceeccCCCCCccccHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN---NYLLVHI--PWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHF  137 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~---gwiVl~v--P~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~  137 (342)
                      ...+++.|.+|||||++|..++......   +-+-+++  |....+.....  .|.- -......|..+...|+.+
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpKg~eLs~~~~--lPHl-~~~Vvtd~~~a~~~L~~l  286 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPKMLELSIYEG--IPHL-LCPVVTDMKEAANALRWS  286 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSSSHHHHTTTT--CTTB-SSSCBCCHHHHHHHHHHH
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCChhhhHhhcC--CCcc-cceeeCCHHHHHHHHHHH
Confidence            5789999999999999999987754432   3343443  44433322110  0110 112356688888888776

>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=95.41  E-value=0.012  Score=53.36  Aligned_cols=36  Identities=25%  Similarity=0.202  Sum_probs=30.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ...++|.|.+||||||+...+..+....||.++++.
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~   39 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLG   39 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEEC
Confidence            356899999999999999998888777899888663

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.41  E-value=0.013  Score=48.95  Aligned_cols=32  Identities=16%  Similarity=0.110  Sum_probs=25.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|.|++||||||+...+...  ..||.++..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~--~~~~~~i~~   34 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAK--NPGFYNINR   34 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH--STTEEEECH
T ss_pred             eEEEEecCCCCCHHHHHHHHHhh--cCCcEEecH
Confidence            35889999999999998887662  568877764

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=95.36  E-value=0.015  Score=53.32  Aligned_cols=37  Identities=14%  Similarity=0.004  Sum_probs=30.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      .++.-++|.|++|||||+++.++....... |+=|+++
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~   70 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLA   70 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            567889999999999999999999877654 8655555

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.31  E-value=0.016  Score=49.00  Aligned_cols=36  Identities=17%  Similarity=0.113  Sum_probs=29.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++..++|+|..||||||++..+..+-...|+-++.+
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~   39 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTL   39 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEE
Confidence            456789999999999999998888766678655555

>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=95.30  E-value=0.019  Score=48.51  Aligned_cols=29  Identities=21%  Similarity=0.312  Sum_probs=23.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      +..++|.|+.||||||+...+....-.+|
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~~~g   31 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLRKEG   31 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHTTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            45799999999999999988887655554

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=95.29  E-value=0.016  Score=48.31  Aligned_cols=30  Identities=27%  Similarity=0.204  Sum_probs=22.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ...++|+|+.||||||++..+..   ..|+.++
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~---~l~~~~i   33 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQ---QLNMEFY   33 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHH---HTTCEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH---HhCCCEE
Confidence            35799999999999999877644   3455444

>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=95.29  E-value=0.0091  Score=50.75  Aligned_cols=35  Identities=20%  Similarity=0.128  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .++..++|.|+.||||||++..+... ...|.+.+.
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~~La~~-~~~g~i~i~   41 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAEALANL-PGVPKVHFH   41 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHHHTC-SSSCEEEEC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHhc-cCCCeEEEc
Confidence            34668999999999999999888664 344655443

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=95.28  E-value=0.015  Score=50.31  Aligned_cols=34  Identities=15%  Similarity=0.128  Sum_probs=27.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|.|+.|||||+++.+++.   ..|--|+|+
T Consensus        18 ~~G~~~~i~G~~GsGKTtl~~~l~~---~~~~~v~~i   51 (220)
T 2cvh_A           18 APGVLTQVYGPYASGKTTLALQTGL---LSGKKVAYV   51 (220)
T ss_dssp             CTTSEEEEECSTTSSHHHHHHHHHH---HHCSEEEEE
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHH---HcCCcEEEE
Confidence            5677899999999999999999988   445555555

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=95.27  E-value=0.011  Score=60.87  Aligned_cols=34  Identities=18%  Similarity=0.243  Sum_probs=29.2

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .-.+|.||+|||||+++.+++.+...+|+=|+-+
T Consensus       206 ~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~  239 (646)
T 4b3f_X          206 ELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCC  239 (646)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            3579999999999999999999999887765544

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.24  E-value=0.016  Score=49.06  Aligned_cols=33  Identities=18%  Similarity=0.327  Sum_probs=28.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++|+|..||||||+...+.......|+-|+..
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~   34 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLY   34 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            478999999999999999888776778877765

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.23  E-value=0.033  Score=48.18  Aligned_cols=45  Identities=13%  Similarity=-0.054  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCe
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNY   96 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gw   96 (342)
                      ..+|++.+.+ . ...+...+.|+|+.||||||++..+.......|.
T Consensus         7 ~~~l~~~~~~-~-~~~~~~~i~i~G~~GsGKstl~~~l~~~~~~~~~   51 (201)
T 1rz3_A            7 IDFLCKTILA-I-KTAGRLVLGIDGLSRSGKTTLANQLSQTLREQGI   51 (201)
T ss_dssp             HHHHHHHHHT-S-CCSSSEEEEEEECTTSSHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHH-h-ccCCCeEEEEECCCCCCHHHHHHHHHHHHhhcCC
Confidence            3446666654 2 2244567999999999999999988877655444

>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=95.15  E-value=0.019  Score=51.47  Aligned_cols=34  Identities=21%  Similarity=0.432  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..+++|.|++||||||+...+...   .|+.++.+
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~---~g~~~is~   60 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKS---HCYCHLST   60 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH---hCCeEEec
Confidence            45678999999999999988887643   27777765

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.10  E-value=0.02  Score=52.92  Aligned_cols=27  Identities=19%  Similarity=0.304  Sum_probs=20.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++...++|+|++|||||++...+...+
T Consensus        34 ~~p~~lLl~GppGtGKT~la~aiA~~l   60 (293)
T 3t15_A           34 KVPLILGIWGGKGQGKSFQCELVFRKM   60 (293)
T ss_dssp             CCCSEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            445789999999999998766554443

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=95.06  E-value=0.025  Score=49.28  Aligned_cols=37  Identities=19%  Similarity=0.070  Sum_probs=31.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++.-++++|+.|+|||++|.++++.+...|.-|+-+
T Consensus         6 ~~g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~   42 (191)
T 1xx6_A            6 DHGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVF   42 (191)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            3456789999999999999999999998887766655

>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=95.04  E-value=0.039  Score=54.18  Aligned_cols=35  Identities=11%  Similarity=0.272  Sum_probs=29.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCe--EEEEeCC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNY--LLVHIPW  103 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gw--iVl~vP~  103 (342)
                      .++|.|++|||||+++.+++.+....|.  |++.-|.
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T   83 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALISTGETGIILAAPT   83 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCc
Confidence            8999999999999999999999988775  4444354

>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=94.98  E-value=0.027  Score=51.80  Aligned_cols=38  Identities=11%  Similarity=0.038  Sum_probs=27.1

Q ss_pred             HHHHHHHhccCCC-CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          52 ELVGYLKSMTNFD-RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        52 el~~~l~~~~~~~-~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+|.++.... ++.+.++|+||+|||||++..-++.
T Consensus        88 ~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           88 YAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            3444555555544 5567899999999999998775544

>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=94.96  E-value=0.022  Score=54.48  Aligned_cols=38  Identities=16%  Similarity=0.186  Sum_probs=33.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|||||++..|++..+..+|--|+||.
T Consensus        61 ~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid   98 (356)
T 1u94_A           61 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   98 (356)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            46678999999999999999999998888877777774

>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=94.96  E-value=0.013  Score=50.21  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=20.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++.|.|+.||||||+|.-+.-.-
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999998887664

>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=94.96  E-value=0.02  Score=48.56  Aligned_cols=33  Identities=12%  Similarity=0.069  Sum_probs=25.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|.+||||||+...+...-   ||.++..
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l---~~~~i~~   36 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGL---RLPLLSK   36 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH---TCCEEEH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc---CCeEecH
Confidence            34578999999999999988776532   7776664

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.88  E-value=0.02  Score=49.12  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=21.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ++.-+.|.|+.||||||++..+...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhh
Confidence            4567899999999999999988765

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=94.86  E-value=0.029  Score=55.23  Aligned_cols=38  Identities=8%  Similarity=0.090  Sum_probs=33.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-++|.|++|+|||+++.|++..+..+|.=|+|+.
T Consensus       195 ~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            46778999999999999999999998888898888884

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=94.79  E-value=0.029  Score=48.82  Aligned_cols=32  Identities=19%  Similarity=0.074  Sum_probs=26.0

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ..+...+.|.|+.||||||++..+...-...|
T Consensus        19 ~~~g~~v~I~G~sGsGKSTl~~~l~~~~~~~g   50 (208)
T 3c8u_A           19 QPGRQLVALSGAPGSGKSTLSNPLAAALSAQG   50 (208)
T ss_dssp             CCSCEEEEEECCTTSCTHHHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhhcC
Confidence            35677889999999999999998887766434

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=94.79  E-value=0.025  Score=49.66  Aligned_cols=37  Identities=22%  Similarity=0.178  Sum_probs=32.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..+.-++++|+-|||||+.|.|+++.+...|-=|+++
T Consensus        18 ~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~   54 (195)
T 1w4r_A           18 TRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVI   54 (195)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEE
Confidence            3466889999999999999999999999888777777

>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=94.78  E-value=0.028  Score=49.40  Aligned_cols=28  Identities=14%  Similarity=0.142  Sum_probs=24.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+..-++|.|+.|||||+++.+++..+.
T Consensus        22 ~~G~~~~i~G~~GsGKTtl~~~l~~~~~   49 (243)
T 1n0w_A           22 ETGSITEMFGEFRTGKTQICHTLAVTCQ   49 (243)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHHHHHh
Confidence            4678899999999999999999988654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.77  E-value=0.021  Score=48.55  Aligned_cols=25  Identities=28%  Similarity=0.386  Sum_probs=21.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ++.-++|.|+.||||||++..+...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            3567899999999999999998775

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.75  E-value=0.033  Score=52.94  Aligned_cols=38  Identities=8%  Similarity=0.110  Sum_probs=33.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++.-++|.|++|+|||+++.|+...+..+|.-|+|+.
T Consensus        44 ~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fS   81 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFS   81 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            46778999999999999999999998888998888873

>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=94.71  E-value=0.029  Score=47.72  Aligned_cols=30  Identities=23%  Similarity=0.350  Sum_probs=22.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      -++|.|+.||||||++..+..  ...|.+.+.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~--~~~g~~~i~   33 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAA--QLDNSAYIE   33 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH--HSSSEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhc--ccCCeEEEc
Confidence            478999999999999998854  344555544

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.71  E-value=0.017  Score=50.18  Aligned_cols=26  Identities=35%  Similarity=0.330  Sum_probs=21.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      +...++|.|+.||||||++..+....
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            46789999999999999999988754

>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=94.70  E-value=0.033  Score=47.38  Aligned_cols=34  Identities=12%  Similarity=0.222  Sum_probs=26.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|+|..|||||++...+....  .||.++..
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~l--~g~~~id~   42 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAEL--DGFQHLEV   42 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHS--TTEEEEEH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhc--CCCEEeeH
Confidence            45689999999999999887664421  58877764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.68  E-value=0.029  Score=48.32  Aligned_cols=32  Identities=22%  Similarity=0.229  Sum_probs=25.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|.|+.||||||+...+...-   |+.++..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l---g~~~i~~   49 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC---GYPFIEG   49 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH---TCCEEEG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh---CCEEEeC
Confidence            4579999999999999888765542   7776654

>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=94.60  E-value=0.025  Score=48.63  Aligned_cols=31  Identities=23%  Similarity=0.178  Sum_probs=25.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      ++.|+|+.||||||++..+..    .|+.+++...
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~----~g~~~i~~d~   33 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE----LGAYVLDADK   33 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH----TTCEEEEHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH----CCCEEEEccH
Confidence            689999999999999888765    3888887643

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.59  E-value=0.03  Score=48.22  Aligned_cols=33  Identities=21%  Similarity=0.168  Sum_probs=24.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .+...++|.|++||||||+...+....   ||.++.
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~~La~~l---~~~~i~   55 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGKAFARKL---NVPFID   55 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH---TCCEEE
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHc---CCCEEc
Confidence            356789999999999999988776543   554443

>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=94.59  E-value=0.031  Score=53.69  Aligned_cols=38  Identities=16%  Similarity=0.123  Sum_probs=32.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|||||+++.|++..+..+|--|+||.
T Consensus        72 ~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~  109 (366)
T 1xp8_A           72 PRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID  109 (366)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEE
Confidence            45678999999999999999999998888777777774

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=94.57  E-value=0.031  Score=50.87  Aligned_cols=28  Identities=21%  Similarity=0.096  Sum_probs=24.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .++.-++|.|+.|||||+++.|+...+.
T Consensus        28 ~~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           28 VAGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            3577899999999999999999998554

>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=94.57  E-value=0.036  Score=47.42  Aligned_cols=35  Identities=11%  Similarity=0.097  Sum_probs=29.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -..+.|.|..||||||++..++.+....|+=|-.|
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~i   38 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTV   38 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEE
Confidence            45788999999999999999999888888755444

>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=94.54  E-value=0.03  Score=48.62  Aligned_cols=28  Identities=18%  Similarity=0.220  Sum_probs=24.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+..-+.|.|+.||||||++.++.....
T Consensus        23 ~~G~~~~l~G~nGsGKSTll~~l~g~~~   50 (231)
T 4a74_A           23 ETQAITEVFGEFGSGKTQLAHTLAVMVQ   50 (231)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4677899999999999999999987544

>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=94.51  E-value=0.033  Score=52.21  Aligned_cols=37  Identities=19%  Similarity=0.106  Sum_probs=29.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC------CeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN------NYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~------gwiVl~v  101 (342)
                      .+..-++|+|++|||||+++.|++..+...      |.-|+||
T Consensus       105 ~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi  147 (324)
T 2z43_A          105 ETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYI  147 (324)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEE
T ss_pred             CCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEE
Confidence            356789999999999999999999876544      5566666

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=94.50  E-value=0.024  Score=52.71  Aligned_cols=44  Identities=14%  Similarity=0.275  Sum_probs=29.2

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ...++.+.++..+   .....++|+|++|||||++...+.......+
T Consensus        10 ~~~~~~~~~~~~a---~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~   53 (304)
T 1ojl_A           10 AMQHLLNEIAMVA---PSDATVLIHGDSGTGKELVARALHACSARSD   53 (304)
T ss_dssp             HHHHHHHHHHHHC---STTSCEEEESCTTSCHHHHHHHHHHHSSCSS
T ss_pred             HHHHHHHHHHHHh---CCCCcEEEECCCCchHHHHHHHHHHhCcccC
Confidence            3445666666622   3467899999999999987666655543333

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=94.48  E-value=0.044  Score=50.57  Aligned_cols=35  Identities=20%  Similarity=0.376  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ....-++|.|++||||||+...+.... ..+|++|.
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~~~-~~~~~~Is   65 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFEET-QGNVIVID   65 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHT-TTCCEEEC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh-CCCeEEEe
Confidence            345679999999999999988776532 24676664

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=94.48  E-value=0.027  Score=48.91  Aligned_cols=30  Identities=20%  Similarity=0.235  Sum_probs=23.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|+|++||||||+...+...   .|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~---~~~~~i~~   31 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEK---YEIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH---HCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCcEeeH
Confidence            6899999999999988877443   36666654

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.48  E-value=0.017  Score=47.39  Aligned_cols=34  Identities=18%  Similarity=0.199  Sum_probs=22.8

Q ss_pred             HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHH
Q psy3261          51 LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        51 ~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      .++.+.++.++   .....++|+|++|||||++...+
T Consensus        14 ~~l~~~~~~~~---~~~~~vll~G~~GtGKt~lA~~i   47 (143)
T 3co5_A           14 QEMNREVEAAA---KRTSPVFLTGEAGSPFETVARYF   47 (143)
T ss_dssp             HHHHHHHHHHH---TCSSCEEEEEETTCCHHHHHGGG
T ss_pred             HHHHHHHHHHh---CCCCcEEEECCCCccHHHHHHHH
Confidence            34555555422   23567999999999999765443

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=94.45  E-value=0.048  Score=52.11  Aligned_cols=39  Identities=26%  Similarity=0.338  Sum_probs=30.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeCCc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIPWV  104 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP~~  104 (342)
                      +...++|.|+.||||||+|.-++.+.... +-.|+.+-+.
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~  161 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDP  161 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCc
Confidence            45589999999999999999988876643 6666666433

>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=94.41  E-value=0.026  Score=48.24  Aligned_cols=32  Identities=19%  Similarity=0.291  Sum_probs=25.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+.|+|+.||||||+...+...    |+.++..
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~~----g~~~id~   38 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRSW----GYPVLDL   38 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHT----TCCEEEH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHC----CCEEEcc
Confidence            4567899999999999998877653    8777754

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.41  E-value=0.042  Score=46.56  Aligned_cols=33  Identities=18%  Similarity=0.202  Sum_probs=25.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|+.||||||+...+...   .||.++..
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~---l~~~~i~~   40 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQK---YGYTHLST   40 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH---hCCeEEcH
Confidence            4678999999999999988777543   37766554

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=94.38  E-value=0.037  Score=49.73  Aligned_cols=33  Identities=21%  Similarity=0.263  Sum_probs=28.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ..++++.|+.|||||++..++.+.+.++|.=|+
T Consensus         6 ~l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~   38 (228)
T 2r8r_A            6 RLKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVM   38 (228)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCCCEE
Confidence            467999999999999999999999888886443

>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=94.36  E-value=0.044  Score=47.83  Aligned_cols=34  Identities=24%  Similarity=0.187  Sum_probs=25.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++...++|.|.+||||||+...+..+   .|+.++..
T Consensus         2 ~~~~~I~l~G~~GsGKsT~a~~La~~---l~~~~i~~   35 (220)
T 1aky_A            2 SESIRMVLIGPPGAGKGTQAPNLQER---FHAAHLAT   35 (220)
T ss_dssp             -CCCEEEEECCTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH---cCceEEeh
Confidence            45678999999999999988777543   36665554

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=94.35  E-value=0.031  Score=51.18  Aligned_cols=30  Identities=23%  Similarity=0.359  Sum_probs=23.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      +...++|+|++|||||++...+.......+
T Consensus        46 ~~~~~ll~G~~GtGKt~la~~la~~~~~~~   75 (311)
T 4fcw_A           46 PIGSFLFLGPTGVGKTELAKTLAATLFDTE   75 (311)
T ss_dssp             CSEEEEEESCSSSSHHHHHHHHHHHHHSCG
T ss_pred             CceEEEEECCCCcCHHHHHHHHHHHHcCCC
Confidence            345799999999999998887777665443

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=94.35  E-value=0.033  Score=46.96  Aligned_cols=30  Identities=17%  Similarity=0.220  Sum_probs=23.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      +..++|.|++||||||+...+...   .|+.++
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~---l~~~~i   33 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQE---LGFKKL   33 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHH---HTCEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH---hCCeEe
Confidence            457999999999999998877543   266544

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.27  E-value=0.03  Score=47.98  Aligned_cols=26  Identities=27%  Similarity=0.285  Sum_probs=22.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++..++|.|+.||||||++..+....
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            46689999999999999998887653

>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=94.27  E-value=0.027  Score=48.93  Aligned_cols=30  Identities=20%  Similarity=0.230  Sum_probs=23.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|+|++||||||+...+..   ..|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~---~~~~~~i~~   31 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE---KYGIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH---HSSCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCcEEeH
Confidence            689999999999998877643   457777765

>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=94.24  E-value=0.028  Score=46.56  Aligned_cols=30  Identities=17%  Similarity=0.058  Sum_probs=22.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++|.|+.||||||+...+...   .||.++..
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~---l~~~~i~~   32 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKE---LKYPIIKG   32 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHH---HCCCEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCeeecC
Confidence            5899999999999998876543   25544433

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.23  E-value=0.021  Score=48.23  Aligned_cols=21  Identities=33%  Similarity=0.298  Sum_probs=18.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVY   86 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q   86 (342)
                      ++.-+.|.|+.||||||++..
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            456789999999999999997

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.17  E-value=0.026  Score=48.95  Aligned_cols=28  Identities=25%  Similarity=0.323  Sum_probs=24.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      .++.|.|+.||||||++.-+..+...+|
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~~~~G   29 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVLKSSG   29 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCChHHHHHHHHHhhcccCC
Confidence            3688999999999999999998777778

>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=94.14  E-value=0.022  Score=49.20  Aligned_cols=34  Identities=12%  Similarity=0.091  Sum_probs=28.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      -++|.|+.||||||++..+..+....|+-|..+.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~~g~~v~~~~   35 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHEEEEEEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            4789999999999999999888777787776553

>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=94.13  E-value=0.049  Score=45.85  Aligned_cols=33  Identities=21%  Similarity=0.274  Sum_probs=24.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|+|.+|||||++...+....   |+.++..
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~~~~---~~~~~~~   42 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELASKS---GLKYINV   42 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHH---CCEEEEH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHh---CCeEEEH
Confidence            35679999999999999888765442   5555443

>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=94.10  E-value=0.055  Score=46.55  Aligned_cols=34  Identities=18%  Similarity=0.029  Sum_probs=27.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ++..++|+|..||||||+...+.......+.-|.
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~~~~~v~   41 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAE   41 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHcCCcEE
Confidence            4678999999999999999998876555555443

>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=94.09  E-value=0.029  Score=48.38  Aligned_cols=29  Identities=24%  Similarity=0.123  Sum_probs=23.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+.|+|+.||||||+...+..    .|+.++.-
T Consensus         4 ~i~l~G~~GsGKST~~~~La~----lg~~~id~   32 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD----LGVPLVDA   32 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT----TTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH----CCCcccch
Confidence            578999999999999888754    58777654

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.09  E-value=0.044  Score=53.81  Aligned_cols=37  Identities=16%  Similarity=0.115  Sum_probs=31.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~v  101 (342)
                      .++.-++|.|++|+|||+++.|+...+.. +|.-|+|+
T Consensus       201 ~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~  238 (454)
T 2r6a_A          201 QRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIF  238 (454)
T ss_dssp             CTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEE
Confidence            36778999999999999999999987764 67766666

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.08  E-value=0.053  Score=49.38  Aligned_cols=35  Identities=20%  Similarity=0.382  Sum_probs=28.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-h-CCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-E-NNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~-~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+..+-. . .|-|++
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~   59 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIIT   59 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEE
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEE
Confidence            5677899999999999999999887654 3 576654

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.06  E-value=0.049  Score=45.93  Aligned_cols=32  Identities=16%  Similarity=0.217  Sum_probs=23.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|.|.+||||||+...+...   .|+.++..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~---~~~~~i~~   34 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEK---YGYTHLSA   34 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH---hCCeEEeH
Confidence            356899999999999988776543   36766543

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=94.05  E-value=0.045  Score=55.62  Aligned_cols=38  Identities=24%  Similarity=0.126  Sum_probs=32.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~~  104 (342)
                      ...++|+|++|||||+++..++..+...|.-|+.+ |..
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~  242 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTG  242 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcH
Confidence            56899999999999999999999988888766665 543

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.05  E-value=0.074  Score=50.46  Aligned_cols=34  Identities=26%  Similarity=0.160  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      ....+++|.|.+|+|||+++.++.......|.=|
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV  110 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGMHLIERGHRV  110 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCE
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHhCCCce
Confidence            4577899999999999999999988776655433

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.04  E-value=0.028  Score=48.57  Aligned_cols=26  Identities=12%  Similarity=-0.020  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+...+.|+|+.||||||++..+...
T Consensus         4 ~~~~~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            4 PKPFVIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             -CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            45667899999999999999887764

>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=93.99  E-value=0.05  Score=51.49  Aligned_cols=25  Identities=20%  Similarity=0.317  Sum_probs=19.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +...++|+|++|||||++...+...
T Consensus        50 ~~~~vll~GppGtGKT~la~~ia~~   74 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETLARL   74 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            5678999999999999965555443

>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=93.93  E-value=0.047  Score=51.64  Aligned_cols=37  Identities=16%  Similarity=0.067  Sum_probs=29.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh------CCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE------NNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~------~gwiVl~v  101 (342)
                      .+..-++|+|++|||||+++.|++..+..      .|--|+||
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi  162 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFI  162 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEE
Confidence            35667899999999999999999988654      35556666

>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=93.93  E-value=0.04  Score=47.99  Aligned_cols=30  Identities=17%  Similarity=0.273  Sum_probs=23.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|.|++||||||....+...-   |+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~---g~~~i~~   31 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY---GIPQIST   31 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH---CCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCeEEeH
Confidence            68999999999999888776532   6666554

>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=93.93  E-value=0.04  Score=48.00  Aligned_cols=26  Identities=27%  Similarity=0.284  Sum_probs=22.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++.-++|.|+.||||||++..+...
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhh
Confidence            35677999999999999999888654

>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=93.93  E-value=0.056  Score=46.27  Aligned_cols=33  Identities=15%  Similarity=0.070  Sum_probs=27.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      -..++|.|+.|||||+++..++......|.-|-
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~~g~~v~   38 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCARGIRPG   38 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHTTCCEE
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccccCCcee
Confidence            467899999999999999999988666665443

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=93.91  E-value=0.046  Score=47.79  Aligned_cols=33  Identities=15%  Similarity=0.217  Sum_probs=25.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|.+||||||....+..+-   |+.++..
T Consensus         4 ~~~~I~l~G~~GsGKsT~a~~La~~l---~~~~i~~   36 (217)
T 3be4_A            4 KKHNLILIGAPGSGKGTQCEFIKKEY---GLAHLST   36 (217)
T ss_dssp             GCCEEEEEECTTSSHHHHHHHHHHHH---CCEEEEH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHh---CceEEeh
Confidence            45689999999999999877765542   6766654

>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=93.88  E-value=0.056  Score=46.41  Aligned_cols=33  Identities=21%  Similarity=0.223  Sum_probs=24.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ....++|.|.+||||||+...+..+   .|+.++.+
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~---l~~~~i~~   51 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEK---LGIPQIST   51 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH---HTCCEEEH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH---hCCcEEeh
Confidence            4568999999999999987777553   26665554

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=93.87  E-value=0.062  Score=48.28  Aligned_cols=35  Identities=17%  Similarity=0.291  Sum_probs=24.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .....++|.|++||||||+...+.... ..+++++.
T Consensus        30 ~~~~~i~l~G~~GsGKSTla~~L~~~l-~~~~~~~~   64 (253)
T 2p5t_B           30 KQPIAILLGGQSGAGKTTIHRIKQKEF-QGNIVIID   64 (253)
T ss_dssp             SSCEEEEEESCGGGTTHHHHHHHHHHT-TTCCEEEC
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHhc-CCCcEEEe
Confidence            345689999999999999887776542 23455543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=93.87  E-value=0.052  Score=45.76  Aligned_cols=32  Identities=19%  Similarity=0.174  Sum_probs=23.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|.|+.||||||+...+...   -||.++..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~---l~~~~i~~   36 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKL---TKRILYDS   36 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH---HCCCEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH---hCCCEEEC
Confidence            467999999999999988776543   36655543

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=93.86  E-value=0.072  Score=45.76  Aligned_cols=31  Identities=26%  Similarity=0.324  Sum_probs=25.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      .++..++|+|..||||||+...+..+....+
T Consensus         8 ~~~~~I~l~G~~GsGKST~~~~L~~~l~~~~   38 (212)
T 2wwf_A            8 KKGKFIVFEGLDRSGKSTQSKLLVEYLKNNN   38 (212)
T ss_dssp             BCSCEEEEEESTTSSHHHHHHHHHHHHHHTT
T ss_pred             hcCCEEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            3467899999999999999998887654444

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.85  E-value=0.046  Score=48.03  Aligned_cols=33  Identities=18%  Similarity=0.112  Sum_probs=25.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|++||||||+...+..   ..|+.++..
T Consensus         6 ~~~~I~l~G~~GsGKsT~a~~La~---~l~~~~i~~   38 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVSSRITT---HFELKHLSS   38 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHHHHHHH---HSSSEEEEH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHH---HcCCeEEec
Confidence            356899999999999998877754   347776654

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=93.84  E-value=0.043  Score=46.05  Aligned_cols=21  Identities=29%  Similarity=0.270  Sum_probs=18.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++|.|++||||||+...+..
T Consensus         6 ~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            689999999999998777643

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=93.84  E-value=0.049  Score=46.67  Aligned_cols=29  Identities=17%  Similarity=0.180  Sum_probs=23.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      +..++|.|..||||||+...+.......|
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~~~g   32 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIELKR   32 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHTTTS
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhhcC
Confidence            45789999999999999999887654444

>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=93.83  E-value=0.026  Score=52.80  Aligned_cols=34  Identities=24%  Similarity=0.237  Sum_probs=26.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      -.-++|+|+.||||||+|.++........|.|+.
T Consensus         4 i~v~~i~G~~GaGKTTll~~l~~~~~~~~~aVi~   37 (318)
T 1nij_A            4 IAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIE   37 (318)
T ss_dssp             EEEEEEEESSSSSCHHHHHHHHHSCCCCCEEEEC
T ss_pred             ccEEEEEecCCCCHHHHHHHHHhhcCCCcEEEEE
Confidence            4568999999999999999998765444555543

>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=93.82  E-value=0.051  Score=47.20  Aligned_cols=34  Identities=18%  Similarity=0.035  Sum_probs=27.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCC--eEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENN--YLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~g--wiVl   99 (342)
                      ++..++|.|..||||||+...+..+-. ..|  ++++
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~   60 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRL   60 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEE
Confidence            466789999999999999998887665 567  4444

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.80  E-value=0.04  Score=46.39  Aligned_cols=25  Identities=20%  Similarity=0.347  Sum_probs=21.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|+.|||||+++.++..
T Consensus        46 ~~~~~i~vvG~~g~GKSsll~~l~~   70 (193)
T 2ged_A           46 SYQPSIIIAGPQNSGKTSLLTLLTT   70 (193)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhc
Confidence            4567999999999999999998765

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.80  E-value=0.06  Score=45.71  Aligned_cols=32  Identities=13%  Similarity=0.167  Sum_probs=24.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|+|.+||||||+...+....   |+.++..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l---~~~~i~~   43 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKY---GFTHLST   43 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH---TCEEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh---CCeEEcH
Confidence            5689999999999999887776542   5665544

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.77  E-value=0.097  Score=45.38  Aligned_cols=30  Identities=17%  Similarity=0.304  Sum_probs=25.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .+..+++|.|..|||||+++.+++......
T Consensus        36 ~~~~~i~ivG~~gvGKTtl~~~l~~~~~~~   65 (226)
T 2hf9_A           36 HGVVAFDFMGAIGSGKTLLIEKLIDNLKDK   65 (226)
T ss_dssp             TTCEEEEEEESTTSSHHHHHHHHHHHHTTT
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            356889999999999999999999876544

>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=93.72  E-value=0.062  Score=49.89  Aligned_cols=38  Identities=26%  Similarity=0.362  Sum_probs=31.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~vP  102 (342)
                      .+...++|.|+.|+||||++..+..+.. .+|.=|+.++
T Consensus       103 ~~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~  141 (296)
T 2px0_A          103 IHSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFIT  141 (296)
T ss_dssp             CCSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            3567899999999999999999998877 4787666664

>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=93.69  E-value=0.051  Score=53.98  Aligned_cols=37  Identities=5%  Similarity=-0.190  Sum_probs=31.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP  102 (342)
                      ++.-++|.|++|+|||+++.|++..+..+ |+-|+|+.
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s  278 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAM  278 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEE
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEe
Confidence            56679999999999999999999888765 88888773

>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=93.67  E-value=0.042  Score=48.76  Aligned_cols=27  Identities=19%  Similarity=0.283  Sum_probs=22.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .++.-++|.||.||||||++..+...-
T Consensus        14 ~~G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           14 AQGTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhccC
Confidence            467889999999999999999887653

>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=93.64  E-value=0.043  Score=47.62  Aligned_cols=27  Identities=26%  Similarity=0.212  Sum_probs=22.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .++..+.|.|+.||||||++.-+.-.-
T Consensus        18 ~~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           18 AVGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             -CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            346788999999999999999887664

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=93.62  E-value=0.041  Score=48.45  Aligned_cols=33  Identities=27%  Similarity=0.368  Sum_probs=26.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .++..+.|.|+.||||||++..+.-.- . |-+.+
T Consensus        21 ~~G~~~~lvGpsGsGKSTLl~~L~g~~-p-G~i~~   53 (218)
T 1z6g_A           21 NNIYPLVICGPSGVGKGTLIKKLLNEF-P-NYFYF   53 (218)
T ss_dssp             -CCCCEEEECSTTSSHHHHHHHHHHHS-T-TTEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhC-C-CcEEE
Confidence            457789999999999999999888754 3 66555

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=93.60  E-value=0.075  Score=52.41  Aligned_cols=45  Identities=27%  Similarity=0.282  Sum_probs=29.8

Q ss_pred             EEechh-HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          44 ILIRNC-MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        44 ~lvR~~-t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ++=|+. ...+++.|..     ...+.++|+|++|||||++...+......
T Consensus       182 iiGr~~~i~~l~~~l~r-----~~~~~~LL~G~pG~GKT~la~~la~~l~~  227 (468)
T 3pxg_A          182 VIGRSKEIQRVIEVLSR-----RTKNNPVLIGEPGVGKTAIAEGLAQQIIN  227 (468)
T ss_dssp             CCCCHHHHHHHHHHHHC-----SSSCEEEEESCTTTTTHHHHHHHHHHHHS
T ss_pred             ccCcHHHHHHHHHHHhc-----cCCCCeEEECCCCCCHHHHHHHHHHHHHh
Confidence            444553 3345555544     34567899999999999987666555433

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=93.60  E-value=0.047  Score=47.17  Aligned_cols=27  Identities=30%  Similarity=0.405  Sum_probs=22.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .+..-++|.|+.||||||+...+....
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            356789999999999999988886653

>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=93.59  E-value=0.06  Score=45.28  Aligned_cols=32  Identities=13%  Similarity=0.192  Sum_probs=24.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|+|..||||||+...+...   .||.++..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~---l~~~~i~~   37 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRD---FGWVHLSA   37 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH---hCCeEeeH
Confidence            357899999999999987776543   36766554

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=93.56  E-value=0.083  Score=46.94  Aligned_cols=37  Identities=16%  Similarity=0.062  Sum_probs=31.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++++|+-|+|||+.|.+.+..+...|.=|+-+
T Consensus        26 ~~G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~   62 (214)
T 2j9r_A           26 QNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVF   62 (214)
T ss_dssp             CSCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            3456677999999999999999999999888766665

>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=93.55  E-value=0.072  Score=44.19  Aligned_cols=30  Identities=17%  Similarity=0.195  Sum_probs=22.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ..++|+|..|||||++...+...   -|+.++.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~---lg~~~id   32 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARA---LGYEFVD   32 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHH---HTCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH---hCCcEEc
Confidence            36899999999999988776553   2565554

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=93.54  E-value=0.082  Score=49.70  Aligned_cols=79  Identities=14%  Similarity=0.161  Sum_probs=52.3

Q ss_pred             ChhhHHhhhhcCCceEEechhHHHHHHHHHhccCC-------------CCCCCeEEEEccCCCcHHHHHHHHHHHHH---
Q psy3261          29 TRVFNEQTQIFNESSILIRNCMLELVGYLKSMTNF-------------DRPSPRFVLYGEHGVGKSMALVYALQYAH---   92 (342)
Q Consensus        29 ~~~~~~~~~~~~~~~~lvR~~t~el~~~l~~~~~~-------------~~~~~r~vL~G~~GsGKS~~L~q~~~~A~---   92 (342)
                      |..+.+.-+..+-|.+-....|-++++.|..+.+.             .-.+..++|.|+.|+|||++...++....   
T Consensus        93 peelie~A~~~~IPVL~T~~~ts~~~~~l~~~l~~~~~~~~~~H~~~v~~~g~~vl~~G~sG~GKSt~a~~l~~~g~~lv  172 (314)
T 1ko7_A           93 PEELIEAAKEHETPLITSKIATTQLMSRLTTFLEHELARTTSLHGVLVDVYGVGVLITGDSGIGKSETALELIKRGHRLV  172 (314)
T ss_dssp             CHHHHHHHHHTTCCEEECCSCHHHHHHHHHHHHHHHTCEEEEEESEEEEETTEEEEEEESTTSSHHHHHHHHHHTTCEEE
T ss_pred             CHHHHHHHHHCCCeEEEECCchhHHHHHHHHHHHHhhccceeeeEEEEEECCEEEEEEeCCCCCHHHHHHHHHhcCCcee
Confidence            44555555555666666666777777766543211             01356899999999999999999988643   


Q ss_pred             hCCeEEEEeCCcccc
Q psy3261          93 ENNYLLVHIPWVLRW  107 (342)
Q Consensus        93 ~~gwiVl~vP~~~~~  107 (342)
                      ..+.+.+..-....+
T Consensus       173 ~dD~~~i~~~~~~~l  187 (314)
T 1ko7_A          173 ADDNVEIREISKDEL  187 (314)
T ss_dssp             ESSEEEEEESSSSCE
T ss_pred             cCCeEEEEEcCCCeE
Confidence            456666666444333

>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=93.53  E-value=0.055  Score=47.13  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=19.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+.|+|+.||||||++..+..
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999887754

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.53  E-value=0.071  Score=52.15  Aligned_cols=37  Identities=14%  Similarity=0.040  Sum_probs=30.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~v  101 (342)
                      .++.-++|.|++|+|||+++.|+...+.. +|.=|+|+
T Consensus       198 ~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~  235 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIY  235 (444)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEE
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEE
Confidence            46778999999999999999999987765 57666666

>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=93.51  E-value=0.027  Score=50.66  Aligned_cols=49  Identities=14%  Similarity=0.066  Sum_probs=30.0

Q ss_pred             eecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCC-CHHHHhhhcc
Q psy3261         292 IHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKR-VPQKMYEFCS  340 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgG-NP~~l~~lc~  340 (342)
                      +.++..+.+|-..+++.+...--+..+.....+..++.| +|+++..+|.
T Consensus       178 i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~  227 (268)
T 2r62_A          178 VLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIIN  227 (268)
T ss_dssp             CBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHH
T ss_pred             EEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence            677778888889999887653222112212234445665 5678887763

>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=93.49  E-value=0.052  Score=45.37  Aligned_cols=33  Identities=18%  Similarity=0.202  Sum_probs=23.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .-++|+|..||||||+...+... ...+|+.+.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~-l~~~~~~~~~   36 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSV-LPEPWLAFGV   36 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH-SSSCEEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh-cCCCeEEecc
Confidence            46899999999999987776543 2345665544

>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=93.49  E-value=0.07  Score=46.38  Aligned_cols=31  Identities=19%  Similarity=0.081  Sum_probs=24.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|+|..||||||++..+..    .|+.++..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~----lg~~~id~   34 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD----LGINVIDA   34 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH----TTCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH----cCCEEEEc
Confidence            45789999999999998887743    57766654

>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=93.48  E-value=0.044  Score=46.85  Aligned_cols=26  Identities=15%  Similarity=0.176  Sum_probs=21.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++..++|.|..||||||+...+....
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            35689999999999999998876643

>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=93.38  E-value=0.049  Score=48.54  Aligned_cols=25  Identities=28%  Similarity=0.247  Sum_probs=21.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +...++|.|+.||||||++..+...
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~   50 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQN   50 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999999887654

>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=93.37  E-value=0.065  Score=45.14  Aligned_cols=31  Identities=29%  Similarity=0.234  Sum_probs=23.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|+|.+|||||++...+..   ..||.++..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~---~lg~~~id~   33 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK---ALGVGLLDT   33 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH---HHTCCEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH---HcCCCEEeC
Confidence            4699999999999998777654   336766654

>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=93.34  E-value=0.07  Score=49.87  Aligned_cols=36  Identities=17%  Similarity=0.185  Sum_probs=28.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|+.||||||++..+..+...+|.=|+.+
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv  138 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLA  138 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEE
Confidence            345688999999999999999998877766544444

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=93.32  E-value=0.085  Score=45.17  Aligned_cols=32  Identities=13%  Similarity=0.269  Sum_probs=24.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|+|..||||||+...+..   ..|+.++..
T Consensus        15 ~~~I~l~G~~GsGKsT~~~~L~~---~~g~~~i~~   46 (203)
T 1ukz_A           15 VSVIFVLGGPGAGKGTQCEKLVK---DYSFVHLSA   46 (203)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH---HSSCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH---HcCceEEeH
Confidence            35789999999999998777654   357777665

>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=93.30  E-value=0.071  Score=51.79  Aligned_cols=27  Identities=22%  Similarity=0.161  Sum_probs=23.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      +..-+.|.|++|||||+++.|+...+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~  203 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQ  203 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhc
Confidence            677899999999999999999876554

>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=93.27  E-value=0.054  Score=50.80  Aligned_cols=48  Identities=13%  Similarity=0.107  Sum_probs=29.9

Q ss_pred             eecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         292 IHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +.++.++.+|...++...... ++-..++...++.-.|.|+||.+.++|
T Consensus       175 ~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll  223 (334)
T 1in4_A          175 LELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  223 (334)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             eeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            566677888888877666432 322244444555567788888776665

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=93.23  E-value=0.082  Score=46.48  Aligned_cols=30  Identities=13%  Similarity=0.233  Sum_probs=23.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++|.|++||||||+...+..+.   |+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l---g~~~i~~   31 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY---SLAHIES   31 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---TCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCeEEch
Confidence            58999999999999888776543   6665554

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=93.20  E-value=0.047  Score=49.29  Aligned_cols=33  Identities=24%  Similarity=0.365  Sum_probs=25.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      -++|.|+.||||||+...+..   .-|+.++.....
T Consensus         3 li~I~G~~GSGKSTla~~La~---~~~~~~i~~D~~   35 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQ---ETGWPVVALDRV   35 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH---HHCCCEEECCSG
T ss_pred             EEEEECCCCcCHHHHHHHHHh---cCCCeEEeccHH
Confidence            478999999999998877743   447777776543

>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=93.18  E-value=0.099  Score=48.75  Aligned_cols=34  Identities=18%  Similarity=0.273  Sum_probs=27.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      +...+.|.|+.||||||++.-+..+....+-=|.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~~~g~V~  134 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVM  134 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEE
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEE
Confidence            4568889999999999999999988775544333

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=93.15  E-value=0.18  Score=44.47  Aligned_cols=34  Identities=15%  Similarity=0.252  Sum_probs=25.6

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      -.+++..+.+       +..+++.|+.|||||+++...+..
T Consensus        66 q~~~i~~i~~-------g~~~~i~g~TGsGKTt~~~~~~~~   99 (235)
T 3llm_A           66 ESEILEAISQ-------NSVVIIRGATGCGKTTQVPQFILD   99 (235)
T ss_dssp             HHHHHHHHHH-------CSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhc-------CCEEEEEeCCCCCcHHhHHHHHhc
Confidence            3455566655       567999999999999988777654

>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=93.13  E-value=0.073  Score=49.50  Aligned_cols=26  Identities=15%  Similarity=0.117  Sum_probs=23.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      +..-++|+|++|||||+++.|+...+
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            56678999999999999999998865

>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=93.11  E-value=0.066  Score=46.91  Aligned_cols=25  Identities=32%  Similarity=0.357  Sum_probs=21.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +..-++|.||.|||||+++..++..
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            5678899999999999999988754

>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=93.11  E-value=0.057  Score=46.82  Aligned_cols=23  Identities=30%  Similarity=0.353  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..+||.||.|+|||+++..++.-
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            45899999999999999887654

>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=93.10  E-value=0.094  Score=49.75  Aligned_cols=26  Identities=19%  Similarity=0.286  Sum_probs=20.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+...++|+|++|||||++...+...
T Consensus        70 ~~~~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           70 LSKSNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             CCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCCCEEEECCCCCCHHHHHHHHHHH
Confidence            34678999999999999776655443

>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=93.03  E-value=0.067  Score=52.53  Aligned_cols=36  Identities=17%  Similarity=0.190  Sum_probs=31.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+++.|+.||||||++..+..+...+|.=|+.+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv  131 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLV  131 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            356788999999999999999999998888777665

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.02  E-value=0.088  Score=45.49  Aligned_cols=28  Identities=14%  Similarity=0.264  Sum_probs=24.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ....++|.|..|+|||+++.+++.....
T Consensus        29 ~~~~i~i~G~~g~GKTTl~~~l~~~~~~   56 (221)
T 2wsm_A           29 GTVAVNIMGAIGSGKTLLIERTIERIGN   56 (221)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            4678999999999999999999887543

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.01  E-value=0.04  Score=48.57  Aligned_cols=25  Identities=24%  Similarity=0.216  Sum_probs=16.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH-HH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL-QY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~-~~   90 (342)
                      ++.-+.|.|+.||||||++..+. ..
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             CCCEEEEECSCC----CHHHHHHC--
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            56789999999999999998887 54

>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=93.00  E-value=0.077  Score=52.23  Aligned_cols=36  Identities=17%  Similarity=0.351  Sum_probs=31.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+++.|+.|+||||+++.+..+..++|.=|+-|
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv  134 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVV  134 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            356889999999999999999999999888877666

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=92.97  E-value=0.064  Score=45.61  Aligned_cols=31  Identities=23%  Similarity=0.409  Sum_probs=23.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .++|.|..||||||+...+..+.   |+.++..|
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l---~~~~~~e~   32 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL---GYEIFKEP   32 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---CCEEECCC
T ss_pred             EEEEECCCccCHHHHHHHHHHhc---CCcEEccc
Confidence            58999999999999988876543   45544433

>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=92.92  E-value=0.089  Score=49.64  Aligned_cols=37  Identities=14%  Similarity=0.269  Sum_probs=29.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...+.|.|+.||||||++.-+..+....+.=|+.+
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l~  163 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIA  163 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEE
Confidence            3567889999999999999999998877665544433

>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=92.87  E-value=0.064  Score=47.99  Aligned_cols=26  Identities=23%  Similarity=0.211  Sum_probs=21.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        29 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcC
Confidence            46778999999999999998876543

>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=92.85  E-value=0.083  Score=50.15  Aligned_cols=28  Identities=18%  Similarity=0.220  Sum_probs=24.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+..-+.|.|++|||||+++.|+...+.
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~~~  156 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVMVQ  156 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3567889999999999999999998763

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=92.85  E-value=0.07  Score=44.10  Aligned_cols=29  Identities=24%  Similarity=0.092  Sum_probs=22.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      +++|+|..||||||+...+...   .|+.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~---l~~~~i~   30 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRS---LNIPFYD   30 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHH---HTCCEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHH---hCCCEEE
Confidence            5899999999999988777653   2555554

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=92.84  E-value=0.087  Score=45.47  Aligned_cols=37  Identities=16%  Similarity=0.221  Sum_probs=27.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH---hCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH---ENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~---~~gwiVl~vP  102 (342)
                      ....++|.|+.|+|||++...++....   ..+++++..-
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~rG~~lvaDD~v~i~~~   54 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALIDRGHQLVCDDVIDLKQE   54 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHHTTCEEEESSEEEEEES
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHcCCeEecCCEEEEEEe
Confidence            356899999999999999999888543   3455555543

>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=92.82  E-value=0.055  Score=44.00  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=21.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...++++.|+.|+|||+++.++..
T Consensus         4 ~~~~i~v~G~~~~GKssl~~~l~~   27 (168)
T 1z2a_A            4 VAIKMVVVGNGAVGKSSMIQRYCK   27 (168)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEEECcCCCCHHHHHHHHHc
Confidence            457899999999999999998874

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=92.82  E-value=0.093  Score=48.85  Aligned_cols=33  Identities=15%  Similarity=0.188  Sum_probs=26.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      ++..+.|.|+.||||||++.-+..+....+.=|
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V  131 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKV  131 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHHTTCCE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHcCCeE
Confidence            456788999999999999999998877554333

>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=92.82  E-value=0.058  Score=44.50  Aligned_cols=25  Identities=20%  Similarity=0.448  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|+.|+|||+++.++..
T Consensus         6 ~~~~~i~v~G~~~~GKSsli~~l~~   30 (182)
T 1ky3_A            6 KNILKVIILGDSGVGKTSLMHRYVN   30 (182)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHh
Confidence            4567999999999999999998875

>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=92.76  E-value=0.068  Score=43.26  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..++++.|..|+|||+++.++..
T Consensus         3 ~~~~i~v~G~~~~GKssl~~~l~~   26 (168)
T 1u8z_A            3 ALHKVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHh
Confidence            356899999999999999988774

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=92.75  E-value=0.064  Score=43.37  Aligned_cols=22  Identities=32%  Similarity=0.428  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++++.|+.|+|||+++.++..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~   23 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLK   23 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4789999999999999998874

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=92.74  E-value=0.11  Score=49.72  Aligned_cols=36  Identities=17%  Similarity=0.237  Sum_probs=29.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...+|.|+.|+|||+++..++......|--|+.+
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~   69 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIII   69 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEE
Confidence            466789999999999999999998777665555445

>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=92.72  E-value=0.047  Score=45.92  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=21.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+..+++|.|+.|+|||+++.++.
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~   37 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLA   37 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHh
Confidence            457899999999999999998865

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.71  E-value=0.058  Score=43.97  Aligned_cols=23  Identities=30%  Similarity=0.531  Sum_probs=20.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..++++.|..|+|||+++.++..
T Consensus         3 ~~~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            3 DYRVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHc
Confidence            46899999999999999998764

>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=92.68  E-value=0.071  Score=47.77  Aligned_cols=33  Identities=21%  Similarity=0.201  Sum_probs=25.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYL   97 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwi   97 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~I   62 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSLLSALLAEMDKVEGHV   62 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTCSEEEEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCCCCCceE
Confidence            4677899999999999999987765432 33544

>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=92.67  E-value=0.1  Score=46.44  Aligned_cols=35  Identities=17%  Similarity=0.235  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .+...++|.|+.||||||++..+..+-.. |.-|+.
T Consensus        24 ~~g~~i~i~G~~GsGKsT~~~~l~~~l~~-~~~~~~   58 (229)
T 4eaq_A           24 AMSAFITFEGPEGSGKTTVINEVYHRLVK-DYDVIM   58 (229)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHTT-TSCEEE
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHhc-CCCcee
Confidence            35678999999999999999998887665 654443

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.67  E-value=0.089  Score=46.23  Aligned_cols=31  Identities=16%  Similarity=0.138  Sum_probs=25.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYL   97 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi   97 (342)
                      +..+.|.|+.||||||+|.-+.-..-..|-|
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl~p~~G~I   52 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQALQSKQV   52 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHHHHHTTSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCcCCee
Confidence            6789999999999999999988772356665

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=92.67  E-value=0.082  Score=46.16  Aligned_cols=25  Identities=12%  Similarity=0.118  Sum_probs=20.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ....++|.|++||||||+...+...
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3467999999999999988777553

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=92.66  E-value=0.081  Score=43.59  Aligned_cols=25  Identities=20%  Similarity=0.240  Sum_probs=21.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus         6 ~~~~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            6 ERPPVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            4678999999999999999988753

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=92.64  E-value=0.1  Score=49.45  Aligned_cols=30  Identities=30%  Similarity=0.270  Sum_probs=25.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .....+.|.|++|+||||++..++.+....
T Consensus        72 ~~~~~v~lvG~pgaGKSTLln~L~~~~~~~  101 (349)
T 2www_A           72 PLAFRVGLSGPPGAGKSTFIEYFGKMLTER  101 (349)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cCceEEEEEcCCCCCHHHHHHHHHHHhhhc
Confidence            346789999999999999999999876554

>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=92.63  E-value=0.13  Score=50.17  Aligned_cols=35  Identities=31%  Similarity=0.441  Sum_probs=27.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl   99 (342)
                      .+..-++|.|+.||||||+|.-++.+-.. .|-|++
T Consensus       165 ~~ggii~I~GpnGSGKTTlL~allg~l~~~~g~I~~  200 (418)
T 1p9r_A          165 RPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILT  200 (418)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEE
T ss_pred             hcCCeEEEECCCCCCHHHHHHHHHhhcCCCCCEEEE
Confidence            45667899999999999999998887643 455554

>1zcb_A G alpha I/13; GTP-binding, lipoprotein, membrane, transducer, signaling PR; HET: GDP; 2.00A {Mus musculus} SCOP: a.66.1.1 c.37.1.8 PDB: 3ab3_A* 3cx8_A* 3cx7_A* 3cx6_A* 1zca_A*

Probab=92.61  E-value=0.081  Score=50.63  Aligned_cols=44  Identities=18%  Similarity=0.172  Sum_probs=24.4

Q ss_pred             HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCe
Q psy3261          52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNY   96 (342)
Q Consensus        52 el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gw   96 (342)
                      +|=+.|++-.....+..|++|-|..||||||++.|.- .-+..||
T Consensus        18 ~Id~~l~~~~~~~~~~~killlG~~~SGKST~~kq~~-i~~~~~~   61 (362)
T 1zcb_A           18 MIDRNLREDGERSARLVKILLLGAGESGKSTFLKQMR-IIHGQDF   61 (362)
T ss_dssp             -------------CCCEEEEEECSTTSSHHHHHHHHH-HHHSCCC
T ss_pred             HHHHHHHHhHHHhcCccEEEEECCCCCcHHHHHHHHH-HHhCCCC
Confidence            3334454412223557899999999999999999983 2234444

>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=92.58  E-value=0.092  Score=50.30  Aligned_cols=35  Identities=20%  Similarity=0.399  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh--CCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE--NNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~--~gwiVl   99 (342)
                      .+...++|.|+.||||||+|.-+..+-..  .|-|++
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~  170 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIIT  170 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEE
Confidence            45667999999999999999999887653  566643

>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=92.58  E-value=0.068  Score=45.56  Aligned_cols=24  Identities=38%  Similarity=0.404  Sum_probs=20.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..+++|.|+.|||||+++..+...
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            368899999999999999988753

>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=92.57  E-value=0.076  Score=42.80  Aligned_cols=22  Identities=36%  Similarity=0.537  Sum_probs=19.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++++.|..|+|||+++.++..
T Consensus         4 ~~i~v~G~~~~GKssl~~~l~~   25 (166)
T 2ce2_X            4 YKLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5799999999999999988864

>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=92.55  E-value=0.066  Score=43.93  Aligned_cols=23  Identities=35%  Similarity=0.414  Sum_probs=20.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +..+++|.|+.|+|||+++.++.
T Consensus         3 ~~~ki~i~G~~~vGKSsl~~~l~   25 (175)
T 2nzj_A            3 ALYRVVLLGDPGVGKTSLASLFA   25 (175)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEEEECCCCccHHHHHHHHh
Confidence            45689999999999999998775

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=92.53  E-value=0.11  Score=48.87  Aligned_cols=36  Identities=28%  Similarity=0.394  Sum_probs=28.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+.+.|+.|+||||++..+..+....|.=|+.+
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVlli  139 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIA  139 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            455788999999999999999998777666655544

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.52  E-value=0.093  Score=60.40  Aligned_cols=38  Identities=16%  Similarity=0.186  Sum_probs=34.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|||||++..|+++-|..+|+-|++|.
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~ 1462 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID 1462 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            46788999999999999999999999999999998884

>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=92.52  E-value=0.083  Score=44.40  Aligned_cols=25  Identities=28%  Similarity=0.349  Sum_probs=21.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++.+++.
T Consensus        21 ~~~~~i~v~G~~~~GKSsli~~l~~   45 (195)
T 1svi_A           21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3568999999999999999998863

>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=92.52  E-value=0.069  Score=43.20  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|+.|+|||+++.++..
T Consensus         3 ~~~i~v~G~~~~GKSsli~~l~~   25 (167)
T 1kao_A            3 EYKVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEEECCCCCCHHHHHHHHHc
Confidence            45899999999999999988775

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.51  E-value=0.085  Score=44.10  Aligned_cols=23  Identities=26%  Similarity=0.264  Sum_probs=20.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ...+++|.|..|+|||+++.+++
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~   44 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALF   44 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            45799999999999999998875

>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=92.50  E-value=0.07  Score=45.39  Aligned_cols=23  Identities=39%  Similarity=0.442  Sum_probs=20.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|+.|||||+++..+..
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~   51 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTR   51 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEECcCCCCHHHHHHHHhc
Confidence            46899999999999999998765

>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=92.50  E-value=0.1  Score=47.68  Aligned_cols=33  Identities=15%  Similarity=0.100  Sum_probs=25.2

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ..++|.|.+||||||+...+...  ..||.++...
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~--~~~~~~i~~D   35 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK--NPGFYNINRD   35 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH--STTEEEECHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh--CCCcEEeccc
Confidence            35899999999999988777651  2488877553

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.48  E-value=0.073  Score=47.21  Aligned_cols=35  Identities=17%  Similarity=0.200  Sum_probs=24.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        28 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~~p~~G~i~~   63 (224)
T 2pcj_A           28 KKGEFVSIIGASGSGKSTLLYILGLLDAPTEGKVFL   63 (224)
T ss_dssp             ETTCEEEEEECTTSCHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            3577889999999999999986654322 2354443

>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=92.42  E-value=0.082  Score=42.95  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..++++.|+.|+|||+++.++..
T Consensus         3 ~~~i~v~G~~~~GKssli~~l~~   25 (170)
T 1ek0_A            3 SIKLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999998864

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=92.41  E-value=0.11  Score=51.93  Aligned_cols=36  Identities=17%  Similarity=0.185  Sum_probs=29.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .++..++|.|+.|||||+++.++......+|--|+|
T Consensus       279 ~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~  314 (525)
T 1tf7_A          279 FKDSIILATGATGTGKTLLVSRFVENACANKERAIL  314 (525)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEE
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEE
Confidence            467889999999999999999999877666653333

>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=92.38  E-value=0.071  Score=44.51  Aligned_cols=24  Identities=25%  Similarity=0.220  Sum_probs=20.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|+.|+|||+++..+..
T Consensus         3 ~~~ki~ivG~~g~GKStLl~~l~~   26 (172)
T 2gj8_A            3 HGMKVVIAGRPNAGKSSLLNALAG   26 (172)
T ss_dssp             -CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            457899999999999999988753

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=92.36  E-value=0.11  Score=48.27  Aligned_cols=23  Identities=17%  Similarity=0.312  Sum_probs=19.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...++|+|++|||||+++..+..
T Consensus        46 ~~~vll~G~pGtGKT~la~~la~   68 (331)
T 2r44_A           46 GGHILLEGVPGLAKTLSVNTLAK   68 (331)
T ss_dssp             TCCEEEESCCCHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHH
Confidence            45899999999999988776544

>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=92.36  E-value=0.086  Score=43.05  Aligned_cols=25  Identities=24%  Similarity=0.329  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..++++.|..|+|||+++.++..
T Consensus         5 ~~~~~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            5 TREMRILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            3467999999999999999998854

>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=92.34  E-value=0.064  Score=45.13  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|.|+.|||||+++..++.
T Consensus         3 ~kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            3 MKLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            5899999999999999998764

>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=92.33  E-value=0.084  Score=44.76  Aligned_cols=25  Identities=16%  Similarity=0.266  Sum_probs=20.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|+.|+|||+++.++..
T Consensus        21 ~~~~ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           21 NKHGKLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             ---CEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            4567999999999999999988764

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.31  E-value=0.1  Score=43.21  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=21.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+..+++|.|+.|+|||+++.++.
T Consensus        16 ~~~~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A           16 NKELRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             SSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             CCccEEEEECCCCCCHHHHHHHHh
Confidence            567899999999999999997654

>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=92.29  E-value=0.047  Score=50.77  Aligned_cols=24  Identities=25%  Similarity=0.414  Sum_probs=19.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ...++|+|++|||||+++..+...
T Consensus        45 ~~~vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHHHHh
Confidence            345999999999999887765553

>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=92.27  E-value=0.083  Score=44.39  Aligned_cols=27  Identities=26%  Similarity=0.196  Sum_probs=22.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .++..+.|.|+.||||||++.-+.-.-
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            456688999999999999999887653

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=92.24  E-value=0.24  Score=46.57  Aligned_cols=26  Identities=19%  Similarity=0.051  Sum_probs=20.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ..-+-|.|+.||||||++..+...-.
T Consensus        92 p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           92 PYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34678999999999999987766544

>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=92.23  E-value=0.089  Score=42.90  Aligned_cols=24  Identities=33%  Similarity=0.337  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...++++.|..|+|||+++.++..
T Consensus         5 ~~~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1z08_A            5 YSFKVVLLGEGCVGKTSLVLRYCE   28 (170)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHHc
Confidence            457899999999999999988764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=92.23  E-value=0.071  Score=44.65  Aligned_cols=23  Identities=30%  Similarity=0.397  Sum_probs=15.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...++|+|..||||||+...+..
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998877643

>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=92.23  E-value=0.2  Score=50.04  Aligned_cols=34  Identities=15%  Similarity=0.268  Sum_probs=27.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl   99 (342)
                      +...+.|.|+.||||||++.-+..+.... |-|.+
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~~G~V~l  326 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQGKSVML  326 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhcCCeEEE
Confidence            45678899999999999999998877654 55554

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=92.22  E-value=0.12  Score=46.46  Aligned_cols=36  Identities=22%  Similarity=0.185  Sum_probs=31.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+.-++++|+-|+|||+.|.+.++.+...|.=|+-+
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~   53 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVI   53 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEE
Confidence            467889999999999999999999999888766665

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=92.21  E-value=1.8  Score=40.13  Aligned_cols=90  Identities=2%  Similarity=0.019  Sum_probs=52.5

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH-hCCCcc
Q psy3261         238 LTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQ  316 (342)
Q Consensus       238 l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~  316 (342)
                      ....|++++.....+..+|.+++.-.....++.  ++..+ ...+       ..+++..++.+|+...+.... +.|+--
T Consensus        93 ~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k--~~~~i-~sr~-------~~~~~~~l~~~~l~~~l~~~~~~~g~~i  162 (343)
T 1jr3_D           93 INEQLLTLTGLLHDDLLLIVRGNKLSKAQENAA--WFTAL-ANRS-------VQVTCQTPEQAQLPRWVAARAKQLNLEL  162 (343)
T ss_dssp             HHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSH--HHHHH-TTTC-------EEEEECCCCTTHHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhH--HHHHH-HhCc-------eEEEeeCCCHHHHHHHHHHHHHHcCCCC
Confidence            456788888765566677777654321111111  22112 1222       137788889999988885544 444322


Q ss_pred             CcchHHHHHHhhCCCHHHHhh
Q psy3261         317 TSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       317 ~e~~~~el~~lSgGNP~~l~~  337 (342)
                      +++....+-..+|||.+.+..
T Consensus       163 ~~~a~~~l~~~~~gdl~~~~~  183 (343)
T 1jr3_D          163 DDAANQVLCYCYEGNLLALAQ  183 (343)
T ss_dssp             CHHHHHHHHHSSTTCHHHHHH
T ss_pred             CHHHHHHHHHHhchHHHHHHH
Confidence            454455566689999987665

>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=92.20  E-value=0.17  Score=49.08  Aligned_cols=48  Identities=17%  Similarity=0.146  Sum_probs=34.2

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEe
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHI  101 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~v  101 (342)
                      .+.+|+.+-.    -.++.|+.|.|++|||||+++.++..++.++  +..++++
T Consensus       161 GiraID~~~p----i~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~I~~  210 (422)
T 3ice_A          161 TARVLDLASP----IGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVL  210 (422)
T ss_dssp             HHHHHHHHSC----CBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred             cceeeeeeee----ecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeEEEE
Confidence            4445554432    2468899999999999999999998887653  4444443

>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=92.19  E-value=0.065  Score=52.54  Aligned_cols=36  Identities=19%  Similarity=0.271  Sum_probs=31.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ...+++.|+.|+||||+.+.+..++.++|+=|+.|.
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            357899999999999999999999988888777773

>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=92.18  E-value=0.09  Score=43.26  Aligned_cols=24  Identities=29%  Similarity=0.419  Sum_probs=21.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|+.|+|||+++..+..
T Consensus         6 ~~~~i~v~G~~~~GKSsli~~l~~   29 (177)
T 1wms_A            6 SLFKVILLGDGGVGKSSLMNRYVT   29 (177)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceeEEEEECCCCCCHHHHHHHHHc
Confidence            457899999999999999998864

>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=92.17  E-value=0.1  Score=44.83  Aligned_cols=26  Identities=19%  Similarity=0.298  Sum_probs=22.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ....+++|.|+.|+|||+++.++...
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            45689999999999999999987653

>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=92.16  E-value=0.092  Score=43.21  Aligned_cols=26  Identities=31%  Similarity=0.442  Sum_probs=22.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+..+++|.|..|+|||+++..+..-
T Consensus         7 ~~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            7 SETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             SCEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhC
Confidence            44679999999999999999888754

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=92.15  E-value=0.094  Score=47.13  Aligned_cols=31  Identities=23%  Similarity=0.274  Sum_probs=23.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      .+...+.|+|+.||||||++..+..   .-|+..
T Consensus        25 ~~g~~I~I~G~~GsGKSTl~k~La~---~Lg~~~   55 (252)
T 4e22_A           25 AIAPVITVDGPSGAGKGTLCKALAE---SLNWRL   55 (252)
T ss_dssp             TTSCEEEEECCTTSSHHHHHHHHHH---HTTCEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH---hcCCCc
Confidence            3467899999999999999887653   335543

>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=92.14  E-value=0.086  Score=43.47  Aligned_cols=22  Identities=32%  Similarity=0.301  Sum_probs=19.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..+++|.|+.|+|||+++..+.
T Consensus         3 ~~~v~lvG~~gvGKStL~~~l~   24 (165)
T 2wji_A            3 SYEIALIGNPNVGKSTIFNALT   24 (165)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHh
Confidence            3578999999999999999885

>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=92.14  E-value=0.086  Score=45.41  Aligned_cols=34  Identities=12%  Similarity=0.009  Sum_probs=24.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+.|+|+.||||||++..+....  .++.++..
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~--~~~~~i~~   53 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL--PNCSVISQ   53 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS--TTEEEEEG
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc--CCcEEEeC
Confidence            45678899999999999887765421  15655554

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.10  E-value=0.09  Score=47.83  Aligned_cols=35  Identities=23%  Similarity=0.288  Sum_probs=25.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        30 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~~p~~G~i~~   65 (262)
T 1b0u_A           30 RAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIV   65 (262)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCCcEEEE
Confidence            4677899999999999999987654432 2354443

>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=92.10  E-value=0.14  Score=45.17  Aligned_cols=36  Identities=22%  Similarity=0.177  Sum_probs=30.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++.-++|.|..||||||....+..+-...|+-|+..
T Consensus         5 ~g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~   40 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLT   40 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHHHHcCCCcccc
Confidence            356789999999999999999999988888766543

>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=92.09  E-value=0.095  Score=42.64  Aligned_cols=22  Identities=32%  Similarity=0.297  Sum_probs=19.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..+++|.|..|+|||+++..+.
T Consensus         2 ~~ki~~vG~~~~GKSsli~~l~   23 (166)
T 3q72_A            2 VYKVLLLGAPGVGKSALARIFG   23 (166)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHC
T ss_pred             eEEEEEECCCCCCHHHHHHHHc
Confidence            4689999999999999998764

>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=92.08  E-value=0.085  Score=46.65  Aligned_cols=35  Identities=17%  Similarity=0.253  Sum_probs=25.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        33 ~~Ge~~~iiG~NGsGKSTLlk~l~Gl~~p~~G~I~~   68 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTLLKTISTYLKPLKGEIIY   68 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCCeEEEE
Confidence            3577899999999999999987654432 2355543

>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=92.04  E-value=0.097  Score=42.60  Aligned_cols=24  Identities=29%  Similarity=0.448  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..++++.|+.|+|||+++..+..
T Consensus         5 ~~~~i~v~G~~~~GKSsli~~l~~   28 (170)
T 1z0j_A            5 RELKVCLLGDTGVGKSSIMWRFVE   28 (170)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHHc
Confidence            346899999999999999998764

>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=92.04  E-value=0.089  Score=42.82  Aligned_cols=23  Identities=39%  Similarity=0.586  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..++++.|+.|+|||+++..+..
T Consensus         3 ~~~i~v~G~~~~GKssli~~l~~   25 (170)
T 1g16_A            3 IMKILLIGDSGVGKSCLLVRFVE   25 (170)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEECcCCCCHHHHHHHHHh
Confidence            35899999999999999998874

>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=92.01  E-value=0.14  Score=46.97  Aligned_cols=31  Identities=19%  Similarity=0.069  Sum_probs=24.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...+.|+|..||||||+...+..    .|+-++..
T Consensus        75 ~~iI~I~G~~GSGKSTva~~La~----lg~~~id~  105 (281)
T 2f6r_A           75 LYVLGLTGISGSGKSSVAQRLKN----LGAYIIDS  105 (281)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHH----HTCEEEEH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH----CCCcEEeh
Confidence            34689999999999999887763    37777665

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=92.01  E-value=0.079  Score=44.26  Aligned_cols=24  Identities=29%  Similarity=0.254  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|+.|+|||+++.++..
T Consensus         6 ~~~~i~lvG~~gvGKStL~~~l~~   29 (188)
T 2wjg_A            6 KSYEIALIGNPNVGKSTIFNALTG   29 (188)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            346899999999999999998863

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=92.00  E-value=0.12  Score=52.74  Aligned_cols=34  Identities=18%  Similarity=0.213  Sum_probs=26.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVH  100 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~  100 (342)
                      ....+|.|++|||||+++..++.+... .++-|+.
T Consensus       195 ~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv  229 (624)
T 2gk6_A          195 RPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLV  229 (624)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEE
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEE
Confidence            346899999999999999999988765 4544433

>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=92.00  E-value=0.084  Score=47.37  Aligned_cols=35  Identities=17%  Similarity=0.318  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   61 (243)
T 1mv5_A           26 QPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITI   61 (243)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSSCCSBSCEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCCcEEEE
Confidence            4677899999999999999988765433 3566655

>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=91.98  E-value=0.091  Score=47.37  Aligned_cols=26  Identities=19%  Similarity=0.304  Sum_probs=22.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        33 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            45778999999999999999877554

>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=91.98  E-value=0.1  Score=47.65  Aligned_cols=26  Identities=23%  Similarity=0.293  Sum_probs=22.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        44 ~~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           44 HPGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            46788999999999999999887764

>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=91.97  E-value=0.25  Score=45.71  Aligned_cols=35  Identities=20%  Similarity=0.133  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH---hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH---ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~---~~gwiVl   99 (342)
                      .+...+.|.|+.||||||++..+.....   ..|-+.+
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~v  115 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVEL  115 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEE
Confidence            4456788999999999999998877543   3455544

>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=91.95  E-value=0.089  Score=45.13  Aligned_cols=27  Identities=22%  Similarity=0.316  Sum_probs=21.4

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..+..+++|.|..|+|||+++..+..-
T Consensus        27 ~~~~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           27 QGQAIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             ---CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cCCeEEEEEECcCCCCHHHHHHHHHhC
Confidence            356789999999999999999887743

>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=91.94  E-value=0.094  Score=46.65  Aligned_cols=35  Identities=14%  Similarity=0.212  Sum_probs=26.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        32 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   67 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKH   67 (229)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCcCCccEEEE
Confidence            3577899999999999999987765433 3466643

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=91.93  E-value=0.061  Score=48.53  Aligned_cols=37  Identities=32%  Similarity=0.462  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -.++++.+..   ...+..+++|.|..|+|||+++..+..
T Consensus        22 l~~~~~~~~~---~~~~~~~I~lvG~~g~GKSSLin~l~~   58 (262)
T 3def_A           22 LIEFFGKLKQ---KDMNSMTVLVLGKGGVGKSSTVNSLIG   58 (262)
T ss_dssp             HHHHHHHHHH---TTCCEEEEEEEECTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHhh---ccCCCcEEEEECCCCCCHHHHHHHHhC
Confidence            3355555544   234578999999999999999988874

>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=91.93  E-value=0.088  Score=43.80  Aligned_cols=25  Identities=28%  Similarity=0.378  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|+.|+|||+++.++..
T Consensus         8 ~~~~ki~v~G~~~~GKSsli~~l~~   32 (186)
T 2bme_A            8 DFLFKFLVIGNAGTGKSCLLHQFIE   32 (186)
T ss_dssp             SEEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHc
Confidence            3457999999999999999998864

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=91.91  E-value=0.098  Score=47.53  Aligned_cols=35  Identities=17%  Similarity=0.267  Sum_probs=26.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-...|-|.+
T Consensus        44 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~~~G~I~i   78 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTIAKLLYRFYDAEGDIKI   78 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSCCEEEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhccCCCCeEEEE
Confidence            46779999999999999999987654323455443

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=91.90  E-value=0.095  Score=46.71  Aligned_cols=26  Identities=15%  Similarity=0.055  Sum_probs=21.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+...+-|+|+.||||||++..+...
T Consensus        23 ~~g~iigI~G~~GsGKSTl~k~L~~~   48 (245)
T 2jeo_A           23 MRPFLIGVSGGTASGKSTVCEKIMEL   48 (245)
T ss_dssp             CCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            34567889999999999999887664

>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=91.88  E-value=0.087  Score=44.72  Aligned_cols=26  Identities=19%  Similarity=0.387  Sum_probs=21.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+..+++|.|..|+|||+++..+...
T Consensus         6 ~~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            6 KVLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CcceEEEEECcCCCCHHHHHHHHHcC
Confidence            45679999999999999999988653

>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=91.87  E-value=0.096  Score=46.94  Aligned_cols=35  Identities=17%  Similarity=0.289  Sum_probs=25.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        30 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   65 (240)
T 1ji0_A           30 PRGQIVTLIGANGAGKTTTLSAIAGLVRAQKGKIIF   65 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            3577899999999999999987765432 2354443

>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=91.87  E-value=0.078  Score=44.08  Aligned_cols=24  Identities=33%  Similarity=0.522  Sum_probs=21.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|..|+|||+++..+..
T Consensus         3 ~~~ki~v~G~~~~GKSsli~~l~~   26 (189)
T 4dsu_A            3 TEYKLVVVGADGVGKSALTIQLIQ   26 (189)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEEECCCCCCHHHHHHHHHh
Confidence            456899999999999999998864

>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=91.85  E-value=0.19  Score=44.29  Aligned_cols=33  Identities=21%  Similarity=0.128  Sum_probs=24.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ....++|.|.+||||||+...+...   .|+.++..
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~~---l~~~~i~~   47 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAKN---FCVCHLAT   47 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH---HTCEEEEH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH---hCCceecH
Confidence            3468999999999999987776554   25555543

>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=91.81  E-value=0.12  Score=44.17  Aligned_cols=25  Identities=20%  Similarity=0.295  Sum_probs=21.5

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..+..+++|.|+.|+|||+++.++.
T Consensus        22 ~~~~~ki~lvG~~~vGKSsLi~~l~   46 (198)
T 1f6b_A           22 YKKTGKLVFLGLDNAGKTTLLHMLK   46 (198)
T ss_dssp             TTCCEEEEEEEETTSSHHHHHHHHS
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHh
Confidence            3456799999999999999999875

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=91.81  E-value=0.11  Score=46.81  Aligned_cols=34  Identities=24%  Similarity=0.268  Sum_probs=25.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .+ ..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl~~p~~G~i~~   57 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGIVKPDRGEVRL   57 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            45 7888999999999999998765433 3455544

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.80  E-value=0.1  Score=47.76  Aligned_cols=35  Identities=23%  Similarity=0.295  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        43 ~~Ge~~~i~G~nGsGKSTLlk~l~Gl~~p~~G~I~~   78 (271)
T 2ixe_A           43 YPGKVTALVGPNGSGKSTVAALLQNLYQPTGGKVLL   78 (271)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCCCCCCEEEE
Confidence            4678899999999999999987765432 3354443

>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=91.80  E-value=0.11  Score=43.91  Aligned_cols=25  Identities=24%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|||||+++..++.
T Consensus        18 ~~~~ki~ivG~~~vGKSsL~~~~~~   42 (184)
T 3ihw_A           18 GPELKVGIVGNLSSGKSALVHRYLT   42 (184)
T ss_dssp             CCEEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhc
Confidence            4567999999999999999988775

>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=91.80  E-value=0.1  Score=42.62  Aligned_cols=21  Identities=38%  Similarity=0.328  Sum_probs=18.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+++|.|..|+|||+++..+.
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            478999999999999998875

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=91.79  E-value=0.15  Score=48.85  Aligned_cols=34  Identities=18%  Similarity=0.257  Sum_probs=27.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl   99 (342)
                      +...+.|.|+.||||||++.-+..+.... |-|.+
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~G~V~l  190 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLM  190 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccccCCEEEE
Confidence            45678899999999999999999887754 44443

>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=91.79  E-value=0.17  Score=46.76  Aligned_cols=42  Identities=19%  Similarity=0.189  Sum_probs=28.2

Q ss_pred             HHHHHHHhc-cCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          52 ELVGYLKSM-TNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        52 el~~~l~~~-~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      .|.+.+.++ .....+...+.|.|+.||||||+...+......
T Consensus        15 ~l~~~i~~~~~~~~~~~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           15 FLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             HHHHHHHHHHTTTCCSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhccCCCCeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            344444442 112344567889999999999998887776554

>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=91.78  E-value=0.1  Score=42.77  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|+.|+|||+++..++.
T Consensus        14 ~~~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           14 KFKLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHc
Confidence            46899999999999999998863

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=91.75  E-value=0.077  Score=43.70  Aligned_cols=24  Identities=29%  Similarity=0.422  Sum_probs=20.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+..+++|.|..|+|||+++..+.
T Consensus         7 ~~~~~i~v~G~~~~GKssl~~~l~   30 (181)
T 3tw8_B            7 DHLFKLLIIGDSGVGKSSLLLRFA   30 (181)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHHC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHh
Confidence            446799999999999999998875

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=91.74  E-value=0.12  Score=43.08  Aligned_cols=26  Identities=35%  Similarity=0.408  Sum_probs=22.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+..+++|.|+.|+|||+++..++.-
T Consensus         5 ~~~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            5 KSSYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHhC
Confidence            35679999999999999999988763

>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=91.73  E-value=0.11  Score=46.92  Aligned_cols=35  Identities=23%  Similarity=0.194  Sum_probs=26.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH---HHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY---AHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~---A~~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.   --..|-|.+
T Consensus        27 ~~Ge~~~l~G~nGsGKSTLlk~l~Gl~~~~p~~G~I~~   64 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTLGKILAGDPEYTVERGEILL   64 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTCTTCEEEEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCCCCCCceEEEE
Confidence            35778999999999999999987764   123455544

>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=91.72  E-value=0.1  Score=47.29  Aligned_cols=35  Identities=14%  Similarity=0.261  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        31 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~~p~~G~i~~   66 (257)
T 1g6h_A           31 NKGDVTLIIGPNGSGKSTLINVITGFLKADEGRVYF   66 (257)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEE
Confidence            4677899999999999999997765432 3355544

>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=91.71  E-value=0.11  Score=47.51  Aligned_cols=35  Identities=23%  Similarity=0.320  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        48 ~~Gei~~liG~NGsGKSTLlk~l~Gl~~p~~G~I~~   83 (263)
T 2olj_A           48 REGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIII   83 (263)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEEcCCCCcHHHHHHHHHcCCCCCCcEEEE
Confidence            4678899999999999999987665432 2354443

>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=91.69  E-value=0.1  Score=47.97  Aligned_cols=26  Identities=23%  Similarity=0.254  Sum_probs=22.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        32 ~~Ge~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           32 KRGEVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            45778999999999999999877654

>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=91.67  E-value=0.1  Score=47.16  Aligned_cols=35  Identities=23%  Similarity=0.278  Sum_probs=25.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-.-.|-|.+
T Consensus        24 ~~Ge~~~liG~NGsGKSTLlk~l~Gl~~p~G~i~~   58 (249)
T 2qi9_C           24 RAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQF   58 (249)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSSCCEEEEEE
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCCCCCeEEEE
Confidence            46778999999999999999977654321154443

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=91.66  E-value=0.14  Score=49.54  Aligned_cols=41  Identities=20%  Similarity=0.132  Sum_probs=32.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CCccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PWVLR  106 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~~~~  106 (342)
                      ....+++.|+.|||||+++..++..+...|.-|+-+ |.+..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dpkge~   93 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDM   93 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHH
T ss_pred             CcceEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCch
Confidence            467899999999999999999998888776555445 66544

>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=91.65  E-value=0.11  Score=42.07  Aligned_cols=23  Identities=35%  Similarity=0.502  Sum_probs=20.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|..|+|||+++..+..
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            6 QFKLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHHc
Confidence            46899999999999999988765

>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=91.64  E-value=0.11  Score=42.56  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=21.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++.++..
T Consensus        14 ~~~~i~v~G~~~~GKSsli~~l~~   37 (179)
T 1z0f_A           14 YIFKYIIIGDMGVGKSCLLHQFTE   37 (179)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHc
Confidence            457999999999999999998865

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.63  E-value=0.11  Score=47.34  Aligned_cols=35  Identities=20%  Similarity=0.252  Sum_probs=25.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        31 ~~Ge~~~liG~nGsGKSTLl~~i~Gl~~p~~G~I~~   66 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTLLQIVAGLIEPTSGDVLY   66 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCCCCCCcEEEE
Confidence            4677899999999999999987654432 2355443

>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=91.62  E-value=0.11  Score=43.16  Aligned_cols=25  Identities=36%  Similarity=0.575  Sum_probs=21.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        16 ~~~~ki~v~G~~~~GKSsl~~~l~~   40 (183)
T 3kkq_A           16 LPTYKLVVVGDGGVGKSALTIQFFQ   40 (183)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHh
Confidence            4567999999999999999998873

>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=91.59  E-value=0.11  Score=42.12  Aligned_cols=23  Identities=39%  Similarity=0.509  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..++++.|..|+|||+++..+..
T Consensus         3 ~~ki~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            3 EYKLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHc
Confidence            35899999999999999998874

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=91.57  E-value=0.15  Score=46.08  Aligned_cols=40  Identities=35%  Similarity=0.470  Sum_probs=28.7

Q ss_pred             chhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          47 RNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        47 R~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++...++++.+..   ...+..++++.|..|+|||+++..+..
T Consensus        22 ~~~l~~~~~~~~~---~~~~~~~I~vvG~~g~GKSSLin~l~~   61 (270)
T 1h65_A           22 QTKLLELLGNLKQ---EDVNSLTILVMGKGGVGKSSTVNSIIG   61 (270)
T ss_dssp             HHHHHHHHHHHHH---TTCCEEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhh---cCCCCeEEEEECCCCCCHHHHHHHHhC
Confidence            3334455555544   234568999999999999999998774

>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=91.56  E-value=0.12  Score=41.95  Aligned_cols=21  Identities=24%  Similarity=0.316  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +++|.|..|+|||+++.++..
T Consensus         2 ki~~~G~~~~GKssl~~~l~~   22 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKL   22 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            789999999999999998865

>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=91.55  E-value=0.1  Score=43.89  Aligned_cols=23  Identities=26%  Similarity=0.268  Sum_probs=18.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      -.+|+|+.|||||++|. ++.++.
T Consensus        28 ~~~i~G~NGsGKStll~-ai~~~l   50 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGD-AILFVL   50 (182)
T ss_dssp             EEEEEECTTSSHHHHHH-HHHHHT
T ss_pred             cEEEECCCCCCHHHHHH-HHHHHH
Confidence            78999999999998875 455543

>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=91.55  E-value=0.21  Score=51.99  Aligned_cols=41  Identities=24%  Similarity=0.152  Sum_probs=29.0

Q ss_pred             ech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          46 IRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        46 vR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      -|+ ...++++.|..     .....++|+|++|||||+++..+....
T Consensus       190 Gr~~~i~~l~~~l~~-----~~~~~vlL~G~~GtGKT~la~~la~~l  231 (758)
T 1r6b_X          190 GREKELERAIQVLCR-----RRKNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_dssp             SCHHHHHHHHHHHTS-----SSSCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhc-----cCCCCeEEEcCCCCCHHHHHHHHHHHH
Confidence            355 33445555544     356789999999999999887777655

>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=91.53  E-value=0.13  Score=42.38  Aligned_cols=25  Identities=24%  Similarity=0.259  Sum_probs=21.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..++++.|..|+|||+++..+..
T Consensus         6 ~~~~ki~v~G~~~~GKssl~~~~~~   30 (182)
T 3bwd_D            6 SRFIKCVTVGDGAVGKTCLLISYTS   30 (182)
T ss_dssp             -CCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999999987764

>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=91.53  E-value=0.2  Score=45.97  Aligned_cols=41  Identities=22%  Similarity=0.314  Sum_probs=29.9

Q ss_pred             HHHHHHHHHhccC----CCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          50 MLELVGYLKSMTN----FDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        50 t~el~~~l~~~~~----~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+++++.|++...    ......++++.|..|+|||+++..++..
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~~~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B            3 LIPVINKLQDVFNTLGSDPLDLPQIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             HHHHHHHHHHHTTTSSSCTTCCCEEEEEECSSSSHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHcCCCCCCCCeEEEEcCCCCCHHHHHHHHHCC
Confidence            4566777765221    1235679999999999999999998754

>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=91.52  E-value=0.09  Score=49.75  Aligned_cols=24  Identities=17%  Similarity=0.099  Sum_probs=20.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..-++|+|++|||||++..|+.+.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            445799999999999999998664

>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=91.50  E-value=0.11  Score=43.30  Aligned_cols=22  Identities=23%  Similarity=0.323  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|.|..|+|||+++.++..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~   23 (190)
T 2cxx_A            2 ATIIFAGRSNVGKSTLIYRLTG   23 (190)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4789999999999999998763

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=91.49  E-value=0.11  Score=49.61  Aligned_cols=23  Identities=35%  Similarity=0.459  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      -++|+|+.|+|||++| .++.||.
T Consensus        25 ~~~i~G~NGaGKTTll-~ai~~al   47 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLF-EAISFAL   47 (365)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHh
Confidence            6789999999999888 6777764

>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=91.49  E-value=0.19  Score=48.37  Aligned_cols=25  Identities=16%  Similarity=0.201  Sum_probs=21.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+...++|.|++||||||++..+..
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHh
Confidence            5677999999999999999987775

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=91.45  E-value=0.12  Score=42.82  Aligned_cols=29  Identities=24%  Similarity=0.109  Sum_probs=21.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .-++|+|..||||||+...+...   .||-++
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~---lg~~~i   36 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLA---LKLEVL   36 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH---HTCCEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH---hCCCEE
Confidence            35889999999999987766442   355444

>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=91.44  E-value=0.11  Score=47.37  Aligned_cols=35  Identities=20%  Similarity=0.258  Sum_probs=26.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        35 ~~Ge~~~liG~nGsGKSTLl~~l~Gl~~p~~G~I~~   70 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTLLRLLTGYLSPSHGECHL   70 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHHHHHHTSSSCCSSCEEEE
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCCCCCCcEEEE
Confidence            4678899999999999999987765432 3455544

>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=91.44  E-value=0.12  Score=42.96  Aligned_cols=24  Identities=29%  Similarity=0.421  Sum_probs=21.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus        10 ~~~ki~v~G~~~~GKSsli~~l~~   33 (195)
T 3bc1_A           10 YLIKFLALGDSGVGKTSVLYQYTD   33 (195)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEEECCCCCCHHHHHHHHhc
Confidence            357999999999999999988764

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=91.43  E-value=0.17  Score=43.83  Aligned_cols=32  Identities=22%  Similarity=0.299  Sum_probs=27.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++-|..||||||....+..+-.++|.=|+..
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~t   34 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVILK   34 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            57889999999999999999999888766554

>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=91.41  E-value=0.12  Score=46.93  Aligned_cols=35  Identities=23%  Similarity=0.312  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        39 ~~Gei~~l~G~NGsGKSTLlk~l~Gl~~p~~G~I~~   74 (256)
T 1vpl_A           39 EEGEIFGLIGPNGAGKTTTLRIISTLIKPSSGIVTV   74 (256)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            4677899999999999999987754432 2355443

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=91.40  E-value=0.18  Score=47.60  Aligned_cols=30  Identities=23%  Similarity=0.170  Sum_probs=26.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .+...+.|.|++||||||+|..+..+....
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~~~~   82 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLLTAA   82 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhhhhC
Confidence            567899999999999999999999876643

>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=91.40  E-value=0.16  Score=49.55  Aligned_cols=32  Identities=22%  Similarity=0.165  Sum_probs=23.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH-ENNYLL   98 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiV   98 (342)
                      ...+.|.|+.|+||||+|.-+.-.-. ..|-|.
T Consensus        69 ~~~valvG~nGaGKSTLln~L~Gl~~p~~GsI~  101 (413)
T 1tq4_A           69 VLNVAVTGETGSGKSSFINTLRGIGNEEEGAAK  101 (413)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHTCCTTSTTSCC
T ss_pred             CeEEEEECCCCCcHHHHHHHHhCCCCccCceEE
Confidence            44888999999999999998875322 345443

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=91.39  E-value=0.11  Score=42.68  Aligned_cols=25  Identities=20%  Similarity=0.238  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus         4 ~~~~ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            4 MRQLKIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             CCEEEEEEECCTTSSHHHHHHHHHG
T ss_pred             CceEEEEEECcCCCCHHHHHHHHHh
Confidence            3467899999999999999998764

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=91.38  E-value=0.1  Score=44.44  Aligned_cols=29  Identities=14%  Similarity=0.218  Sum_probs=24.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNY   96 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gw   96 (342)
                      ..+.|.|+.||||||++.-++-+....|+
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~g~   31 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRERGL   31 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhcCC
Confidence            36789999999999999999888776654

>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=91.34  E-value=0.13  Score=42.52  Aligned_cols=24  Identities=29%  Similarity=0.513  Sum_probs=21.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++.++..
T Consensus        11 ~~~ki~v~G~~~~GKSsli~~l~~   34 (181)
T 2efe_B           11 INAKLVLLGDVGAGKSSLVLRFVK   34 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHHc
Confidence            457899999999999999988864

>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=91.32  E-value=0.12  Score=49.38  Aligned_cols=35  Identities=17%  Similarity=0.379  Sum_probs=26.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        28 ~~Ge~~~llGpsGsGKSTLLr~iaGl~~p~~G~I~i   63 (359)
T 3fvq_A           28 DPGEILFIIGASGCGKTTLLRCLAGFEQPDSGEISL   63 (359)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCchHHHHHHHHhcCCCCCCcEEEE
Confidence            4577889999999999999987765443 3465544

>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=91.31  E-value=0.11  Score=42.81  Aligned_cols=25  Identities=32%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus         8 ~~~~~i~v~G~~~~GKssli~~l~~   32 (180)
T 2g6b_A            8 DVAFKVMLVGDSGVGKTCLLVRFKD   32 (180)
T ss_dssp             SEEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcceEEEEECcCCCCHHHHHHHHHh
Confidence            4467999999999999999988764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=91.29  E-value=0.18  Score=52.55  Aligned_cols=42  Identities=29%  Similarity=0.317  Sum_probs=28.0

Q ss_pred             EEech-hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          44 ILIRN-CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        44 ~lvR~-~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ++-|+ ....++..|..     ...+.++|+|++|||||++...+...
T Consensus       182 iiG~~~~i~~l~~~l~~-----~~~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          182 VIGRSKEIQRVIEVLSR-----RTKNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             CCCCHHHHHHHHHHHHC-----SSSCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             ccCchHHHHHHHHHHhC-----CCCCCeEEECCCCCCHHHHHHHHHHH
Confidence            34455 34445555544     44567999999999999976555444

>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=91.28  E-value=0.12  Score=46.23  Aligned_cols=24  Identities=21%  Similarity=0.105  Sum_probs=19.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +...+.|+|+.||||||+...+..
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            345789999999999998876655

>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=91.26  E-value=0.17  Score=44.97  Aligned_cols=36  Identities=25%  Similarity=0.281  Sum_probs=27.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...+++.|+.|+||||++.++..+.. .|.=|+-|
T Consensus        12 ~~~~i~~~~GkgGvGKTTl~~~La~~l~-~g~~v~vv   47 (262)
T 1yrb_A           12 MASMIVVFVGTAGSGKTTLTGEFGRYLE-DNYKVAYV   47 (262)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHT-TTSCEEEE
T ss_pred             cceEEEEEeCCCCCCHHHHHHHHHHHHH-CCCeEEEE
Confidence            3456788899999999999999998776 66444333

>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=91.24  E-value=0.21  Score=43.24  Aligned_cols=32  Identities=19%  Similarity=0.130  Sum_probs=24.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...+.|+|..||||||+...+...   .|+-|+..
T Consensus        12 ~~iIgltG~~GSGKSTva~~L~~~---lg~~vid~   43 (192)
T 2grj_A           12 HMVIGVTGKIGTGKSTVCEILKNK---YGAHVVNV   43 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh---cCCEEEEC
Confidence            457889999999999998877654   26666553

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=91.21  E-value=0.12  Score=46.72  Aligned_cols=33  Identities=21%  Similarity=0.287  Sum_probs=24.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYL   97 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwi   97 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|
T Consensus        29 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~I   62 (253)
T 2nq2_C           29 NKGDILAVLGQNGCGKSTLLDLLLGIHRPIQGKI   62 (253)
T ss_dssp             ETTCEEEEECCSSSSHHHHHHHHTTSSCCSEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCCCCCCcEE
Confidence            3577899999999999999987765432 33555

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=91.17  E-value=0.24  Score=46.63  Aligned_cols=35  Identities=23%  Similarity=0.269  Sum_probs=27.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcc
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVL  105 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~  105 (342)
                      ..++|.|+.|||||++...+   |...|+.++.+.+..
T Consensus         6 ~~i~i~GptGsGKTtla~~L---a~~l~~~iis~Ds~q   40 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMAL---ADALPCELISVDSAL   40 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHH---HHHSCEEEEEECTTT
T ss_pred             cEEEEECCCCCCHHHHHHHH---HHHcCCcEEeccchh
Confidence            47899999999999986655   456789998886543

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=91.14  E-value=0.24  Score=44.85  Aligned_cols=25  Identities=24%  Similarity=0.312  Sum_probs=21.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|.+|+|||+++..++.
T Consensus        24 ~~~~~i~vvG~~~~GKSSLln~l~g   48 (299)
T 2aka_B           24 LDLPQIAVVGGQSAGKSSVLENFVG   48 (299)
T ss_dssp             CCCCEEEEEEBTTSCHHHHHHHHHT
T ss_pred             CCCCeEEEEeCCCCCHHHHHHHHHC
Confidence            3567999999999999999998864

>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=91.13  E-value=0.15  Score=42.90  Aligned_cols=25  Identities=32%  Similarity=0.518  Sum_probs=22.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++.++..
T Consensus         6 ~~~~ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A            6 SNDYRVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCeeEEEEECCCCCcHHHHHHHHHc
Confidence            4567999999999999999998875

>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=91.13  E-value=0.13  Score=42.57  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=21.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|..|+|||+++..+..
T Consensus        17 ~~~ki~v~G~~~~GKSsli~~l~~   40 (187)
T 2a9k_A           17 ALHKVIMVGSGGVGKSALTLQFMY   40 (187)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHhh
Confidence            457999999999999999988774

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=91.13  E-value=0.14  Score=44.61  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .-.+|+|+.|+|||++|- ++.||.
T Consensus        24 ~~~~I~G~NgsGKStil~-ai~~~l   47 (203)
T 3qks_A           24 GINLIIGQNGSGKSSLLD-AILVGL   47 (203)
T ss_dssp             EEEEEECCTTSSHHHHHH-HHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHH-HHHHHh
Confidence            467899999999999874 556655

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=91.12  E-value=0.11  Score=43.57  Aligned_cols=24  Identities=33%  Similarity=0.434  Sum_probs=21.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++.++..
T Consensus        15 ~~~ki~v~G~~~~GKSsli~~l~~   38 (196)
T 3tkl_A           15 YLFKLLLIGDSGVGKSCLLLRFAD   38 (196)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHHc
Confidence            457999999999999999988863

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=91.11  E-value=0.13  Score=46.61  Aligned_cols=31  Identities=19%  Similarity=0.214  Sum_probs=23.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ...++|+|+.||||||++..+...   -||-++.
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~---lg~~~~d   78 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARS---LGYTFFD   78 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHH---HTCEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh---cCCcEEe
Confidence            568999999999999998776543   3665444

>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=91.10  E-value=0.15  Score=47.26  Aligned_cols=35  Identities=14%  Similarity=0.216  Sum_probs=28.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...+++.|+.|+||||++..+..+....|.=|+.+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~  132 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLV  132 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            45678899999999999999998887777655555

>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=91.08  E-value=0.12  Score=42.82  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=20.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|..|+|||+++.++..
T Consensus         4 ~~~~i~~~G~~~~GKssl~~~l~~   27 (186)
T 1mh1_A            4 QAIKCVVVGDGAVGKTCLLISYTT   27 (186)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEEEECCCCCCHHHHHHHHHc
Confidence            456899999999999999988764

>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=91.07  E-value=0.14  Score=49.03  Aligned_cols=35  Identities=17%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   62 (359)
T 2yyz_A           27 KDGEFVALLGPSGCGKTTTLLMLAGIYKPTSGEIYF   62 (359)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             cCCCEEEEEcCCCchHHHHHHHHHCCCCCCccEEEE
Confidence            4577899999999999999987765433 3466654

>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=91.06  E-value=0.14  Score=42.93  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=22.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus        14 ~~~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           14 HQEHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            4678999999999999999998763

>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=91.03  E-value=0.11  Score=45.81  Aligned_cols=32  Identities=22%  Similarity=0.273  Sum_probs=24.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .++.-+.|.|+.||||||++..+..+   .|-+++
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~---~g~v~~   49 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY---KNDICL   49 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG---TTTEEE
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc---cCCeEE
Confidence            45667899999999999999887766   553443

>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=91.02  E-value=0.1  Score=44.51  Aligned_cols=24  Identities=25%  Similarity=0.220  Sum_probs=20.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+..+++|.|+.|||||+++..+.
T Consensus        24 ~~~~~v~lvG~~g~GKSTLl~~l~   47 (210)
T 1pui_A           24 DTGIEVAFAGRSNAGKSSALNTLT   47 (210)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHh
Confidence            457789999999999999997654

>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=91.01  E-value=0.14  Score=49.42  Aligned_cols=35  Identities=23%  Similarity=0.286  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~Ge~~~llGpsGsGKSTLLr~iaGl~~p~~G~I~i   62 (381)
T 3rlf_A           27 HEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI   62 (381)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEEcCCCchHHHHHHHHHcCCCCCCeEEEE
Confidence            4577899999999999999987765443 3466654

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.00  E-value=0.13  Score=47.30  Aligned_cols=35  Identities=23%  Similarity=0.422  Sum_probs=25.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        45 ~~Ge~~~liG~NGsGKSTLlk~l~Gl~~p~~G~I~~   80 (279)
T 2ihy_A           45 AKGDKWILYGLNGAGKTTLLNILNAYEPATSGTVNL   80 (279)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCCCCCCeEEEE
Confidence            4677899999999999999987765432 3455544

>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=90.98  E-value=0.14  Score=43.29  Aligned_cols=25  Identities=32%  Similarity=0.569  Sum_probs=21.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        26 ~~~~ki~v~G~~~vGKSsli~~l~~   50 (196)
T 2atv_A           26 SAEVKLAIFGRAGVGKSALVVRFLT   50 (196)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHh
Confidence            4578999999999999999988775

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=90.91  E-value=0.14  Score=48.93  Aligned_cols=35  Identities=20%  Similarity=0.228  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   62 (362)
T 2it1_A           27 KDGEFMALLGPSGSGKSTLLYTIAGIYKPTSGKIYF   62 (362)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCchHHHHHHHHhcCCCCCceEEEE
Confidence            4577889999999999999987765433 3466655

>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=90.91  E-value=0.14  Score=42.74  Aligned_cols=24  Identities=33%  Similarity=0.497  Sum_probs=21.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..++++.|..|+|||+++.++..
T Consensus        20 ~~~ki~vvG~~~~GKSsli~~l~~   43 (190)
T 3con_A           20 TEYKLVVVGAGGVGKSALTIQLIQ   43 (190)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceeEEEEECcCCCCHHHHHHHHHc
Confidence            346899999999999999999875

>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=90.91  E-value=0.13  Score=47.97  Aligned_cols=54  Identities=15%  Similarity=0.089  Sum_probs=33.4

Q ss_pred             HHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHH
Q psy3261         239 TRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYE  310 (342)
Q Consensus       239 ~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~  310 (342)
                      ...|++++.....+..+|++|+...      .  ++..+..+          .++++.++.+|+...+....
T Consensus        99 ~naLLk~LEep~~~t~fIl~t~~~~------k--l~~tI~SR----------~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           99 ANAFLKALEEPPEYAVIVLNTRRWH------Y--LLPTIKSR----------VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             HHHTHHHHHSCCTTEEEEEEESCGG------G--SCHHHHTT----------SEEEECCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCeEEEEEECChH------h--ChHHHHce----------eEeCCCCCHHHHHHHHHHHh
Confidence            4667788776667777777775421      1  22222222          27788888888888876554

>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=90.88  E-value=0.13  Score=43.11  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|+.|+|||+++.++..
T Consensus         5 ~~~~ki~v~G~~~vGKSsli~~l~~   29 (184)
T 1m7b_A            5 NVKCKIVVVGDSQCGKTALLHVFAK   29 (184)
T ss_dssp             -CEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEEEECCCCCCHHHHHHHHhc
Confidence            4567899999999999999998775

>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=90.87  E-value=0.28  Score=46.05  Aligned_cols=38  Identities=16%  Similarity=0.124  Sum_probs=28.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVL  105 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~  105 (342)
                      +....++|.||.|||||++...+   |...+..|+...+.+
T Consensus         8 ~~~~~i~i~GptgsGKt~la~~L---a~~~~~~iis~Ds~q   45 (316)
T 3foz_A            8 SLPKAIFLMGPTASGKTALAIEL---RKILPVELISVDSAL   45 (316)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHH---HHHSCEEEEECCTTT
T ss_pred             CCCcEEEEECCCccCHHHHHHHH---HHhCCCcEEeccccc
Confidence            33457889999999999997666   455688888875543

>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=90.86  E-value=0.12  Score=45.69  Aligned_cols=24  Identities=38%  Similarity=0.437  Sum_probs=20.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ....+++|.|+.|+|||+++..++
T Consensus        27 ~~~~~i~lvG~~g~GKStlin~l~   50 (239)
T 3lxx_A           27 NSQLRIVLVGKTGAGKSATGNSIL   50 (239)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHc
Confidence            356799999999999999998876

>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=90.85  E-value=0.15  Score=49.06  Aligned_cols=35  Identities=20%  Similarity=0.319  Sum_probs=26.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        35 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   70 (372)
T 1v43_A           35 KDGEFLVLLGPSGCGKTTTLRMIAGLEEPTEGRIYF   70 (372)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCChHHHHHHHHHcCCCCCceEEEE
Confidence            4577899999999999999987765433 3466655

>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=90.83  E-value=0.12  Score=49.19  Aligned_cols=35  Identities=23%  Similarity=0.464  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        24 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~~   59 (348)
T 3d31_A           24 ESGEYFVILGPTGAGKTLFLELIAGFHVPDSGRILL   59 (348)
T ss_dssp             CTTCEEEEECCCTHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCccHHHHHHHHHcCCCCCCcEEEE
Confidence            4567899999999999999998765433 3466655

>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=90.83  E-value=0.14  Score=42.42  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +..+++|.|..|+|||+++..++
T Consensus         5 ~~~ki~~~G~~~~GKSsli~~l~   27 (181)
T 3t5g_A            5 KSRKIAILGYRSVGKSSLTIQFV   27 (181)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHH
T ss_pred             ceEEEEEECcCCCCHHHHHHHHH
Confidence            45789999999999999999887

>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=90.79  E-value=0.13  Score=43.11  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=21.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus        18 ~~~~ki~v~G~~~~GKSsli~~l~~   42 (189)
T 1z06_A           18 SRIFKIIVIGDSNVGKTCLTYRFCA   42 (189)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHc
Confidence            3457999999999999999998764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=90.79  E-value=0.16  Score=44.88  Aligned_cols=35  Identities=20%  Similarity=0.237  Sum_probs=26.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      +..++|.|..||||||+...+..+.  +++.++..|-
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l--~~~~~~~Ep~   36 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTY--PEWHVATEPV   36 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHC--TTSEEECCCG
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHc--CCCeeeecch
Confidence            3568999999999999988876653  3566655553

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=90.78  E-value=0.14  Score=48.81  Aligned_cols=35  Identities=20%  Similarity=0.256  Sum_probs=26.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        39 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   74 (355)
T 1z47_A           39 REGEMVGLLGPSGSGKTTILRLIAGLERPTKGDVWI   74 (355)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCCCCCccEEEE
Confidence            3577899999999999999997765433 3466654

>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=90.78  E-value=0.14  Score=43.57  Aligned_cols=24  Identities=38%  Similarity=0.567  Sum_probs=20.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|+.|+|||+++..+..
T Consensus        19 ~~~~i~v~G~~~~GKSsli~~l~~   42 (213)
T 3cph_A           19 SIMKILLIGDSGVGKSCLLVRFVE   42 (213)
T ss_dssp             -CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHh
Confidence            467999999999999999988764

>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=90.76  E-value=0.15  Score=47.29  Aligned_cols=33  Identities=15%  Similarity=0.266  Sum_probs=25.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYL   97 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwi   97 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|
T Consensus        62 ~~Ge~~~i~G~NGsGKSTLlk~l~Gl~~p~~G~I   95 (290)
T 2bbs_A           62 ERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKI   95 (290)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHTTSSCEEEEEE
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCCCCCCcEE
Confidence            4677899999999999999987765432 34554

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=90.75  E-value=0.18  Score=44.55  Aligned_cols=33  Identities=12%  Similarity=0.177  Sum_probs=24.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .+...+.|+|+.|||||++...+..   ..|+.++.
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~---~lg~~~~d   46 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAK---DFGFTYLD   46 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHH---HHCCEEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH---HcCCceec
Confidence            5667899999999999998876654   23654443

>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=90.74  E-value=0.15  Score=42.79  Aligned_cols=24  Identities=38%  Similarity=0.389  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus        24 ~~~ki~v~G~~~~GKSsLi~~l~~   47 (193)
T 2oil_A           24 FVFKVVLIGESGVGKTNLLSRFTR   47 (193)
T ss_dssp             EEEEEEEESSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHhc
Confidence            357899999999999999988765

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=90.74  E-value=0.21  Score=50.97  Aligned_cols=38  Identities=18%  Similarity=0.178  Sum_probs=29.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh----CC-eEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE----NN-YLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~----~g-wiVl~vP~~  104 (342)
                      ..-++|+|++|||||+++..++.....    .+ -+++--|..
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg  206 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTG  206 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCCh
Confidence            567999999999999999999887663    34 344545754

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=90.71  E-value=0.2  Score=50.16  Aligned_cols=36  Identities=17%  Similarity=0.229  Sum_probs=29.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|..||||||++..+..++.+.|.=|+-|
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllV  135 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLI  135 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            345788999999999999999999988877755544

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=90.70  E-value=0.12  Score=51.00  Aligned_cols=37  Identities=27%  Similarity=0.328  Sum_probs=30.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCC-e-EEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENN-Y-LLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~g-w-iVl~v  101 (342)
                      .++.++.|.|+.||||||+|.-+.-++. ..| - |.+.-
T Consensus       136 ~~Ge~v~IvGpnGsGKSTLlr~L~Gl~~p~~G~~pI~vdg  175 (460)
T 2npi_A          136 FEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINL  175 (460)
T ss_dssp             SSCCCEEEEESTTSSHHHHHHHHHHTTHHHHCCCCEEEEC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCcccccCCceeEEEcC
Confidence            4688999999999999999999999886 446 3 55543

>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=90.68  E-value=0.22  Score=46.09  Aligned_cols=36  Identities=17%  Similarity=0.193  Sum_probs=28.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+.+.|+.|+||||++..+..+....|.=|+.+
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~  132 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            455788889999999999999998777665544444

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=90.67  E-value=0.14  Score=48.79  Aligned_cols=35  Identities=20%  Similarity=0.300  Sum_probs=26.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVH  100 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~  100 (342)
                      +...++|.|+.||||||+|.-+..+-. ..|-|.+.
T Consensus       174 ~G~~i~ivG~sGsGKSTll~~l~~~~~~~~g~I~ie  209 (361)
T 2gza_A          174 LERVIVVAGETGSGKTTLMKALMQEIPFDQRLITIE  209 (361)
T ss_dssp             TTCCEEEEESSSSCHHHHHHHHHTTSCTTSCEEEEE
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHhcCCCCceEEEEC
Confidence            467899999999999999998877543 34555443

>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=90.66  E-value=0.13  Score=43.31  Aligned_cols=25  Identities=16%  Similarity=0.141  Sum_probs=21.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++..+++|.|..|+|||+++.++..
T Consensus        20 ~~~~ki~v~G~~~~GKSsli~~l~~   44 (188)
T 1zd9_A           20 KEEMELTLVGLQYSGKTTFVNVIAS   44 (188)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCHHHHHHHHHc
Confidence            3467899999999999999998864

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=90.66  E-value=0.18  Score=47.86  Aligned_cols=28  Identities=29%  Similarity=0.284  Sum_probs=25.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .++-++.|.|+.||||||+|..+.-...
T Consensus        69 ~~Gq~~gIiG~nGaGKTTLl~~I~g~~~   96 (347)
T 2obl_A           69 GIGQRIGIFAGSGVGKSTLLGMICNGAS   96 (347)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            5688999999999999999998888864

>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=90.65  E-value=0.13  Score=48.88  Aligned_cols=25  Identities=16%  Similarity=0.173  Sum_probs=22.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ..++.|.|+.||||||++..+.-.-
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~  194 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVF  194 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999999887763

>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=90.64  E-value=0.13  Score=42.89  Aligned_cols=25  Identities=16%  Similarity=0.224  Sum_probs=20.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus        19 ~~~~~i~v~G~~~~GKSsli~~l~~   43 (181)
T 2h17_A           19 SQEHKVIIVGLDNAGKTTILYQFSM   43 (181)
T ss_dssp             --CEEEEEEEETTSSHHHHHHHHHT
T ss_pred             CceeEEEEECCCCCCHHHHHHHHhc
Confidence            3567999999999999999998864

>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=90.64  E-value=0.17  Score=41.79  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .-.+|+|+.|||||++|- ++.||.
T Consensus        24 g~~~I~G~NGsGKStil~-Ai~~~l   47 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLD-AILVGL   47 (149)
T ss_dssp             EEEEEECCTTSSHHHHHH-HHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHH
Confidence            467899999999999854 666665

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=90.62  E-value=0.2  Score=56.89  Aligned_cols=38  Identities=16%  Similarity=0.186  Sum_probs=34.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|||||+++.|++..+..+|--|+||.
T Consensus       381 ~~G~lilI~G~pGsGKTtLaLq~a~~~~~~G~~vlyis  418 (1706)
T 3cmw_A          381 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  418 (1706)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEE
Confidence            36778999999999999999999999998888888884

>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=90.62  E-value=0.16  Score=43.45  Aligned_cols=26  Identities=19%  Similarity=0.240  Sum_probs=21.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+..+++|.|..|+|||+++.++..-
T Consensus         5 ~~~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            5 SSQRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             ---CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            45689999999999999999988764

>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=90.61  E-value=0.13  Score=42.97  Aligned_cols=25  Identities=20%  Similarity=0.231  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..++++.|..|+|||+++.++..
T Consensus        16 ~~~~~i~v~G~~~~GKssl~~~l~~   40 (186)
T 1ksh_A           16 ERELRLLMLGLDNAGKTTILKKFNG   40 (186)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999999988763

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=90.58  E-value=0.18  Score=42.22  Aligned_cols=23  Identities=22%  Similarity=0.283  Sum_probs=20.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      ++..++++.|..|+|||+++.++
T Consensus        20 ~~~~~i~v~G~~~~GKssli~~l   42 (189)
T 2x77_A           20 DRKIRVLMLGLDNAGKTSILYRL   42 (189)
T ss_dssp             TSCEEEEEEEETTSSHHHHHHHT
T ss_pred             CCceEEEEECCCCCCHHHHHHHH
Confidence            46789999999999999999876

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=90.58  E-value=0.35  Score=42.54  Aligned_cols=30  Identities=23%  Similarity=0.247  Sum_probs=26.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNY   96 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gw   96 (342)
                      +.-+++.|..||||||....+..+-...|.
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~   32 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETLEQLGI   32 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHTTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence            456889999999999999999999888886

>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=90.57  E-value=0.14  Score=42.36  Aligned_cols=25  Identities=28%  Similarity=0.333  Sum_probs=21.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.+.+.
T Consensus         5 ~~~~ki~~vG~~~vGKTsli~~l~~   29 (178)
T 2iwr_A            5 IPELRLGVLGDARSGKSSLIHRFLT   29 (178)
T ss_dssp             CCEEEEEEECCGGGCHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHh
Confidence            3567899999999999999998765

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=90.56  E-value=0.43  Score=50.13  Aligned_cols=48  Identities=19%  Similarity=0.281  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH-hC--Ce-EEEEeCC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH-EN--NY-LLVHIPW  103 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~--gw-iVl~vP~  103 (342)
                      ...+|...++.       +..++|.|+.|||||+++.+++.... ..  |- +++-.|.
T Consensus        98 q~~~i~~~l~~-------~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~  149 (773)
T 2xau_A           98 QRDEFLKLYQN-------NQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPR  149 (773)
T ss_dssp             GHHHHHHHHHH-------CSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESC
T ss_pred             HHHHHHHHHhC-------CCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCch
Confidence            34455666655       55799999999999998888755433 12  44 4444575

>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=90.56  E-value=0.16  Score=49.15  Aligned_cols=35  Identities=29%  Similarity=0.405  Sum_probs=26.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-...|-|.+
T Consensus        45 ~~Ge~~~llGpsGsGKSTLLr~iaGl~~~~G~I~i   79 (390)
T 3gd7_A           45 SPGQRVGLLGRTGSGKSTLLSAFLRLLNTEGEIQI   79 (390)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTCSEEEEEEEE
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCCCCCCeEEEE
Confidence            46789999999999999999877654334455544

>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=90.55  E-value=0.15  Score=42.91  Aligned_cols=25  Identities=20%  Similarity=0.215  Sum_probs=21.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ...+++|.|..|+|||+++..+..-
T Consensus        22 ~~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           22 YMFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             ECEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeeEEEEECCCCcCHHHHHHHHhcC
Confidence            4579999999999999999988754

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=90.53  E-value=0.2  Score=52.94  Aligned_cols=32  Identities=19%  Similarity=0.248  Sum_probs=25.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHE-NNYLLV   99 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl   99 (342)
                      .-.+|.|++|||||+++..++.+..+ .+.-|+
T Consensus       372 ~~~lI~GppGTGKT~ti~~~i~~l~~~~~~~il  404 (800)
T 2wjy_A          372 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVL  404 (800)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHTTCSSCEE
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEE
Confidence            46899999999999999999988775 444443

>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=90.52  E-value=0.15  Score=43.02  Aligned_cols=25  Identities=24%  Similarity=0.343  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus        12 ~~~~ki~v~G~~~~GKSsli~~l~~   36 (206)
T 2bov_A           12 LALHKVIMVGSGGVGKSALTLQFMY   36 (206)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHh
Confidence            3457999999999999999988774

>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=90.51  E-value=0.16  Score=42.65  Aligned_cols=24  Identities=29%  Similarity=0.477  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|..|+|||+++..+..
T Consensus        20 ~~~ki~v~G~~~~GKSsli~~l~~   43 (191)
T 2a5j_A           20 YLFKYIIIGDTGVGKSCLLLQFTD   43 (191)
T ss_dssp             EEEEEEEESSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHhc
Confidence            356899999999999999988764

>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=90.51  E-value=0.16  Score=48.83  Aligned_cols=35  Identities=17%  Similarity=0.339  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   62 (372)
T 1g29_1           27 KDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYI   62 (372)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCcHHHHHHHHHHcCCCCCccEEEE
Confidence            3577889999999999999988765433 3466654

>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=90.46  E-value=0.14  Score=45.21  Aligned_cols=25  Identities=28%  Similarity=0.347  Sum_probs=21.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ....++|.|++|+|||++...++..
T Consensus        33 ~g~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHHHHHTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            3568999999999999998887654

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=90.41  E-value=0.99  Score=38.14  Aligned_cols=23  Identities=17%  Similarity=0.395  Sum_probs=17.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++.++.|||||.+....+.
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~   60 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIA   60 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEECCCCChHHHHHHHHHH
Confidence            35699999999999987544443

>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=90.40  E-value=0.17  Score=42.73  Aligned_cols=24  Identities=33%  Similarity=0.484  Sum_probs=21.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|..|+|||+++..+..
T Consensus        22 ~~~ki~vvG~~~~GKSsli~~l~~   45 (192)
T 2fg5_A           22 RELKVCLLGDTGVGKSSIVCRFVQ   45 (192)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CceEEEEECcCCCCHHHHHHHHhc
Confidence            457999999999999999988864

>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=90.35  E-value=0.17  Score=42.90  Aligned_cols=24  Identities=21%  Similarity=0.297  Sum_probs=21.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+..+++|.|+.|+|||+++.++.
T Consensus        27 ~~~~ki~v~G~~~vGKSsLi~~l~   50 (192)
T 2b6h_A           27 KKQMRILMVGLDAAGKTTILYKLK   50 (192)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHC
T ss_pred             CCccEEEEECCCCCCHHHHHHHHH
Confidence            567899999999999999999764

>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=90.35  E-value=0.15  Score=42.93  Aligned_cols=25  Identities=28%  Similarity=0.355  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.+++.
T Consensus        19 ~~~~ki~vvG~~~vGKTsLi~~l~~   43 (187)
T 3c5c_A           19 PLEVNLAILGRRGAGKSALTVKFLT   43 (187)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHh
Confidence            4567999999999999999998774

>1of1_A Thymidine kinase; transferase, antiviral drug, enzyme- prodrug gene, DNA synthesis, ATP-binding; HET: SCT; 1.95A {Herpes simplex virus} SCOP: c.37.1.1

Probab=90.33  E-value=0.13  Score=49.60  Aligned_cols=38  Identities=21%  Similarity=0.362  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+...++|.|.-||||||++..+..+....|+++..-|
T Consensus        47 ~~~~fIt~EG~dGsGKTT~~~~Lae~L~~~gvv~trEP   84 (376)
T 1of1_A           47 PTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEP   84 (376)
T ss_dssp             CEEEEEEECSSTTSSHHHHHHHHHC----CCEEEECCC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHhhhCCEEEEeCC
Confidence            34567899999999999999999988888884444445

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=90.30  E-value=0.15  Score=46.55  Aligned_cols=23  Identities=22%  Similarity=0.410  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .+.|.|+.||||||++.-+.-.-
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            57889999999999999887653

>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=90.29  E-value=0.18  Score=42.14  Aligned_cols=24  Identities=33%  Similarity=0.523  Sum_probs=21.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|..|+|||+++..+..
T Consensus        14 ~~~~i~v~G~~~~GKssli~~l~~   37 (195)
T 1x3s_A           14 TTLKILIIGESGVGKSSLLLRFTD   37 (195)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHc
Confidence            357999999999999999988864

>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=90.28  E-value=0.41  Score=44.96  Aligned_cols=31  Identities=23%  Similarity=0.134  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      .+...+.|.|+.|+||||++..+.......|
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~~~~~   84 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLLIREG   84 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHHHhcC
Confidence            5678899999999999999999988776544

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=90.26  E-value=0.76  Score=39.55  Aligned_cols=32  Identities=9%  Similarity=0.090  Sum_probs=21.5

Q ss_pred             chhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHH
Q psy3261          47 RNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALV   85 (342)
Q Consensus        47 R~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~   85 (342)
                      |.-=.+.+..+.+       +..+++.++.|||||.+..
T Consensus        38 ~~~Q~~~i~~~~~-------~~~~lv~~pTGsGKT~~~~   69 (224)
T 1qde_A           38 SAIQQRAIMPIIE-------GHDVLAQAQSGTGKTGTFS   69 (224)
T ss_dssp             CHHHHHHHHHHHT-------TCCEEEECCTTSSHHHHHH
T ss_pred             cHHHHHHHHHHhc-------CCCEEEECCCCCcHHHHHH
Confidence            4433345555544       3459999999999998733

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=90.26  E-value=0.24  Score=48.45  Aligned_cols=35  Identities=14%  Similarity=0.261  Sum_probs=30.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      ...+++.|+.|+||||+...+.++...+ |.=|+-|
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllv  135 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVV  135 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEE
Confidence            4577888999999999999999988887 8777766

>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=90.25  E-value=0.17  Score=42.44  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=20.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|..|+|||+++.++..
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~   44 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYAD   44 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHc
Confidence            46899999999999999988764

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=90.20  E-value=0.56  Score=41.16  Aligned_cols=19  Identities=21%  Similarity=0.392  Sum_probs=15.6

Q ss_pred             CeEEEEccCCCcHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVY   86 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q   86 (342)
                      ..+++.++.|||||.+..-
T Consensus        67 ~~~l~~a~TGsGKT~~~~l   85 (245)
T 3dkp_A           67 RELLASAPTGSGKTLAFSI   85 (245)
T ss_dssp             CCEEEECCTTSCHHHHHHH
T ss_pred             CCEEEECCCCCcHHHHHHH
Confidence            4589999999999987433

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=90.20  E-value=0.14  Score=43.00  Aligned_cols=25  Identities=16%  Similarity=0.243  Sum_probs=21.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++.++..
T Consensus        15 ~~~~ki~v~G~~~~GKSsl~~~l~~   39 (199)
T 4bas_A           15 KTKLQVVMCGLDNSGKTTIINQVKP   39 (199)
T ss_dssp             -CEEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhc
Confidence            3567999999999999999988753

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=90.19  E-value=0.44  Score=49.08  Aligned_cols=69  Identities=16%  Similarity=0.063  Sum_probs=41.7

Q ss_pred             CCChhhHHhhhhcCCceEEechhHHHHHHH-HHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEEe-CC
Q psy3261          27 GITRVFNEQTQIFNESSILIRNCMLELVGY-LKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVHI-PW  103 (342)
Q Consensus        27 ~l~~~~~~~~~~~~~~~~lvR~~t~el~~~-l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~v-P~  103 (342)
                      ++|+.+.+.++.++-  .-.+..=.+++.. +.+       +..+++.|+.|||||+...+.+..+.. +|--++++ |.
T Consensus        14 ~l~~~~~~~l~~~g~--~~l~~~Q~~~i~~~~~~-------~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~   84 (715)
T 2va8_A           14 KLPSNVIEIIKKRGI--KKLNPPQTEAVKKGLLE-------GNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPL   84 (715)
T ss_dssp             SSCHHHHHHHHTTSC--CBCCHHHHHHHHTTTTT-------TCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSC
T ss_pred             CCCHHHHHHHHhCCC--CCCCHHHHHHHHHHhcC-------CCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCc
Confidence            466666555544321  1234433344443 222       578999999999999999888865543 55555555 85


Q ss_pred             c
Q psy3261         104 V  104 (342)
Q Consensus       104 ~  104 (342)
                      -
T Consensus        85 r   85 (715)
T 2va8_A           85 R   85 (715)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=90.18  E-value=0.17  Score=42.90  Aligned_cols=25  Identities=32%  Similarity=0.416  Sum_probs=20.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|+.|+|||+++..+..
T Consensus        26 ~~~~ki~v~G~~~~GKSsli~~l~~   50 (199)
T 2p5s_A           26 QKAYKIVLAGDAAVGKSSFLMRLCK   50 (199)
T ss_dssp             --CEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHh
Confidence            4568999999999999999988764

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=90.18  E-value=0.52  Score=41.79  Aligned_cols=50  Identities=16%  Similarity=0.134  Sum_probs=31.2

Q ss_pred             EechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          45 LIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        45 lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      -.|+.=.+.+..+.+       ..+.+|.|+.|+|||.+...++...  .+.+++-+|.
T Consensus        93 ~l~~~Q~~ai~~~~~-------~~~~ll~~~tG~GKT~~a~~~~~~~--~~~~liv~P~  142 (237)
T 2fz4_A           93 SLRDYQEKALERWLV-------DKRGCIVLPTGSGKTHVAMAAINEL--STPTLIVVPT  142 (237)
T ss_dssp             CCCHHHHHHHHHHTT-------TSEEEEEESSSTTHHHHHHHHHHHS--CSCEEEEESS
T ss_pred             CcCHHHHHHHHHHHh-------CCCEEEEeCCCCCHHHHHHHHHHHc--CCCEEEEeCC
Confidence            445544455554433       2459999999999999876665543  3444444443

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=90.17  E-value=0.23  Score=50.68  Aligned_cols=42  Identities=21%  Similarity=0.324  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHhc-cCCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSM-TNFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        49 ~t~el~~~l~~~-~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +.+++++.+... .+.+-.-+.+.|.|+.||||||+|.-++-.
T Consensus        26 ~ll~~id~l~~~gv~~~l~lp~iaIvG~nGsGKSTLL~~I~Gl   68 (608)
T 3szr_A           26 PCIDLIDSLRALGVEQDLALPAIAVIGDQSSGKSSVLEALSGV   68 (608)
T ss_dssp             HHHHHHHHHHHHSCCSSCCCCCEECCCCTTSCHHHHHHHHHSC
T ss_pred             HHHHHHHHHHhCCCCCcccCCeEEEECCCCChHHHHHHHHhCC
Confidence            456677777652 112234467999999999999999988764

>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=90.15  E-value=0.17  Score=47.32  Aligned_cols=28  Identities=18%  Similarity=0.005  Sum_probs=23.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .++..+.|.|+.||||||++..+...-.
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            4566788999999999999988776654

>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=90.14  E-value=0.2  Score=50.45  Aligned_cols=27  Identities=26%  Similarity=0.272  Sum_probs=21.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .+...++|+|++|||||+++..+....
T Consensus       106 ~~g~~vll~Gp~GtGKTtlar~ia~~l  132 (543)
T 3m6a_A          106 LKGPILCLAGPPGVGKTSLAKSIAKSL  132 (543)
T ss_dssp             CCSCEEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            367789999999999998887665544

>1e2k_A Thymidine kinase; transferase, antiviral drug, enzyme-prodrug gene therapy, sugar ring pucker; HET: TMC; 1.7A {Herpes simplex virus} SCOP: c.37.1.1 PDB: 1e2i_A* 1e2h_A* 1e2m_A* 1e2n_A* 1e2p_A* 1ki2_A* 1ki3_A* 1ki4_A* 1ki6_B* 1ki7_A* 1ki8_A* 3rdp_A* 2ki5_A* 1kim_A* 1qhi_A* 1p7c_A* 1vtk_A* 2vtk_A* 3vtk_A* 3f0t_A* ...

Probab=90.12  E-value=0.13  Score=48.63  Aligned_cols=36  Identities=22%  Similarity=0.389  Sum_probs=25.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ...++|-|.-||||||++..+..+....|+++..-|
T Consensus         4 ~~fI~~EG~dGsGKTT~~~~La~~L~~~gv~~trEP   39 (331)
T 1e2k_A            4 LLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEP   39 (331)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC----CCEEEECCC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhhhCCEEEEeCC
Confidence            356889999999999999999988888884444444

>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=90.11  E-value=0.17  Score=42.93  Aligned_cols=23  Identities=43%  Similarity=0.444  Sum_probs=20.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +..+++|.|.+|+|||+++.+.+
T Consensus         5 ~~~kv~lvG~~~vGKSsL~~~~~   27 (192)
T 2cjw_A            5 TYYRVVLIGEQGVGKSTLANIFA   27 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHH
T ss_pred             ceEEEEEECCCCCCHHHHHHHHh
Confidence            45789999999999999998866

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.07  E-value=0.23  Score=57.18  Aligned_cols=38  Identities=16%  Similarity=0.186  Sum_probs=33.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|+|||+++.|++..+..+|.-|+||.
T Consensus       381 ~~G~lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis  418 (2050)
T 3cmu_A          381 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  418 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             cCCcEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            36778999999999999999999999998887788874

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=90.05  E-value=0.27  Score=49.79  Aligned_cols=29  Identities=21%  Similarity=0.400  Sum_probs=25.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      ....++|.|++|||||++|.+-+.|..++
T Consensus        21 ~~~~~lV~a~aGsGKT~~l~~ri~~l~~~   49 (647)
T 3lfu_A           21 PRSNLLVLAGAGSGKTRVLVHRIAWLMSV   49 (647)
T ss_dssp             CSSCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHh
Confidence            35668999999999999999999988765

>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=90.05  E-value=0.18  Score=42.75  Aligned_cols=23  Identities=22%  Similarity=0.304  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|..|+|||+++..+..
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~   30 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYAD   30 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999988753

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=90.02  E-value=0.48  Score=46.04  Aligned_cols=50  Identities=12%  Similarity=0.062  Sum_probs=36.4

Q ss_pred             hhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHh--CCeEEEEe
Q psy3261          48 NCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHE--NNYLLVHI  101 (342)
Q Consensus        48 ~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~--~gwiVl~v  101 (342)
                      +..+.+|+.|--    -.++-|..|.|++|+|||+++.++...+..  .+..+|++
T Consensus       160 ~tGiraID~l~P----igrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~V~~  211 (427)
T 3l0o_A          160 IYSTRLIDLFAP----IGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIRIIL  211 (427)
T ss_dssp             CHHHHHHHHHSC----CBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred             hccchhhhhccc----ccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeEEEEE
Confidence            355566666633    246889999999999999999888877654  36555554

>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=89.98  E-value=0.19  Score=42.76  Aligned_cols=24  Identities=33%  Similarity=0.397  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~   30 (206)
T 2bcg_Y            7 YLFKLLLIGNSGVGKSCLLLRFSD   30 (206)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999988764

>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=89.96  E-value=0.33  Score=43.55  Aligned_cols=32  Identities=25%  Similarity=0.300  Sum_probs=27.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYL   97 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi   97 (342)
                      ++.-++|.|..||||||.+..+..+-...|.-
T Consensus        26 ~~~~i~~eG~~GsGKsT~~~~l~~~l~~~~~~   57 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTAIQVVVETLQQNGID   57 (236)
T ss_dssp             CCCEEEEEESTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCC
Confidence            45689999999999999999999988877754

>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=89.95  E-value=0.18  Score=42.98  Aligned_cols=25  Identities=28%  Similarity=0.369  Sum_probs=21.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++.+++.
T Consensus        23 ~~~~ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           23 DFLFKFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             CEEEEEEEEESTTSSHHHHHHHHHC
T ss_pred             CcceEEEEECcCCCCHHHHHHHHHh
Confidence            3457999999999999999998864

>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=89.90  E-value=0.19  Score=43.79  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++..++.
T Consensus        27 ~~~~kI~vvG~~~vGKSsLin~l~~   51 (228)
T 2qu8_A           27 PHKKTIILSGAPNVGKSSFMNIVSR   51 (228)
T ss_dssp             TTSEEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            4568999999999999999988753

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=89.90  E-value=0.49  Score=40.18  Aligned_cols=41  Identities=17%  Similarity=0.207  Sum_probs=29.1

Q ss_pred             EechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          45 LIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        45 lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      -.|+-=.+.+..+.+       ...++|.++.|+|||.+...++....
T Consensus        33 ~l~~~Q~~~i~~~~~-------~~~~li~~~tGsGKT~~~~~~~~~~~   73 (216)
T 3b6e_A           33 QLRPYQMEVAQPALE-------GKNIIICLPTGSGKTRVAVYIAKDHL   73 (216)
T ss_dssp             CCCHHHHHHHHHHHT-------TCCEEEECSCHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHhc-------CCCEEEEcCCCCCHHHHHHHHHHHHH
Confidence            355544555665544       35799999999999998877776543

>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=89.89  E-value=0.17  Score=43.63  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++.++..
T Consensus        26 ~~~~ki~vvG~~~vGKSsLi~~l~~   50 (205)
T 1gwn_A           26 NVKCKIVVVGDSQCGKTALLHVFAK   50 (205)
T ss_dssp             -CEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceeeEEEEECCCCCCHHHHHHHHhc
Confidence            3567999999999999999998775

>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=89.88  E-value=0.2  Score=42.16  Aligned_cols=25  Identities=24%  Similarity=0.406  Sum_probs=21.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        21 ~~~~ki~~vG~~~~GKSsl~~~l~~   45 (194)
T 3reg_A           21 KKALKIVVVGDGAVGKTCLLLAFSK   45 (194)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceeeEEEEECcCCCCHHHHHHHHhc
Confidence            3467999999999999999988764

>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=89.83  E-value=0.22  Score=44.63  Aligned_cols=31  Identities=19%  Similarity=0.042  Sum_probs=22.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ...+.|+|+.||||||+...+...   .|+.++.
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~---lg~~~~d   39 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARA---LGARYLD   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH---HTCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH---hCCCccc
Confidence            467999999999999988766433   3555443

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=89.82  E-value=0.26  Score=56.03  Aligned_cols=37  Identities=16%  Similarity=0.197  Sum_probs=32.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-++|+|++|+|||+++.|++..+..+|.-|+||
T Consensus       730 ~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~Vlyi  766 (1706)
T 3cmw_A          730 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFI  766 (1706)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEE
Confidence            3567899999999999999999999998888777777

>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=89.81  E-value=0.13  Score=48.99  Aligned_cols=35  Identities=20%  Similarity=0.277  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        29 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   64 (353)
T 1oxx_K           29 ENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYF   64 (353)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCCCCCceEEEE
Confidence            4577899999999999999987765433 3466654

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=89.78  E-value=0.29  Score=43.51  Aligned_cols=34  Identities=21%  Similarity=0.057  Sum_probs=26.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .+.=.+++|+-|||||+.|.+.+..+...|--|+
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvl   60 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRLRRGIYAKQKVV   60 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHHHcCCceE
Confidence            3566789999999999988888887776654443

>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=89.75  E-value=0.18  Score=44.95  Aligned_cols=25  Identities=40%  Similarity=0.517  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..++.
T Consensus        20 ~~~~~I~lvG~~g~GKStl~n~l~~   44 (260)
T 2xtp_A           20 RSELRIILVGKTGTGKSAAGNSILR   44 (260)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhC
Confidence            3567999999999999999998864

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=89.73  E-value=0.19  Score=42.69  Aligned_cols=25  Identities=20%  Similarity=0.191  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        22 ~~~~ki~vvG~~~~GKSsli~~l~~   46 (201)
T 3oes_A           22 VRYRKVVILGYRCVGKTSLAHQFVE   46 (201)
T ss_dssp             -CEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCcCHHHHHHHHHh
Confidence            3567999999999999999998874

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=89.73  E-value=0.32  Score=45.95  Aligned_cols=24  Identities=25%  Similarity=0.340  Sum_probs=21.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .-++++|.|+.|||||++|..++.
T Consensus        33 ~lp~I~vvG~~~sGKSSLln~l~g   56 (360)
T 3t34_A           33 SLPAIAVVGGQSSGKSSVLESIVG   56 (360)
T ss_dssp             CCCEEEEECBTTSSHHHHHHHHHT
T ss_pred             cCCEEEEECCCCCcHHHHHHHHhC
Confidence            345999999999999999999886

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=89.72  E-value=0.27  Score=51.32  Aligned_cols=34  Identities=21%  Similarity=0.328  Sum_probs=24.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|+|++|||||.+...+.......+.-+++|
T Consensus       522 ~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i  555 (758)
T 3pxi_A          522 GSFIFLGPTGVGKTELARALAESIFGDEESMIRI  555 (758)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEE
Confidence            3699999999999988777766665444333333

>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=89.71  E-value=0.2  Score=41.78  Aligned_cols=23  Identities=26%  Similarity=0.270  Sum_probs=19.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++ +.+.
T Consensus        13 ~~~ki~vvG~~~~GKssL~-~~l~   35 (198)
T 3t1o_A           13 INFKIVYYGPGLSGKTTNL-KWIY   35 (198)
T ss_dssp             EEEEEEEECSTTSSHHHHH-HHHH
T ss_pred             cccEEEEECCCCCCHHHHH-HHHH
Confidence            4579999999999999998 5444

>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=89.68  E-value=0.17  Score=47.29  Aligned_cols=35  Identities=23%  Similarity=0.443  Sum_probs=25.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        78 ~~Ge~vaivG~sGsGKSTLl~ll~gl~~p~~G~I~i  113 (306)
T 3nh6_A           78 MPGQTLALVGPSGAGKSTILRLLFRFYDISSGCIRI  113 (306)
T ss_dssp             CTTCEEEEESSSCHHHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCchHHHHHHHHHcCCCCCCcEEEE
Confidence            5688999999999999999976654322 3455443

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=89.64  E-value=0.24  Score=48.57  Aligned_cols=28  Identities=32%  Similarity=0.494  Sum_probs=24.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .++.++.|.|+.||||||+|..+.-+..
T Consensus       155 ~~Gq~~~IvG~sGsGKSTLl~~Iag~~~  182 (438)
T 2dpy_A          155 GRGQRMGLFAGSGVGKSVLLGMMARYTR  182 (438)
T ss_dssp             BTTCEEEEEECTTSSHHHHHHHHHHHSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcccC
Confidence            5688999999999999999988887754

>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=89.64  E-value=0.32  Score=48.19  Aligned_cols=46  Identities=22%  Similarity=0.328  Sum_probs=33.1

Q ss_pred             HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q psy3261          52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHI  101 (342)
Q Consensus        52 el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~v  101 (342)
                      ..|+.|..+    .++.+.+|.|++|+|||+++.+++.... ..+-+.+++
T Consensus       140 r~ID~L~pi----~kGq~~~i~G~sGvGKTtL~~~l~~~~~~~~~~i~V~~  186 (473)
T 1sky_E          140 KVVDLLAPY----IKGGKIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFA  186 (473)
T ss_dssp             HHHHHHSCE----ETTCEEEEECCSSSCHHHHHHHHHHHHHHHTCCCEEEE
T ss_pred             hHHHHHhhh----ccCCEEEEECCCCCCccHHHHHHHhhhhhccCcEEEEe
Confidence            356666441    2466899999999999999999988644 455555554

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=89.63  E-value=0.41  Score=45.72  Aligned_cols=38  Identities=21%  Similarity=0.145  Sum_probs=25.0

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +-++++.++. .-.......++|.|+.|||||++...+.
T Consensus         8 ~~~il~~l~~-~i~~g~~~~i~l~G~~G~GKTTl~~~la   45 (359)
T 2ga8_A            8 ADDVLQLLDN-RIEDNYRVCVILVGSPGSGKSTIAEELC   45 (359)
T ss_dssp             HHHHHHHHHH-TTTTCSCEEEEEECCTTSSHHHHHHHHH
T ss_pred             HHHHHHHHHH-HhccCCeeEEEEECCCCCcHHHHHHHHH
Confidence            3445666654 2222334569999999999999886543

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=89.63  E-value=0.16  Score=50.74  Aligned_cols=25  Identities=20%  Similarity=0.150  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ...++|+|++|||||++...+...+
T Consensus        41 ~~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           41 GESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TCEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             CCeeEeecCchHHHHHHHHHHHHHH
Confidence            4689999999999998776665543

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=89.60  E-value=0.19  Score=42.45  Aligned_cols=25  Identities=28%  Similarity=0.337  Sum_probs=20.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        18 ~~~~ki~~~G~~~~GKssl~~~l~~   42 (201)
T 2q3h_A           18 GRGVKCVLVGDGAVGKTSLVVSYTT   42 (201)
T ss_dssp             --CEEEEEECSTTSSHHHHHHHHHC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHh
Confidence            4577999999999999999988764

>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=89.50  E-value=0.23  Score=43.50  Aligned_cols=28  Identities=21%  Similarity=0.388  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      +++|.|++||||+|....+.   ...|+..|
T Consensus         2 ~Iil~GpPGsGKgTqa~~La---~~~g~~~i   29 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLA---KEKGFVHI   29 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHH---HHHCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHHCCeEE
Confidence            57899999999998655554   34465443

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=89.49  E-value=0.17  Score=50.71  Aligned_cols=34  Identities=15%  Similarity=0.224  Sum_probs=24.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl   99 (342)
                      +...++|.|+.||||||+|.-++.+-.. .|-+.+
T Consensus       259 ~g~~i~I~GptGSGKTTlL~aL~~~i~~~~giiti  293 (511)
T 2oap_1          259 HKFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSI  293 (511)
T ss_dssp             TTCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEE
Confidence            3455999999999999999887765432 344333

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=89.46  E-value=0.39  Score=42.41  Aligned_cols=36  Identities=17%  Similarity=0.213  Sum_probs=27.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ++.-+++.|..||||||....+..+-.. ...++..|
T Consensus         4 ~g~~i~~eG~~g~GKst~~~~l~~~l~~-~~~~~~ep   39 (216)
T 3tmk_A            4 RGKLILIEGLDRTGKTTQCNILYKKLQP-NCKLLKFP   39 (216)
T ss_dssp             CCCEEEEEECSSSSHHHHHHHHHHHHCS-SEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcc-cceEEEec
Confidence            4678999999999999999988887654 33444444

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=89.43  E-value=0.22  Score=43.48  Aligned_cols=19  Identities=26%  Similarity=0.489  Sum_probs=15.9

Q ss_pred             eEEEEccCCCcHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~   87 (342)
                      -++++|++|||||+.....
T Consensus         7 i~l~tG~pGsGKT~~a~~~   25 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSM   25 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHH
Confidence            5789999999999986553

>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=89.39  E-value=0.22  Score=42.78  Aligned_cols=24  Identities=33%  Similarity=0.330  Sum_probs=21.2

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++.++..
T Consensus        25 ~~~ki~lvG~~~vGKSsLi~~l~~   48 (201)
T 2ew1_A           25 FLFKIVLIGNAGVGKTCLVRRFTQ   48 (201)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHHh
Confidence            357999999999999999998765

>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=89.39  E-value=0.23  Score=42.06  Aligned_cols=23  Identities=30%  Similarity=0.382  Sum_probs=18.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      .+..+++|.|..|+|||+++..+
T Consensus        18 ~~~~ki~~vG~~~vGKTsLi~~l   40 (196)
T 3llu_A           18 GSKPRILLMGLRRSGKSSIQKVV   40 (196)
T ss_dssp             --CCEEEEEESTTSSHHHHHHHH
T ss_pred             CcceEEEEECCCCCCHHHHHHHH
Confidence            45789999999999999998743

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=89.38  E-value=0.21  Score=45.50  Aligned_cols=33  Identities=15%  Similarity=0.301  Sum_probs=24.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      +..+.|.|+.||||||+|.-+.-.--..|-|.+
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~p~~G~I~~   62 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLLPYSGNIFI   62 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSSCCEEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCCCCCcEEEE
Confidence            678999999999999999887654322355543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=89.35  E-value=0.21  Score=48.57  Aligned_cols=37  Identities=24%  Similarity=0.158  Sum_probs=28.3

Q ss_pred             CCeEEEEccCCCcHHHH-HHHHHHHHHhCCeEEEEe-CC
Q psy3261          67 SPRFVLYGEHGVGKSMA-LVYALQYAHENNYLLVHI-PW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~-L~q~~~~A~~~gwiVl~v-P~  103 (342)
                      +..+++.|+.|||||.+ +..++..+..+|.-++++ |.
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt   40 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPT   40 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcH
Confidence            45789999999999998 577776777777555554 64

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=89.28  E-value=0.27  Score=49.07  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++..+.|.|+.||||||++.+++
T Consensus        37 ~~Ge~~~l~G~nGsGKSTL~~~~l   60 (525)
T 1tf7_A           37 PIGRSTLVSGTSGTGKTLFSIQFL   60 (525)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHH
Confidence            467899999999999999999964

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=89.26  E-value=0.21  Score=42.16  Aligned_cols=23  Identities=22%  Similarity=0.394  Sum_probs=20.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|..|+|||+++.++..
T Consensus        26 ~~ki~vvG~~~~GKSsLi~~l~~   48 (192)
T 2il1_A           26 KLQVIIIGSRGVGKTSLMERFTD   48 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999998753

>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=89.24  E-value=0.22  Score=42.71  Aligned_cols=24  Identities=25%  Similarity=0.328  Sum_probs=20.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus        24 ~~~ki~vvG~~~~GKSsLi~~l~~   47 (217)
T 2f7s_A           24 YLIKLLALGDSGVGKTTFLYRYTD   47 (217)
T ss_dssp             EEEEEEEESCTTSSHHHHHHHHHC
T ss_pred             eeEEEEEECcCCCCHHHHHHHHhc
Confidence            357899999999999999987753

>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=89.22  E-value=0.31  Score=47.60  Aligned_cols=36  Identities=17%  Similarity=0.193  Sum_probs=29.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...+++.|+.||||||++..+..+....|.=|+-+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllv  132 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            455688889999999999999999888777666554

>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=89.20  E-value=0.17  Score=42.53  Aligned_cols=25  Identities=12%  Similarity=0.097  Sum_probs=20.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        19 ~~~~ki~v~G~~~~GKSsli~~l~~   43 (190)
T 2h57_A           19 SKEVHVLCLGLDNSGKTTIINKLKP   43 (190)
T ss_dssp             --CEEEEEEECTTSSHHHHHHHTSC
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            3567999999999999999988754

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=89.19  E-value=0.37  Score=41.57  Aligned_cols=31  Identities=23%  Similarity=0.193  Sum_probs=22.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..+.|+|+.|||||++...+.   ...|+-++..
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~---~~~g~~~~~~   34 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVA---SELSMIYVDT   34 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHH---HHTTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHH---HhcCCceecC
Confidence            468999999999999877653   3346655443

>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=89.10  E-value=0.21  Score=48.45  Aligned_cols=32  Identities=28%  Similarity=0.278  Sum_probs=24.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..-++|.|.+||||||+..++.   ...||.+|..
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~---~~~~~~~i~~  289 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHL---VSAGYVHVNR  289 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHT---GGGTCEECCG
T ss_pred             CEEEEEECCCCCCHHHHHHHHH---HhcCcEEEcc
Confidence            4578899999999999887754   3447776643

>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=89.09  E-value=0.21  Score=43.11  Aligned_cols=25  Identities=32%  Similarity=0.424  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++..+..
T Consensus        32 ~~~~ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           32 VRSVKVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             CCEEEEEEEECTTSSHHHHHHHHHC
T ss_pred             cceEEEEEECcCCCCHHHHHHHHHc
Confidence            3467999999999999999988763

>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=89.05  E-value=0.44  Score=44.83  Aligned_cols=35  Identities=20%  Similarity=0.141  Sum_probs=26.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ..-++|.||.|||||++...+   |...+..||...+.
T Consensus         3 ~~~i~i~GptgsGKt~la~~L---a~~~~~~iis~Ds~   37 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVML---AKRLNGEVISGDSM   37 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHH---HHTTTEEEEECCGG
T ss_pred             CcEEEEECCCcCCHHHHHHHH---HHhCccceeecCcc
Confidence            346889999999999997666   45567777776554

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=89.01  E-value=0.28  Score=43.72  Aligned_cols=35  Identities=20%  Similarity=0.230  Sum_probs=25.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC----CeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN----NYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~----gwiVl   99 (342)
                      .++.-++|.|+.||||||....+..+-...    |.-|+
T Consensus        23 ~~g~~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~   61 (227)
T 3v9p_A           23 ARGKFITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVV   61 (227)
T ss_dssp             CCCCEEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEE
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHhhccccceeee
Confidence            356789999999999999999998887665    65443

>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=88.99  E-value=0.22  Score=44.96  Aligned_cols=22  Identities=23%  Similarity=0.235  Sum_probs=19.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..+++|.|++|||||+++..+.
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~   24 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALT   24 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHh
Confidence            4689999999999999999875

>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=88.98  E-value=0.26  Score=48.73  Aligned_cols=57  Identities=12%  Similarity=0.242  Sum_probs=43.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC----CeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHh
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN----NYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQ  140 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~----gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~  140 (342)
                      .++-|..|.|.+|+|||+++.|+..++..|    |.++||+--+++                    +....++++.|...
T Consensus       150 grGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER--------------------~~Ev~e~~~~~~~~  209 (469)
T 2c61_A          150 VRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGIT--------------------NEEAQYFMSDFEKT  209 (469)
T ss_dssp             BTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEEC--------------------HHHHHHHHHHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCC--------------------cHHHHHHHHHHHhc
Confidence            468899999999999999999999988754    467777743322                    23667788888754


Q ss_pred             C
Q psy3261         141 N  141 (342)
Q Consensus       141 N  141 (342)
                      .
T Consensus       210 g  210 (469)
T 2c61_A          210 G  210 (469)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=88.97  E-value=0.25  Score=42.24  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus        24 ~~~ki~vvG~~~~GKSsli~~l~~   47 (207)
T 2fv8_A           24 IRKKLVVVGDGACGKTCLLIVFSK   47 (207)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             cCcEEEEECcCCCCHHHHHHHHhc
Confidence            356899999999999999988765

>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=88.92  E-value=0.25  Score=41.98  Aligned_cols=23  Identities=22%  Similarity=0.431  Sum_probs=20.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|..|+|||+++..+..
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~   47 (201)
T 2gco_A           25 RKKLVIVGDGACGKTCLLIVFSK   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999987764

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=88.88  E-value=0.17  Score=43.62  Aligned_cols=25  Identities=24%  Similarity=0.344  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ....+++|.|..|+|||+++..++.
T Consensus        27 ~~~~~i~v~G~~~~GKSslin~l~~   51 (223)
T 4dhe_A           27 TVQPEIAFAGRSNAGKSTAINVLCN   51 (223)
T ss_dssp             CCSCEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHhC
Confidence            3568999999999999999988753

>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=88.87  E-value=0.24  Score=42.09  Aligned_cols=21  Identities=19%  Similarity=0.121  Sum_probs=18.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+.|+|+.|||||++...+..
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            688999999999998877654

>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=88.80  E-value=0.13  Score=42.74  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=11.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus         7 ~~~ki~v~G~~~~GKssl~~~l~~   30 (183)
T 2fu5_C            7 YLFKLLLIGDSGVGKTCVLFRFSE   30 (183)
T ss_dssp             EEEEEEEECCCCC-----------
T ss_pred             CceEEEEECCCCCCHHHHHHHHHh
Confidence            357899999999999999988764

>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=88.80  E-value=0.27  Score=47.15  Aligned_cols=35  Identities=20%  Similarity=0.271  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        52 ~~Gei~~IiGpnGaGKSTLlr~i~GL~~p~~G~I~i   87 (366)
T 3tui_C           52 PAGQIYGVIGASGAGKSTLIRCVNLLERPTEGSVLV   87 (366)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             cCCCEEEEEcCCCchHHHHHHHHhcCCCCCceEEEE
Confidence            4677899999999999999877665433 3455544

>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=88.76  E-value=0.12  Score=46.46  Aligned_cols=36  Identities=19%  Similarity=0.247  Sum_probs=26.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+...++|.|..||||||+...+..+.  .++.++..|
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~~l--~~~~~i~ep   57 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQLC--EDWEVVPEP   57 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGGGC--TTEEEECCC
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHhc--CCCEEEecc
Confidence            345789999999999999988776553  256666554

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=88.75  E-value=0.16  Score=47.74  Aligned_cols=34  Identities=15%  Similarity=0.350  Sum_probs=24.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      +...+.|.|+.||||||+|.-+..+-. ..|-|.+
T Consensus       170 ~g~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i  204 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISI  204 (330)
T ss_dssp             HTCCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEE
Confidence            356899999999999999887776533 3344433

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=88.68  E-value=0.89  Score=40.71  Aligned_cols=20  Identities=20%  Similarity=0.436  Sum_probs=16.0

Q ss_pred             CeEEEEccCCCcHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~   87 (342)
                      ..+++.++.|||||.+..-.
T Consensus        92 ~~~lv~a~TGsGKT~~~~l~  111 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAFLIP  111 (262)
T ss_dssp             CCCEECCCTTSCHHHHHHHH
T ss_pred             CcEEEEccCCCCchHHHHHH
Confidence            46899999999999874433

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=88.67  E-value=0.29  Score=51.64  Aligned_cols=27  Identities=19%  Similarity=0.290  Sum_probs=23.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      ....+|.|++|||||+++.+++.+...
T Consensus       375 ~~~~lI~GppGTGKT~~i~~~i~~l~~  401 (802)
T 2xzl_A          375 RPLSLIQGPPGTGKTVTSATIVYHLSK  401 (802)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHh
Confidence            346899999999999999999987654

>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=88.66  E-value=0.25  Score=44.56  Aligned_cols=21  Identities=19%  Similarity=0.238  Sum_probs=18.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++++|.|.+|||||+++..+.
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~   22 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALT   22 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            478999999999999999874

>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=88.60  E-value=0.29  Score=51.85  Aligned_cols=36  Identities=22%  Similarity=0.361  Sum_probs=24.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|+|++|||||++...+.......+.-+++|
T Consensus       587 p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i  622 (854)
T 1qvr_A          587 PIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI  622 (854)
T ss_dssp             CSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEE
Confidence            345899999999999987766666555434333333

>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=88.57  E-value=0.21  Score=42.58  Aligned_cols=22  Identities=36%  Similarity=0.329  Sum_probs=19.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      ...+++|.|..|+|||+++.++
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l   43 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTF   43 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHT
T ss_pred             cEEEEEEECCCCCCHHHHHHHH
Confidence            4579999999999999999876

>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=88.55  E-value=0.28  Score=42.41  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.+++.
T Consensus        25 ~~~~ki~vvG~~~vGKSsL~~~l~~   49 (214)
T 3q3j_B           25 VARCKLVLVGDVQCGKTAMLQVLAK   49 (214)
T ss_dssp             --CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEEECcCCCCHHHHHHHHhc
Confidence            3467999999999999999998875

>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=88.53  E-value=0.27  Score=45.47  Aligned_cols=34  Identities=21%  Similarity=0.030  Sum_probs=22.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      ....+.|.|+.||||||+|..+.-... ..|-|.+
T Consensus       168 ~geiv~l~G~sG~GKSTll~~l~g~~~~~~G~i~~  202 (301)
T 1u0l_A          168 KGKISTMAGLSGVGKSSLLNAINPGLKLRVSEVSE  202 (301)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHSTTCCCC------
T ss_pred             cCCeEEEECCCCCcHHHHHHHhcccccccccceec
Confidence            356788999999999999998875443 3355554

>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=88.52  E-value=0.26  Score=43.05  Aligned_cols=23  Identities=43%  Similarity=0.444  Sum_probs=20.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ...+++|.|.+|+|||+++.+.+
T Consensus        36 ~~~kVvlvG~~~vGKSSLl~r~~   58 (211)
T 2g3y_A           36 TYYRVVLIGEQGVGKSTLANIFA   58 (211)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHH
Confidence            34689999999999999998765

>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=88.52  E-value=0.28  Score=41.14  Aligned_cols=24  Identities=25%  Similarity=0.307  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++.++..
T Consensus        17 ~~~ki~v~G~~~~GKssli~~l~~   40 (194)
T 2atx_A           17 LMLKCVVVGDGAVGKTCLLMSYAN   40 (194)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEEECCCCCCHHHHHHHHhc
Confidence            346999999999999999988774

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=88.46  E-value=0.28  Score=41.81  Aligned_cols=25  Identities=24%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..+++|.|..|+|||+++.++..
T Consensus         7 ~~~~ki~i~G~~~~GKTsli~~l~~   31 (212)
T 2j0v_A            7 SKFIKCVTVGDGAVGKTCMLICYTS   31 (212)
T ss_dssp             CCEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCCHHHHHHHHhc
Confidence            4567999999999999999988763

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=88.39  E-value=0.31  Score=43.14  Aligned_cols=30  Identities=17%  Similarity=0.200  Sum_probs=20.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLL   98 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiV   98 (342)
                      +..-++|.|++||||+|....+..   ..|+..
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~---~~g~~h   57 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQ---KFHFNH   57 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHH---HHCCEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH---HHCCce
Confidence            445567899999999996655543   335543

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=88.33  E-value=1.1  Score=40.93  Aligned_cols=24  Identities=21%  Similarity=0.231  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ..+++.++.|||||.+....+...
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~~~   68 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLIEL   68 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHHHH
Confidence            679999999999999876655443

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=88.30  E-value=0.25  Score=44.02  Aligned_cols=36  Identities=22%  Similarity=0.125  Sum_probs=28.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVH  100 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~  100 (342)
                      .++.-+++.|..||||||....+..+-.. .|.-|+.
T Consensus        19 ~~~~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~   55 (223)
T 3ld9_A           19 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVV   55 (223)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhhccCceeeE
Confidence            45778999999999999999999888776 6654433

>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=88.28  E-value=0.29  Score=41.68  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++.++..
T Consensus        28 ~~~ki~vvG~~~vGKSsli~~l~~   51 (201)
T 2hup_A           28 FLFKLVLVGDASVGKTCVVQRFKT   51 (201)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             cceEEEEECcCCCCHHHHHHHHhh
Confidence            357899999999999999998754

>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=88.28  E-value=0.3  Score=45.23  Aligned_cols=33  Identities=24%  Similarity=0.157  Sum_probs=24.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      ....+.|.|+.|+||||++..+. ... ..|-|-+
T Consensus       164 ~G~i~~l~G~sG~GKSTLln~l~-~~~~~~G~i~~  197 (302)
T 2yv5_A          164 EGFICILAGPSGVGKSSILSRLT-GEELRTQEVSE  197 (302)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHH-SCCCCCSCC--
T ss_pred             cCcEEEEECCCCCCHHHHHHHHH-HhhCccccccc
Confidence            35678999999999999999988 433 3465555

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=88.27  E-value=1.4  Score=40.87  Aligned_cols=40  Identities=15%  Similarity=0.236  Sum_probs=26.4

Q ss_pred             chhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          47 RNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        47 R~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      |..=.+.+..+-+     .....+++.++.|+|||.+....+...
T Consensus        29 ~~~Q~~~i~~~~~-----~~~~~~lv~a~TGsGKT~~~~~~~~~~   68 (395)
T 3pey_A           29 SKIQERALPLLLH-----NPPRNMIAQSQSGTGKTAAFSLTMLTR   68 (395)
T ss_dssp             CHHHHHHHHHHHC-----SSCCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHc-----CCCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            3333345555544     234789999999999998766655544

>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=88.14  E-value=0.3  Score=46.63  Aligned_cols=26  Identities=31%  Similarity=0.335  Sum_probs=21.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ++..+.|.|+.|+||||++..+.-..
T Consensus       214 ~G~~~~lvG~sG~GKSTLln~L~g~~  239 (358)
T 2rcn_A          214 TGRISIFAGQSGVGKSSLLNALLGLQ  239 (358)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHCCS
T ss_pred             CCCEEEEECCCCccHHHHHHHHhccc
Confidence            35689999999999999998887543

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=88.10  E-value=2.1  Score=37.18  Aligned_cols=20  Identities=20%  Similarity=0.351  Sum_probs=16.4

Q ss_pred             CCeEEEEccCCCcHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVY   86 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q   86 (342)
                      +..+++.++.|||||.+...
T Consensus        62 ~~~~li~a~TGsGKT~~~~~   81 (236)
T 2pl3_A           62 GKDVLGAAKTGSGKTLAFLV   81 (236)
T ss_dssp             TCCEEEECCTTSCHHHHHHH
T ss_pred             CCCEEEEeCCCCcHHHHHHH
Confidence            45699999999999997444

>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=88.08  E-value=0.31  Score=47.94  Aligned_cols=80  Identities=13%  Similarity=0.261  Sum_probs=47.5

Q ss_pred             EEEEeCccccccCCCcCCCCCCCcccCCccc---hHHHHHHhhcCC----------CCCeEEEEEeCCCCCCCCCccCcc
Q psy3261         207 FVCVDGYNSFFAEKTNCKPEDKSKVLPSRVT---LTRSVINLVQSD----------WNNGAIVLALSPRANLPDRRESHL  273 (342)
Q Consensus       207 LvavD~~n~~~~~s~~y~~~~~~~I~~~~l~---l~~~~~~~~~~~----------~~~G~vv~AtS~~~~~~~~~~~~~  273 (342)
                      ++.+|++-.+...+..         ...+.+   +=+.|++++.+.          -.+-.+|+|..-..  .++.. .+
T Consensus       253 il~~DEidki~~~~~~---------~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~--~~~~d-li  320 (444)
T 1g41_A          253 IVFIDEIDKICKKGEY---------SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQV--ARPSD-LI  320 (444)
T ss_dssp             EEEEETGGGGSCCSSC---------SSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSS--CCGGG-SC
T ss_pred             eeeHHHHHHHhhccCC---------CCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEecccccc--CChhh-cc
Confidence            4459999777654321         122332   446888888763          35556666643221  12222 23


Q ss_pred             hhHHhhhcCCCCCCCcceeecCCCCHHHHHHHH
Q psy3261         274 PLYMLKKAGFESIDPFVPIHVPELNDEEFHNLL  306 (342)
Q Consensus       274 p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll  306 (342)
                      | ++.|+  |+.     .++++.|+.+|+..++
T Consensus       321 p-el~~R--~~i-----~i~l~~lt~~e~~~Il  345 (444)
T 1g41_A          321 P-ELQGR--LPI-----RVELTALSAADFERIL  345 (444)
T ss_dssp             H-HHHTT--CCE-----EEECCCCCHHHHHHHH
T ss_pred             h-HHhcc--cce-----eeeCCCCCHHHHHHHH
Confidence            4 56666  321     3688999999999988

>1osn_A Thymidine kinase, VZV-TK; chickenpox, BVDU-MP, transferase; HET: BVP ADP; 3.20A {Human herpesvirus 3} SCOP: c.37.1.1

Probab=88.02  E-value=0.2  Score=47.57  Aligned_cols=40  Identities=28%  Similarity=0.312  Sum_probs=31.1

Q ss_pred             CCCeEEEEccCCCcHHHHH-HHHHHHHHhCCeEEEEeCCccc
Q psy3261          66 PSPRFVLYGEHGVGKSMAL-VYALQYAHENNYLLVHIPWVLR  106 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L-~q~~~~A~~~gwiVl~vP~~~~  106 (342)
                      +...++|.|.-||||||++ ..+..+....|- |++++++-.
T Consensus        11 ~~~~I~iEG~~GaGKTT~~~~~L~~~l~~~g~-vv~trEPgg   51 (341)
T 1osn_A           11 GVLRIYLDGAYGIGKTTAAEEFLHHFAITPNR-ILLIGEPLS   51 (341)
T ss_dssp             EEEEEEEEESSSSCTTHHHHHHHHTTTTSGGG-EEEECCCHH
T ss_pred             CceEEEEeCCCCCCHHHHHHHHHHHHHhhCCc-EEEEeCCCc
Confidence            4578899999999999999 777777666663 666666544

>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=87.98  E-value=0.31  Score=42.77  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=20.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .-+++|-|..|+|||+++.+.+.
T Consensus        13 ~~KivlvGd~~VGKTsLi~r~~~   35 (216)
T 4dkx_A           13 KFKLVFLGEQSVGKTSLITRFMY   35 (216)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEEECcCCcCHHHHHHHHHh
Confidence            35899999999999999998764

>1knx_A Probable HPR(Ser) kinase/phosphatase; HPR kinase, HPR kinase/phosphatase, HPRK/P, P-loop, walker A BOX, catabolite repression; 2.50A {Mycoplasma pneumoniae} SCOP: c.98.2.1 c.91.1.2

Probab=87.98  E-value=0.33  Score=45.54  Aligned_cols=36  Identities=19%  Similarity=0.265  Sum_probs=26.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHH---hCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAH---ENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~---~~gwiVl~v  101 (342)
                      .+..++|.|+.|+|||++....+....   ..+++.+..
T Consensus       146 ~g~gvli~G~sG~GKStlal~l~~~G~~lv~DD~v~i~~  184 (312)
T 1knx_A          146 FGVGVLLTGRSGIGKSECALDLINKNHLFVGDDAIEIYR  184 (312)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHTTTCEEEEEEEEEEEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHcCCEEEeCCEEEEEE
Confidence            356899999999999999988876443   335555554

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=87.96  E-value=1.8  Score=39.15  Aligned_cols=35  Identities=14%  Similarity=0.249  Sum_probs=23.3

Q ss_pred             chhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          47 RNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        47 R~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      |..=.+++..+.+       ...+++.++.|+|||.+....+
T Consensus        18 ~~~Q~~~i~~i~~-------~~~~lv~~~TGsGKT~~~~~~~   52 (337)
T 2z0m_A           18 TEVQSKTIPLMLQ-------GKNVVVRAKTGSGKTAAYAIPI   52 (337)
T ss_dssp             CHHHHHHHHHHHT-------TCCEEEECCTTSSHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc-------CCCEEEEcCCCCcHHHHHHHHH
Confidence            3333345555544       3579999999999998755443

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=87.94  E-value=1.7  Score=36.74  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=17.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +..+++.++.|+|||.+..-.+
T Consensus        40 ~~~~lv~apTGsGKT~~~~~~~   61 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYLIPL   61 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHHHHH
T ss_pred             CCCEEEECCCCCchHHHHHHHH
Confidence            3569999999999997655433

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=87.89  E-value=0.24  Score=45.62  Aligned_cols=39  Identities=15%  Similarity=0.074  Sum_probs=24.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWV  104 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~  104 (342)
                      +...+.|+|+.||||||+...+.......  ...|++...-
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~   44 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   44 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchh
Confidence            35568999999999999998887743322  2456654433

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=87.82  E-value=0.54  Score=44.55  Aligned_cols=37  Identities=22%  Similarity=0.185  Sum_probs=29.1

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVL  105 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~  105 (342)
                      +..-++|.|+.|||||++...+   |..-|+-||...+.+
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~L---A~~l~~eiIs~Ds~q   75 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDL---AAHFPLEVINSDKMQ   75 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHH---HTTSCEEEEECCSST
T ss_pred             CCceEEEECCCCCCHHHHHHHH---HHHCCCcEEcccccc
Confidence            3457999999999999987655   566788888876653

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=87.69  E-value=0.36  Score=47.62  Aligned_cols=56  Identities=7%  Similarity=0.207  Sum_probs=41.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh-----------CCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE-----------NNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMW  133 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~-----------~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~  133 (342)
                      .+.-|..|.|.+|+|||+++.++..++..           .++++||+--+++                    +....++
T Consensus       145 grGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR--------------------~~Ev~e~  204 (464)
T 3gqb_B          145 VRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGIT--------------------QRELSYF  204 (464)
T ss_dssp             BTTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEEC--------------------HHHHHHH
T ss_pred             ccCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCc--------------------hHHHHHH
Confidence            46789999999999999999999888764           3567777743322                    2366777


Q ss_pred             HHHHHHh
Q psy3261         134 LRHFQKQ  140 (342)
Q Consensus       134 L~~~~~~  140 (342)
                      ++.|...
T Consensus       205 ~~~l~~~  211 (464)
T 3gqb_B          205 IQEFERT  211 (464)
T ss_dssp             HHHHHHT
T ss_pred             HHHhhhc
Confidence            8887664

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=87.54  E-value=0.35  Score=41.87  Aligned_cols=24  Identities=38%  Similarity=0.404  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...+++|.|..|+|||+++..+..
T Consensus        12 ~~~ki~v~G~~~vGKSsli~~l~~   35 (223)
T 3cpj_B           12 LLFKIVLIGDSGVGKSNLLSRFTK   35 (223)
T ss_dssp             EEEEEEEESCTTSSHHHHHHHHHH
T ss_pred             eeeEEEEECcCCCCHHHHHHHHhc
Confidence            346899999999999999988764

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=87.53  E-value=0.45  Score=49.13  Aligned_cols=36  Identities=17%  Similarity=0.072  Sum_probs=28.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCcc
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVL  105 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~  105 (342)
                      ..++|+|.||.|||+++--+++.+..+.  +|.-|...
T Consensus       193 ~~~vlta~RGRGKSa~lG~~~a~~~~~~--~vtAP~~~  228 (671)
T 2zpa_A          193 GVAAVTAARGRGKSALAGQLISRIAGRA--IVTAPAKA  228 (671)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHSSSCE--EEECSSCC
T ss_pred             CeEEEecCCCCCHHHHHHHHHHHHHhCc--EEECCCHH
Confidence            4689999999999999999999887654  44455443

>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=87.53  E-value=0.29  Score=45.30  Aligned_cols=23  Identities=26%  Similarity=0.392  Sum_probs=19.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ...++|.|+.|+|||++|..+..
T Consensus        18 ~~~I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           18 EFTLMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHC
T ss_pred             CEEEEEECCCCCCHHHHHHHHhC
Confidence            45779999999999999999653

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=87.51  E-value=0.47  Score=48.86  Aligned_cols=38  Identities=16%  Similarity=0.141  Sum_probs=28.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~vP~~  104 (342)
                      +..+++.||.|||||++..+.+..+..+ +-+|+-.|.-
T Consensus        40 ~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r   78 (702)
T 2p6r_A           40 GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLR   78 (702)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcH
Confidence            5679999999999999998888766554 4444444854

>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=87.49  E-value=0.35  Score=47.74  Aligned_cols=57  Identities=9%  Similarity=0.206  Sum_probs=42.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh----CCeEEEEeCCccccccCCcceeccCCCCCccccHHHHHHHHHHHHHh
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE----NNYLLVHIPWVLRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQ  140 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~----~gwiVl~vP~~~~~~~~~~~~~~s~~~~~~~~qP~~a~~~L~~~~~~  140 (342)
                      .+.-|..|.|.+|+|||+++.++..++..    .++++||+--+++                    +....++++.|...
T Consensus       149 grGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR--------------------~~Ev~e~~~~~~~~  208 (465)
T 3vr4_D          149 VRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGIT--------------------FEEAEFFMEDFRQT  208 (465)
T ss_dssp             BTTCBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEEC--------------------HHHHHHHHHHHHHH
T ss_pred             ccCCEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCC--------------------cHHHHHHHHHHhhc
Confidence            46889999999999999999998888865    3567777744422                    23667778888664


Q ss_pred             C
Q psy3261         141 N  141 (342)
Q Consensus       141 N  141 (342)
                      .
T Consensus       209 g  209 (465)
T 3vr4_D          209 G  209 (465)
T ss_dssp             T
T ss_pred             C
Confidence            3

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	342
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.05
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.65
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.6
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.33
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.29
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.23
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.18
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.16
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.94
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.8
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.73
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.65
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.63
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.52
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.47
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.47
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.44
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.34
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.05
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.87
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.81
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.78
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.78
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.73
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.7
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.64
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.62
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.53
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.1
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.03
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.03
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.98
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.95
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	95.93
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.9
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	95.89
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.86
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	95.84
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.79
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.77
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	95.74
d1okkd2	207	GTPase domain of the signal recognition particle r	95.7
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.62
d1ls1a2	207	GTPase domain of the signal sequence recognition p	95.59
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.57
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.57
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	95.56
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	95.56
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.55
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.55
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.54
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	95.54
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	95.44
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.41
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.34
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.32
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.32
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.26
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.22
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.2
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.15
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.07
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.04
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.04
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.98
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	94.95
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.92
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.88
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.87
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	94.84
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.84
d2qy9a2	211	GTPase domain of the signal recognition particle r	94.83
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	94.83
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.74
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.7
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	94.67
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.65
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.64
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	94.63
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.54
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.53
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.45
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.44
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.31
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.3
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.27
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	94.2
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.17
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.11
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	94.03
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	93.97
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.8
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	93.78
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	93.69
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	93.66
d1tuea_	205	Replication protein E1 helicase domain {Human papi	93.57
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.55
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	93.52
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	93.52
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.49
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	93.47
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	93.47
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.44
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.43
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	93.43
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	93.38
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.33
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.29
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	93.24
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.21
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.19
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	93.14
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.14
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.14
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	93.11
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.11
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.1
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.09
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	93.02
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	92.99
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.97
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.96
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	92.95
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	92.95
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.94
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	92.92
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.9
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	92.88
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	92.86
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	92.82
d1nrjb_	209	Signal recognition particle receptor beta-subunit	92.77
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.75
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	92.67
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.65
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	92.61
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	92.6
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	92.6
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	92.52
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	92.5
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.47
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	92.47
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.44
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	92.34
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.28
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	92.28
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.26
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.24
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	92.24
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	92.21
d2awna2	232	Maltose transport protein MalK, N-terminal domain	92.18
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.15
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	92.12
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	92.07
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.04
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	92.04
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.02
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	92.01
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	91.97
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	91.94
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	91.92
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	91.87
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	91.87
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	91.83
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	91.81
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	91.77
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	91.75
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	91.64
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	91.64
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.59
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	91.56
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.55
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	91.53
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	91.52
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	91.52
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	91.5
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.41
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	91.4
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	91.38
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.37
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	91.34
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	91.26
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	91.25
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.23
d1xpua3	289	Transcription termination factor Rho, ATPase domai	91.17
d1g2912	240	Maltose transport protein MalK, N-terminal domain	91.13
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	91.05
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	91.03
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	90.98
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	90.92
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.74
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	90.72
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	90.7
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	90.67
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	90.51
d2fh5b1	207	Signal recognition particle receptor beta-subunit	90.44
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.42
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	90.32
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	90.3
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	90.17
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	90.17
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	90.04
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	89.99
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	89.6
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	89.58
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	89.45
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	89.29
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	89.29
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	89.12
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	89.01
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	88.93
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	88.92
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	88.64
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	88.61
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	88.42
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	88.4
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	88.38
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.31
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	88.21
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	88.02
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	87.97
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	87.94
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	87.78
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	87.77
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	87.76
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	87.27
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	87.08
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	87.06
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	86.6
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	86.49
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	86.24
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	86.21
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	86.02
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	85.72
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	84.91
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	84.49
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	84.41
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	84.33
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	84.01
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	83.77
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	83.1
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	82.46
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	82.14
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	82.06
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	81.92
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	81.66
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	81.14
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	80.52
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	80.5

>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=99.05  E-value=7.8e-10  Score=97.93  Aligned_cols=123  Identities=12%  Similarity=0.064  Sum_probs=73.1

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPD  267 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~  267 (342)
                      +..+++.+...   .+.++++++|++..+.....              ..+...+..+......- ..+++.+...    
T Consensus       123 ~~~~l~~l~~~---~~~~~~i~id~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~-~~i~~~~~~~----  180 (283)
T d2fnaa2         123 FANLLESFEQA---SKDNVIIVLDEAQELVKLRG--------------VNLLPALAYAYDNLKRI-KFIMSGSEMG----  180 (283)
T ss_dssp             HHHHHHHHHHT---CSSCEEEEEETGGGGGGCTT--------------CCCHHHHHHHHHHCTTE-EEEEEESSHH----
T ss_pred             HHHHHHHHHhh---cccccccccchhhhhcccch--------------HHHHHHHHHHHHhhhhh-hhhhccccch----
Confidence            44455566554   37789999999987765543              34566666666544333 3333333221    


Q ss_pred             CccCcchhHHhhhcCCC---CCCCcceeecCCCCHHHHHHHHHHHH-hCCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         268 RRESHLPLYMLKKAGFE---SIDPFVPIHVPELNDEEFHNLLNLYE-SKKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       268 ~~~~~~p~~llg~~g~~---~~dP~~~i~v~~~s~~E~~~ll~yy~-~~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           .+..+.......   .-..+.++.+++|+.+|+..++.-.. ..+ + +.+..++++-.|||+|.-|..+|
T Consensus       181 -----~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~-~-~~~~~~~i~~~~~G~P~~L~~~~  249 (283)
T d2fnaa2         181 -----LLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEAD-I-DFKDYEVVYEKIGGIPGWLTYFG  249 (283)
T ss_dssp             -----HHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHT-C-CCCCHHHHHHHHCSCHHHHHHHH
T ss_pred             -----HHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcC-C-CHHHHHHHHHHhCCCHHHHHHHH
Confidence                 111122111110   01123468999999999999986543 333 3 34456789999999999887776

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.65  E-value=1.5e-06  Score=77.72  Aligned_cols=122  Identities=13%  Similarity=0.107  Sum_probs=72.5

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.++.+||+-+++.... ...   ..-+...-.++..|+..+.+ .-+.+++|.|||...       ..++..+.+..
T Consensus       103 ~~P~il~iDeiD~l~~~r~-~~~---~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~-------~~ld~al~R~g  171 (256)
T d1lv7a_         103 AAPCIIFIDEIDAVGRQRG-AGL---GGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRP-------DVLDPALLRPG  171 (256)
T ss_dssp             TCSEEEEETTHHHHTCCCS-TTS---CCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCT-------TTSCGGGGSTT
T ss_pred             cCCEEEEEEChhhhCccCC-CCC---CCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCc-------ccCCHhHcCCC
Confidence            4677888999988876432 111   11111222466677777764 334556655555432       11445555433


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHH-hhCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAF-LTKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~-lSgGNP~~l~~lc~  340 (342)
                      .|++     .|+++..+.+|-..++..|....-+..+.....+-. ..|-+++++..+|.
T Consensus       172 Rfd~-----~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~  226 (256)
T d1lv7a_         172 RFDR-----QVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (256)
T ss_dssp             SSCE-----EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCCE-----EEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHH
Confidence            4653     388998999999999998876554432333344444 44558899988873

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.60  E-value=8.1e-07  Score=79.14  Aligned_cols=122  Identities=13%  Similarity=0.084  Sum_probs=71.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCC-CCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSD-WNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~-~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      .-|.+|.+||+-++++... ...   ..-....-.++..|+..+.+- -+.+++|.+||...     .  .++..+++..
T Consensus       100 ~~p~Ii~iDeid~l~~~r~-~~~---~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~-----~--~ld~al~R~~  168 (247)
T d1ixza_         100 HAPCIVFIDEIDAVGRKRG-SGV---GGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRP-----D--ILDPALLRPG  168 (247)
T ss_dssp             SSSEEEEEETHHHHHC-------------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCG-----G--GSCGGGGSTT
T ss_pred             cCCEEEEEEChhhhCccCC-CCC---CCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCc-----c--ccCHhHcCCC
Confidence            4588888999988876421 110   011112234677777777653 24556655544321     1  1334455333


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhh-CCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLT-KRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lS-gGNP~~l~~lc~  340 (342)
                      .|+.     .|+|+..+.+|-+.+++.|....-+..+....+|-..| |-+++++..+|.
T Consensus       169 Rf~~-----~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~  223 (247)
T d1ixza_         169 RFDR-----QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  223 (247)
T ss_dssp             SSCE-----EEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCcE-----EEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHHH
Confidence            4643     38999999999999999888765553232334455554 558888888874

>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=98.33  E-value=3.5e-06  Score=73.61  Aligned_cols=57  Identities=26%  Similarity=0.266  Sum_probs=37.6

Q ss_pred             EechhHH-HHHHHHHhc-cCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q psy3261          45 LIRNCML-ELVGYLKSM-TNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN-NYLLVHI  101 (342)
Q Consensus        45 lvR~~t~-el~~~l~~~-~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~-gwiVl~v  101 (342)
                      .-|+..+ +|.+.|..+ .+.......++|+|++|||||+++..+....... +..++++
T Consensus        19 ~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~   78 (276)
T d1fnna2          19 PHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYI   78 (276)
T ss_dssp             TTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEe
Confidence            4466443 455666552 1334566789999999999999998887776544 3334433

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.29  E-value=9.6e-06  Score=72.18  Aligned_cols=119  Identities=13%  Similarity=0.204  Sum_probs=71.8

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcC-CCCCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS-DWNNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~-~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.+|++-.++.......+       ...-++...++..+.+ ..+.+++|++||....       .++..+.+..
T Consensus        96 ~~p~il~iDeid~l~~~r~~~~~-------~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~-------~ld~al~r~g  161 (258)
T d1e32a2          96 NAPAIIFIDELDAIAPKREKTHG-------EVERRIVSQLLTLMDGLKQRAHVIVMAATNRPN-------SIDPALRRFG  161 (258)
T ss_dssp             TCSEEEEESSGGGTCCHHHHCCC-------TTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGG-------GSCGGGTSTT
T ss_pred             cCCeEEEehhhhhhccCCCCCCC-------chHHHHHHHhccccccccccCCccEEEeCCCcc-------ccchhhhhcc
Confidence            46888899999888876321111       1112456666666654 3455666665554321       1233444322


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHh-hCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFL-TKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~l-SgGNP~~l~~lc~  340 (342)
                      .|+.     .|+|+.-+.++-+.+++.|....-+..+....+|--. -|-+++++..+|.
T Consensus       162 Rfd~-----~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~  216 (258)
T d1e32a2         162 RFDR-----EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  216 (258)
T ss_dssp             SSCE-----EEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             cccc-----eeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHH
Confidence            3543     4889989999999999998765444322234455444 4669999988873

>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=98.23  E-value=6.1e-06  Score=73.90  Aligned_cols=122  Identities=9%  Similarity=0.100  Sum_probs=69.2

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCC-CCeEEEEEeCCCCCCCCCccCcchhHHhhhc
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDW-NNGAIVLALSPRANLPDRRESHLPLYMLKKA  281 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~-~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~  281 (342)
                      ..|.+|.+||+-.++.......+.    -....-.++..|+..+.+-. +++++|.+|+...  .     .+|..+....
T Consensus        99 ~~p~il~ideid~l~~~~~~~~~~----~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~--~-----~ld~al~r~g  167 (265)
T d1r7ra3          99 AAPCVLFFDELDSIAKARGGNIGD----GGGAADRVINQILTEMDGMSTKKNVFIIGATNRP--D-----IIDPAILRPG  167 (265)
T ss_dssp             TCSEEEEESSGGGTCCHHHHCCCT----THHHHHHHHHHHHHTCC------CCEEEECCBSC--T-----TTSCGGGSST
T ss_pred             cCCcceeHHhhhhccccCCCcCCC----CcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCc--h-----hCCHHHhCCC
Confidence            469999999998888753201110    00011135677777776532 3445555555432  1     1444454333


Q ss_pred             CCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHH-HHhhCCCHHHHhhhcc
Q psy3261         282 GFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEI-AFLTKRVPQKMYEFCS  340 (342)
Q Consensus       282 g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el-~~lSgGNP~~l~~lc~  340 (342)
                      .|+.     .|+++..+.+|-+.++..+.....+..+....++ ....|-+++++..+|.
T Consensus       168 Rf~~-----~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~  222 (265)
T d1r7ra3         168 RLDQ-----LIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  222 (265)
T ss_dssp             TSEE-----EEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHHH
T ss_pred             CccE-----EEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHHH
Confidence            3543     3899999999999999888765544322223344 3467789999998874

>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=98.18  E-value=6.1e-06  Score=71.94  Aligned_cols=100  Identities=12%  Similarity=0.077  Sum_probs=61.2

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      ...++.+|+++.+...                  ....+++++.....+..+|++++....        ++..+..+  +
T Consensus       131 ~~~iiiide~d~l~~~------------------~~~~l~~~~e~~~~~~~~Il~tn~~~~--------i~~~l~sR--~  182 (252)
T d1sxje2         131 RYKCVIINEANSLTKD------------------AQAALRRTMEKYSKNIRLIMVCDSMSP--------IIAPIKSQ--C  182 (252)
T ss_dssp             CCEEEEEECTTSSCHH------------------HHHHHHHHHHHSTTTEEEEEEESCSCS--------SCHHHHTT--S
T ss_pred             CceEEEeccccccccc------------------cchhhhcccccccccccceeeeccccc--------hhhhhhcc--h
Confidence            3457888999765322                  234556666544455666777655331        22233322  2


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHhC-CCcc-CcchHHHHHHhhCCCHHHHhh
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQ-TSEGREEIAFLTKRVPQKMYE  337 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~-~e~~~~el~~lSgGNP~~l~~  337 (342)
                            ..|+++.++.+|+..++.+-... ++-- .++...++-..|+||+|....
T Consensus       183 ------~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~ai~  232 (252)
T d1sxje2         183 ------LLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLL  232 (252)
T ss_dssp             ------EEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHH
T ss_pred             ------heeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHHHHH
Confidence                  24889999999999999865443 3321 344445677799999997543

>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=98.16  E-value=4.1e-05  Score=68.61  Aligned_cols=67  Identities=22%  Similarity=0.287  Sum_probs=48.8

Q ss_pred             eCHHHHHHhhhcCCCChhhHHhhhhcCCceEEechhH-HHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          14 LPDEVRSAIFELGGITRVFNEQTQIFNESSILIRNCM-LELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        14 ~~~~~~~~l~~~g~l~~~~~~~~~~~~~~~~lvR~~t-~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      |+...++.....|.+|+          ++.+..|+.- .+|++.|.+..+  ....-+.|+|..|+|||++..++...+.
T Consensus         2 ~~~~~~~~~l~~~~~p~----------~~~~~gR~~~~~~i~~~L~~~~~--~~~~~v~I~GmgGiGKTtLA~~v~~~~~   69 (277)
T d2a5yb3           2 FSRQMLDRKLLLGNVPK----------QMTCYIREYHVDRVIKKLDEMCD--LDSFFLFLHGRAGSGKSVIASQALSKSD   69 (277)
T ss_dssp             CCHHHHHHHHHHTTCBC----------CCCSCCCHHHHHHHHHHHHHHTT--SSSEEEEEECSTTSSHHHHHHHHHHHCS
T ss_pred             cchhhhcccccccCCCC----------CCceeCcHHHHHHHHHHHHhccC--CCceEEEEECCCCCCHHHHHHHHHHhhh
Confidence            56778888888888997          2334568844 477788866222  2344567999999999999999987654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.94  E-value=0.00014  Score=63.27  Aligned_cols=102  Identities=11%  Similarity=0.133  Sum_probs=66.1

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      ...++.||++-.+-                  -.....|++++.....+..+|++|.....        +...+..+   
T Consensus       115 ~~kviiIde~d~l~------------------~~~q~~Llk~lE~~~~~~~~il~tn~~~~--------i~~~i~SR---  165 (239)
T d1njfa_         115 RFKVYLIDEVHMLS------------------RHSFNALLKTLEEPPEHVKFLLATTDPQK--------LPVTILSR---  165 (239)
T ss_dssp             SSEEEEEETGGGSC------------------HHHHHHHHHHHHSCCTTEEEEEEESCGGG--------SCHHHHTT---
T ss_pred             CCEEEEEECcccCC------------------HHHHHHHHHHHhcCCCCeEEEEEcCCccc--------cChhHhhh---
Confidence            34577889996541                  23346688888765667778888765321        11112211   


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ...+.++.++.+|+...+..... .+.-.+++..+.+-..|+||+|.+..+|
T Consensus       166 -----c~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         166 -----CLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             -----SEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             -----hcccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                 22488999999999988765543 3332256666778889999999987765

>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=97.80  E-value=0.00044  Score=58.91  Aligned_cols=115  Identities=10%  Similarity=0.029  Sum_probs=71.5

Q ss_pred             hHHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCC
Q psy3261         185 SDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRAN  264 (342)
Q Consensus       185 ~~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~  264 (342)
                      .+.+..+++.+...+. ....-++.+|++..+-.                  .....|++++....++..+|++|+....
T Consensus        90 ~~~ir~l~~~~~~~~~-~~~~kviIide~d~l~~------------------~a~n~Llk~lEep~~~~~fIl~t~~~~~  150 (207)
T d1a5ta2          90 VDAVREVTEKLNEHAR-LGGAKVVWVTDAALLTD------------------AAANALLKTLEEPPAETWFFLATREPER  150 (207)
T ss_dssp             HHHHHHHHHHTTSCCT-TSSCEEEEESCGGGBCH------------------HHHHHHHHHHTSCCTTEEEEEEESCGGG
T ss_pred             cchhhHHhhhhhhccc-cCccceEEechhhhhhh------------------hhhHHHHHHHHhhcccceeeeeecChhh
Confidence            3444455556544332 23345778999955532                  3457888999877788888888765431


Q ss_pred             CCCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHHHhCCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         265 LPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       265 ~~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      +       +| -+..+        ...+.++.++.+|+...+.   +..-+ +++....+-.+|+|+||....+
T Consensus       151 l-------l~-tI~SR--------c~~i~~~~~~~~~~~~~L~---~~~~~-~~~~~~~i~~~s~Gs~r~al~~  204 (207)
T d1a5ta2         151 L-------LA-TLRSR--------CRLHYLAPPPEQYAVTWLS---REVTM-SQDALLAALRLSAGSPGAALAL  204 (207)
T ss_dssp             S-------CH-HHHTT--------SEEEECCCCCHHHHHHHHH---HHCCC-CHHHHHHHHHHTTTCHHHHHHT
T ss_pred             h-------hh-hhcce--------eEEEecCCCCHHHHHHHHH---HcCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            1       22 12211        1237888999999988774   22223 4444445666999999998765

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.73  E-value=0.0001  Score=63.34  Aligned_cols=103  Identities=12%  Similarity=0.166  Sum_probs=68.1

Q ss_pred             CceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcC
Q psy3261         203 VCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG  282 (342)
Q Consensus       203 ~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g  282 (342)
                      ..+.++.+|++..+....                  ...|+.++.....+..+|+++.....        ++..+..+  
T Consensus       108 ~~~~iilide~d~~~~~~------------------~~~ll~~l~~~~~~~~~i~~~n~~~~--------i~~~l~sR--  159 (231)
T d1iqpa2         108 ASFKIIFLDEADALTQDA------------------QQALRRTMEMFSSNVRFILSCNYSSK--------IIEPIQSR--  159 (231)
T ss_dssp             CSCEEEEEETGGGSCHHH------------------HHHHHHHHHHTTTTEEEEEEESCGGG--------SCHHHHHT--
T ss_pred             CCceEEeehhhhhcchhH------------------HHHHhhhcccCCcceEEEeccCChhh--------chHhHhCc--
Confidence            456678899996554432                  34567777666667777877765431        22233322  


Q ss_pred             CCCCCCcceeecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         283 FESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       283 ~~~~dP~~~i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                            +..+.+..++..+....+......--+. +++...++--.|+|+.|.+...+
T Consensus       160 ------~~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~gdiR~ai~~L  211 (231)
T d1iqpa2         160 ------CAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINIL  211 (231)
T ss_dssp             ------EEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ------cccccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  2248899999999999998776654443 55555566678999999887544

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.65  E-value=7.9e-05  Score=63.97  Aligned_cols=102  Identities=15%  Similarity=0.096  Sum_probs=64.6

Q ss_pred             ceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCC
Q psy3261         204 CRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGF  283 (342)
Q Consensus       204 ~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~  283 (342)
                      .+-++.+|++..+.....                  ..++..+.....+..++.++.....        ++..+..+   
T Consensus       101 ~~kviiiDe~d~~~~~~~------------------~~ll~~~e~~~~~~~~i~~~~~~~~--------i~~~l~sr---  151 (224)
T d1sxjb2         101 KHKIVILDEADSMTAGAQ------------------QALRRTMELYSNSTRFAFACNQSNK--------IIEPLQSQ---  151 (224)
T ss_dssp             CCEEEEEESGGGSCHHHH------------------HTTHHHHHHTTTTEEEEEEESCGGG--------SCHHHHTT---
T ss_pred             ceEEEEEecccccchhHH------------------HHHhhhccccccceeeeeccCchhh--------hhhHHHHH---
Confidence            345677999977755432                  2345555555566677777654331        12223222   


Q ss_pred             CCCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhhc
Q psy3261         284 ESIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       284 ~~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                           ...++++.++.+|+..++...... |+--+++...++-..|+|++|.+...+
T Consensus       152 -----~~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~Gd~R~ai~~L  203 (224)
T d1sxjb2         152 -----CAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNL  203 (224)
T ss_dssp             -----SEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             -----HHHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence                 234899999999999999776543 443255556667779999999876553

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.63  E-value=0.00019  Score=61.41  Aligned_cols=100  Identities=8%  Similarity=0.090  Sum_probs=61.1

Q ss_pred             eEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCCCCCccCcchhHHhhhcCCC
Q psy3261         205 RTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE  284 (342)
Q Consensus       205 pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~~~~~~~~~p~~llg~~g~~  284 (342)
                      ..++.||++..+....                  -..|++.+....++..+++++.....        ++..+..+    
T Consensus       100 ~kiiiiDe~d~~~~~~------------------~~~Ll~~le~~~~~~~~~~~~~~~~~--------i~~~i~sr----  149 (227)
T d1sxjc2         100 FKLIILDEADAMTNAA------------------QNALRRVIERYTKNTRFCVLANYAHK--------LTPALLSQ----  149 (227)
T ss_dssp             CEEEEETTGGGSCHHH------------------HHHHHHHHHHTTTTEEEEEEESCGGG--------SCHHHHTT----
T ss_pred             eEEEEEeccccchhhH------------------HHHHHHHhhhcccceeeccccCcHHH--------hHHHHHHH----
Confidence            3467789996654332                  24566666544455566666543321        12222211    


Q ss_pred             CCCCcceeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         285 SIDPFVPIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       285 ~~dP~~~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                          ...+.+..++.+|+..++...... |+-.+++..+++--.|+|+.|.+..+
T Consensus       150 ----~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~Gd~R~ain~  200 (227)
T d1sxjc2         150 ----CTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNV  200 (227)
T ss_dssp             ----SEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ----HhhhccccccccccccccccccccccccCCHHHHHHHHHHcCCcHHHHHHH
Confidence                234889999999999999876544 44325555556777999999987554

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.52  E-value=0.00094  Score=57.75  Aligned_cols=50  Identities=12%  Similarity=0.115  Sum_probs=33.6

Q ss_pred             eeecCCCCHHHHHHHHHHHHhCCCcc---CcchHHHHHHhh------CCCHHHHhhhcc
Q psy3261         291 PIHVPELNDEEFHNLLNLYESKKWLQ---TSEGREEIAFLT------KRVPQKMYEFCS  340 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~~~l~---~e~~~~el~~lS------gGNP~~l~~lc~  340 (342)
                      ++.++.|+.+|...++..-.+.+...   +++....+--++      .|+||...++|.
T Consensus       203 ~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~  261 (287)
T d1w5sa2         203 KLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALK  261 (287)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHH
T ss_pred             eeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHH
Confidence            48899999999999998765533221   343333333344      699998877763

>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=97.47  E-value=0.0019  Score=57.46  Aligned_cols=91  Identities=13%  Similarity=0.188  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhcCCCCCeEEEEEeCCCCCC
Q psy3261         186 DVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQSDWNNGAIVLALSPRANL  265 (342)
Q Consensus       186 ~~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~~~~~~G~vv~AtS~~~~~  265 (342)
                      .-+..+++|+.+     ..++++.||++..+++... .        ....+.+...|+.+++..  .--+|+||+...  
T Consensus        97 ~r~~~i~~~~~~-----~~~iIlfiDeih~l~~~g~-~--------~g~~~d~a~~Lkp~L~rg--~i~vIgatT~ee--  158 (268)
T d1r6bx2          97 KRFKALLKQLEQ-----DTNSILFIDEIHTIIGAGA-A--------SGGQVDAANLIKPLLSSG--KIRVIGSTTYQE--  158 (268)
T ss_dssp             HHHHHHHHHHSS-----SSCEEEEETTTTTTTTSCC-S--------SSCHHHHHHHHSSCSSSC--CCEEEEEECHHH--
T ss_pred             HHHHHHHHHhhc-----cCCceEEecchHHHhcCCC-C--------CCccccHHHHhhHHHhCC--CCeEEEeCCHHH--
Confidence            345567778864     5679999999999987632 0        123467788888777621  234677776432  


Q ss_pred             CCCccCcchhHHhhhcCCCCCCC-----cceeecCCCCHHHHHHHHHH
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDP-----FVPIHVPELNDEEFHNLLNL  308 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP-----~~~i~v~~~s~~E~~~ll~y  308 (342)
                                  ..+  +...||     |.+|.|...|.++...++..
T Consensus       159 ------------y~~--~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~  192 (268)
T d1r6bx2         159 ------------FSN--IFEKDRALARRFQKIDITEPSIEETVQIING  192 (268)
T ss_dssp             ------------HHC--CCCCTTSSGGGEEEEECCCCCHHHHHHHHHH
T ss_pred             ------------HHH--HHhhcHHHHhhhcccccCCCCHHHHHHHHHH
Confidence                        000  111233     56799999999999998854

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.47  E-value=0.00065  Score=57.94  Aligned_cols=48  Identities=8%  Similarity=0.005  Sum_probs=35.6

Q ss_pred             eeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         291 PIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      .+++..++.+|+..++.....+ ++--+++..+.+--.|+|+.|....+
T Consensus       161 ~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~gd~R~ai~~  209 (237)
T d1sxjd2         161 KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITL  209 (237)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHH
T ss_pred             hhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCCCHHHHHHH
Confidence            4889999999999999876554 33215555566777999999975543

>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=97.44  E-value=0.0039  Score=53.44  Aligned_cols=48  Identities=8%  Similarity=0.080  Sum_probs=36.8

Q ss_pred             eeecCCCCHHHHHHHHHHHHhC-CCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         291 PIHVPELNDEEFHNLLNLYESK-KWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       291 ~i~v~~~s~~E~~~ll~yy~~~-~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      .++++.++.++....++....+ |+--+++..+++...|+|+.|.+...
T Consensus       178 ~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~GDiR~ai~~  226 (253)
T d1sxja2         178 DIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINL  226 (253)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHH
T ss_pred             eeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCCcHHHHHHH
Confidence            4899999999999999877654 54225666677888999999887543

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=6.1e-05  Score=61.17  Aligned_cols=34  Identities=21%  Similarity=0.218  Sum_probs=28.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|+|++|||||+++.+++......|-.|..+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~~~~v~~~   35 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSSGVPVDGF   35 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHTTCCCEEE
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            5689999999999999999999998777655433

>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=97.05  E-value=0.00022  Score=57.35  Aligned_cols=34  Identities=18%  Similarity=0.106  Sum_probs=29.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +-+.|+|..||||||++.+++.+..++|+-|..+
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~   36 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALCARGIRPGLI   36 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEe
Confidence            3578999999999999999999999999866555

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=96.87  E-value=0.00043  Score=60.78  Aligned_cols=37  Identities=24%  Similarity=0.271  Sum_probs=26.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      .+...++|+||+|||||++...+   |.+-|+-++.|-.+
T Consensus        38 ~p~~~vLL~GppGtGKT~la~al---A~~~~~~~~~i~~~   74 (246)
T d1d2na_          38 TPLVSVLLEGPPHSGKTALAAKI---AEESNFPFIKICSP   74 (246)
T ss_dssp             CSEEEEEEECSTTSSHHHHHHHH---HHHHTCSEEEEECG
T ss_pred             CCCeEEEEECcCCCCHHHHHHHH---hhcccccccccccc
Confidence            45567999999999998887665   44556666666443

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.81  E-value=0.00049  Score=59.02  Aligned_cols=38  Identities=16%  Similarity=0.187  Sum_probs=35.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+..-.+|+|++|||||+++.|+++.+..+|.-++|+.
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            56788999999999999999999999999999888884

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=96.78  E-value=0.00071  Score=58.01  Aligned_cols=48  Identities=13%  Similarity=0.133  Sum_probs=37.7

Q ss_pred             eecCCCCHHHHHHHHHHHHhCCCcc-CcchHHHHHHhhCCCHHHHhhhc
Q psy3261         292 IHVPELNDEEFHNLLNLYESKKWLQ-TSEGREEIAFLTKRVPQKMYEFC  339 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~~~~l~-~e~~~~el~~lSgGNP~~l~~lc  339 (342)
                      +.++.++.+|...+++.+...--.. .++...++...|+|++|.+..+|
T Consensus       159 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         159 LELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             EEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHHHHHH
Confidence            5788899999999998766654443 55566778889999999988766

>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=96.78  E-value=0.0011  Score=56.88  Aligned_cols=39  Identities=23%  Similarity=0.237  Sum_probs=32.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ..+.++|+|++|||||-+|.-+...+..++--|+|++..
T Consensus        35 ~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~   73 (213)
T d1l8qa2          35 LYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD   73 (213)
T ss_dssp             SCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechH
Confidence            345699999999999999888888888888777777544

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.73  E-value=0.0059  Score=54.06  Aligned_cols=38  Identities=16%  Similarity=0.123  Sum_probs=33.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ....-..++|+.|||||++..|++.-|.+.|-.|+||.
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiD   92 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID   92 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEE
Confidence            45667889999999999999999999999998888873

>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=96.70  E-value=0.00038  Score=56.62  Aligned_cols=24  Identities=25%  Similarity=0.454  Sum_probs=20.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      |++|+|+.||||||+|..++..-.
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCC
Confidence            789999999999999988877543

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=96.64  E-value=0.0092  Score=55.53  Aligned_cols=94  Identities=13%  Similarity=0.117  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc-CCCCCeEEEEEeCCCCCC
Q psy3261         187 VVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ-SDWNNGAIVLALSPRANL  265 (342)
Q Consensus       187 ~~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~-~~~~~G~vv~AtS~~~~~  265 (342)
                      -+..+++|+...    +.++++.||++..+++... -         .....+...|+.+++ |+   --||+|||...- 
T Consensus       102 r~~~i~~~~~~~----~~~~ilfide~h~l~~~g~-~---------~g~~d~a~~Lkp~L~rg~---~~~I~~tT~~ey-  163 (387)
T d1qvra2         102 RLKAVIQEVVQS----QGEVILFIDELHTVVGAGK-A---------EGAVDAGNMLKPALARGE---LRLIGATTLDEY-  163 (387)
T ss_dssp             HHHHHHHHHHTT----CSSEEEEECCC-----------------------------HHHHHTTC---CCEEEEECHHHH-
T ss_pred             HHHHHHHHhccC----CCceEEEeccHHHHhcCCC-C---------CCcccHHHHHHHHHhCCC---cceeeecCHHHH-
Confidence            345667787653    5689999999999987532 0         112567788888885 43   246888874320 


Q ss_pred             CCCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHHHHH
Q psy3261         266 PDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLLNLY  309 (342)
Q Consensus       266 ~~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll~yy  309 (342)
                               +..-...++  ..-|.+|.|...|.++...++...
T Consensus       164 ---------~~~e~d~al--~rrF~~v~v~ep~~~~~~~il~~~  196 (387)
T d1qvra2         164 ---------REIEKDPAL--ERRFQPVYVDEPTVEETISILRGL  196 (387)
T ss_dssp             ---------HHHTTCTTT--CSCCCCEEECCCCHHHHHHHHHHH
T ss_pred             ---------HHhcccHHH--HHhcccccCCCCcHHHHHHHHHHH
Confidence                     111011112  222667999999999999998543

>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=96.62  E-value=0.00067  Score=57.15  Aligned_cols=38  Identities=18%  Similarity=0.108  Sum_probs=32.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH-HHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ-YAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~-~A~~~gwiVl~vP  102 (342)
                      .+..-++|+|++|+|||+++.|++. .|..++|.|+|+.
T Consensus        24 ~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            5788999999999999999999655 6778889998873

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=96.53  E-value=0.002  Score=55.13  Aligned_cols=47  Identities=15%  Similarity=-0.017  Sum_probs=32.3

Q ss_pred             eecCCCCHHHHHHHHHHHHh-CCCccCcchHHHHHHhhCCCHHHHhhh
Q psy3261         292 IHVPELNDEEFHNLLNLYES-KKWLQTSEGREEIAFLTKRVPQKMYEF  338 (342)
Q Consensus       292 i~v~~~s~~E~~~ll~yy~~-~~~l~~e~~~~el~~lSgGNP~~l~~l  338 (342)
                      +.+...+.++...++..... .++-..++...++-..|+|++|....+
T Consensus       160 ~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~~  207 (239)
T d1ixsb2         160 EHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRL  207 (239)
T ss_dssp             EECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHHH
T ss_pred             eEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHHH
Confidence            67888999999988875544 333324444455666999999987654

>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=96.10  E-value=0.0033  Score=54.17  Aligned_cols=34  Identities=24%  Similarity=0.384  Sum_probs=23.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      ....++|+||+|||||++. ++++-....+.+++.
T Consensus        31 ~P~~ilL~GpPGtGKT~la-~~la~~~~~~~~~i~   64 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLR-SAIFEETQGNVIVID   64 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHH-HHHHHHTTTCCEEEC
T ss_pred             CCEEEEEECCCCCCHHHHH-HHHHHHhhcceEEEe
Confidence            3456999999999999975 444444444566554

>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=96.03  E-value=0.0023  Score=51.32  Aligned_cols=25  Identities=16%  Similarity=0.215  Sum_probs=21.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +++.+++|+|++||||||+...+..
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHH
Confidence            5688999999999999998766653

>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=96.03  E-value=0.0017  Score=53.10  Aligned_cols=31  Identities=13%  Similarity=0.059  Sum_probs=27.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      .++.-++|+|++|||||+++.|+++.+...+
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~~~~~~   51 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVTCQLPI   51 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTTSCG
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHHHHHhh
Confidence            5788999999999999999999999887654

>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=95.98  E-value=0.0028  Score=51.20  Aligned_cols=33  Identities=12%  Similarity=0.140  Sum_probs=29.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +-++|..||||||++.+++.+...+|+=|..|-
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            349999999999999999999999998887763

>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=95.95  E-value=0.0035  Score=51.68  Aligned_cols=34  Identities=21%  Similarity=0.130  Sum_probs=26.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++.|++|.|++||||||.-..+.   ...|+..|.+
T Consensus         1 p~~~riil~G~pGSGKsT~a~~La---~~~g~~~i~~   34 (190)
T d1ak2a1           1 PKGVRAVLLGPPGAGKGTQAPKLA---KNFCVCHLAT   34 (190)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHH---HHHTCEEEEH
T ss_pred             CCccEEEEECCCCCCHHHHHHHHH---HHhCCeEEeH
Confidence            367899999999999999876654   3447776664

>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=95.93  E-value=0.0029  Score=49.79  Aligned_cols=31  Identities=16%  Similarity=0.149  Sum_probs=21.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -++|+|++||||||+...++.  ...|+.++..
T Consensus         4 lIii~G~pGsGKTTla~~L~~--~~~~~~~~~~   34 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIA--KNPGFYNINR   34 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH--HSTTEEEECH
T ss_pred             EEEEECCCCCCHHHHHHHHHH--hCCCCEEech
Confidence            378899999999999876543  2235554443

>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=95.90  E-value=0.0021  Score=51.36  Aligned_cols=31  Identities=23%  Similarity=0.368  Sum_probs=24.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+++|+|++||||||+...+.   .+-|+-++.+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La---~~l~~~~i~~   35 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELA---SKSGLKYINV   35 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH---HHHCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHH---HHHCCcEEec
Confidence            578999999999999887664   3447777765

>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=95.89  E-value=0.0066  Score=49.34  Aligned_cols=35  Identities=14%  Similarity=0.048  Sum_probs=27.3

Q ss_pred             CCeEE-EEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFV-LYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~v-L~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+.+| |+|+.||||||+..++.......+-.+..+
T Consensus        21 ~~~iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~   56 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (198)
T ss_dssp             SSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhccccccceec
Confidence            44455 999999999999999998877776555444

>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=95.86  E-value=0.0039  Score=54.38  Aligned_cols=38  Identities=13%  Similarity=0.064  Sum_probs=32.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH-HHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ-YAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~-~A~~~gwiVl~vP  102 (342)
                      .++.-++|.|++|+|||+++.|++. +|..+|+=|+|+.
T Consensus        33 ~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s   71 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (277)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEee
Confidence            4677899999999999999999986 5778899888873

>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=95.84  E-value=0.0022  Score=51.40  Aligned_cols=33  Identities=15%  Similarity=0.043  Sum_probs=25.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ..+++|.|++||||||+...+..+   -|.-.+...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~---~~~~~i~~~   39 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV---FNTTSAWEY   39 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH---TTCEEECCT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH---hCCCeEeee
Confidence            568999999999999998877665   355555443

>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=95.79  E-value=0.0035  Score=50.40  Aligned_cols=33  Identities=18%  Similarity=0.194  Sum_probs=26.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      .-++|+|++||||||++..+..+....|+=+..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~~~~~~~   34 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKM   34 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHcCCCeEE
Confidence            347899999999999999999887766554433

>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=95.77  E-value=0.0034  Score=55.46  Aligned_cols=37  Identities=16%  Similarity=0.197  Sum_probs=33.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..-..|+|++|||||+++.|++.-|.+.|-.|+||
T Consensus        52 ~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyi   88 (263)
T d1u94a1          52 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFI   88 (263)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEE
Confidence            4677889999999999999999999999998888886

>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=95.74  E-value=0.0029  Score=49.53  Aligned_cols=30  Identities=27%  Similarity=0.234  Sum_probs=20.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .++|+|++||||||+-. .++-  .-|+-++..
T Consensus         4 ~I~l~G~~GsGKSTvak-~La~--~L~~~~id~   33 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGR-QLAQ--QLNMEFYDS   33 (169)
T ss_dssp             CEEEECCTTSCHHHHHH-HHHH--HTTCEEEEH
T ss_pred             eEEEECCCCCCHHHHHH-HHHH--HhCCCeEee
Confidence            58999999999996544 4433  346665543

>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=95.70  E-value=0.0054  Score=52.25  Aligned_cols=36  Identities=17%  Similarity=0.247  Sum_probs=30.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...++|.|+.|+||||+++-+.+|+..+|.=|.-|
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~li   40 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFC   40 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            456678899999999999999999998888766544

>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=95.62  E-value=0.0053  Score=52.54  Aligned_cols=36  Identities=17%  Similarity=0.185  Sum_probs=29.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +..-++|.|+.|+||||+++-+.+|...+|+=|.-|
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~li   45 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLA   45 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEE
Confidence            445678899999999999999999998887655444

>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=95.59  E-value=0.0051  Score=52.37  Aligned_cols=34  Identities=18%  Similarity=0.213  Sum_probs=28.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +-++|.|+.|+||||+++-+.++..++|+=|.-|
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~li   44 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV   44 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            3467799999999999999999999888766644

>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=95.57  E-value=0.0058  Score=50.33  Aligned_cols=34  Identities=12%  Similarity=0.218  Sum_probs=25.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++...++|.|++||||||....+.   ...||+.+..
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La---~~~g~~~i~~   37 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIV---RDFGWVHLSA   37 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHH---HHHCCEEEEH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHH---HHHCCceEch
Confidence            455688999999999999765554   3448876643

>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=95.57  E-value=0.0035  Score=50.22  Aligned_cols=33  Identities=27%  Similarity=0.231  Sum_probs=23.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      +.-++|.|++||||||+...+   |.+.|+-+++++
T Consensus         4 g~iI~l~G~~GsGKSTia~~L---a~~lg~~~~~~~   36 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEAL---ANLPGVPKVHFH   36 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHH---HTCSSSCEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHH---HHHhCCCEEEec
Confidence            344789999999999975433   556677666663

>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=95.56  E-value=0.0052  Score=50.39  Aligned_cols=34  Identities=24%  Similarity=0.193  Sum_probs=26.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...-++|.|.+||||||+..+.   +...||+++.-
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l---~~~~~~~~i~~   45 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEH---LVSAGYVHVNR   45 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHH---TGGGTCEEEEH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHH---HHhcCCEEEch
Confidence            45568899999999999987654   55678887643

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=95.56  E-value=0.016  Score=50.12  Aligned_cols=46  Identities=17%  Similarity=0.232  Sum_probs=37.6

Q ss_pred             HHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-C
Q psy3261          52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-P  102 (342)
Q Consensus        52 el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P  102 (342)
                      +|.+.+.+     ......+|.|..|||||..-..++..|.++|.=|+.+ |
T Consensus        66 ~i~~~~~~-----~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~P  112 (233)
T d2eyqa3          66 AVLSDMCQ-----PLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVP  112 (233)
T ss_dssp             HHHHHHHS-----SSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECS
T ss_pred             HHHHHHhc-----cCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEcc
Confidence            45555555     5567889999999999999999999999998877665 5

>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=95.55  E-value=0.0071  Score=54.90  Aligned_cols=49  Identities=16%  Similarity=0.163  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC--eEEEEe
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENN--YLLVHI  101 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g--wiVl~v  101 (342)
                      ..+|++.+-.   .+....++=|+|++|+|||+++.+++.+.+..|  --|+.+
T Consensus        37 ~~~~~~~~~~---~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViav   87 (323)
T d2qm8a1          37 VRDLIDAVLP---QTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAV   87 (323)
T ss_dssp             HHHHHHHHGG---GCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHhhh---ccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeec
Confidence            3444444432   446788999999999999999999998877654  455666

>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=95.55  E-value=0.0046  Score=52.30  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=25.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCC-eEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENN-YLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~g-wiVl~v  101 (342)
                      +++.|+.|+||||++.++.++..... ..||..
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn~   35 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNL   35 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTTSCEEEEEC
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEec
Confidence            68999999999999999998876554 444554

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.54  E-value=0.011  Score=53.60  Aligned_cols=49  Identities=16%  Similarity=0.162  Sum_probs=37.0

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC--eEEEEe
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENN--YLLVHI  101 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g--wiVl~v  101 (342)
                      +.++++.+..   .+....++=|+|++|+|||+++..++.+.+..|  --|+-|
T Consensus        40 ~~~ll~~~~~---~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlav   90 (327)
T d2p67a1          40 STQLLDAIMP---YCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAV   90 (327)
T ss_dssp             HHHHHHHHGG---GCSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHhhh---ccCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecC
Confidence            3445554433   346789999999999999999999999888876  345655

>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=95.54  E-value=0.0036  Score=49.66  Aligned_cols=20  Identities=30%  Similarity=0.448  Sum_probs=17.3

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      -++|+|++||||||+..++.
T Consensus         4 lI~i~G~~GsGKTTva~~L~   23 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLA   23 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999977664

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

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: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=95.44  E-value=0.0038  Score=47.89  Aligned_cols=37  Identities=16%  Similarity=0.077  Sum_probs=28.3

Q ss_pred             CCCeEEEEccCCCcHHHHH-HHHHHHHHhCCeEEEEeC
Q psy3261          66 PSPRFVLYGEHGVGKSMAL-VYALQYAHENNYLLVHIP  102 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L-~q~~~~A~~~gwiVl~vP  102 (342)
                      ++.+.+|.++.|||||... ..++.++.+.+..++.++
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~   43 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLA   43 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEE
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeee
Confidence            4788999999999999555 456677777776666663

>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=95.41  E-value=0.006  Score=49.16  Aligned_cols=32  Identities=25%  Similarity=0.186  Sum_probs=26.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|..||||||+...+..+...+|.-+..+
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~   35 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDNQGINNKII   35 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            57899999999999999988877777655444

>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=95.34  E-value=0.0071  Score=49.98  Aligned_cols=32  Identities=19%  Similarity=0.226  Sum_probs=25.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ...++|.|++||||||....+   |...||..|..
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~L---a~~~g~~~is~   39 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKI---VQKYGYTHLST   39 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHH---HHHTCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHH---HHHhCCeeEec
Confidence            567899999999999966554   55678877655

>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=95.32  E-value=0.0057  Score=49.56  Aligned_cols=30  Identities=20%  Similarity=0.202  Sum_probs=22.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      |++|.|++||||||....+   |..-||..+..
T Consensus         2 ~I~i~G~pGSGKsT~a~~L---a~~~~~~~i~~   31 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKI---VAAYGIPHIST   31 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHH---HHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHHCCceech
Confidence            7899999999999976554   33448876655

>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=95.32  E-value=0.0095  Score=47.39  Aligned_cols=34  Identities=21%  Similarity=0.196  Sum_probs=25.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ....-++|.|++||||||+...+....   ||..+..
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l---~~~~~~~   37 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQL---HAAFLDG   37 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHH---TCEEEEG
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh---CCCeech
Confidence            345668889999999999988775543   6655554

>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=95.26  E-value=0.0053  Score=49.47  Aligned_cols=30  Identities=30%  Similarity=0.256  Sum_probs=22.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ++|++|.|.+||||||+-..+..   .-||-.+
T Consensus         1 ~p~IvliG~~G~GKSTig~~La~---~l~~~fi   30 (165)
T d2iyva1           1 APKAVLVGLPGSGKSTIGRRLAK---ALGVGLL   30 (165)
T ss_dssp             CCSEEEECSTTSSHHHHHHHHHH---HHTCCEE
T ss_pred             CCcEEEECCCCCCHHHHHHHHHH---HhCCCeE
Confidence            46899999999999998766643   3355444

>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=95.22  E-value=0.0074  Score=51.53  Aligned_cols=37  Identities=14%  Similarity=0.202  Sum_probs=25.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +...-++|.|+.|+||||+++-+.++...+|+=|.-|
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~li   46 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLV   46 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHHTTCCEEEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEE
Confidence            3455677899999999999999999988887655443

>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=95.20  E-value=0.0062  Score=48.83  Aligned_cols=25  Identities=20%  Similarity=0.295  Sum_probs=21.8

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++..|++|.|.+|||||+++.++.
T Consensus        10 ~~k~~kI~lvG~~~vGKTsLl~~l~   34 (186)
T d1f6ba_          10 YKKTGKLVFLGLDNAGKTTLLHMLK   34 (186)
T ss_dssp             TTCCEEEEEEEETTSSHHHHHHHHS
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHh
Confidence            3667899999999999999998863

>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=0.0067  Score=49.57  Aligned_cols=32  Identities=25%  Similarity=0.229  Sum_probs=25.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +.|++|.|++||||||....+..   .-||..|..
T Consensus         2 ~mrIvl~G~pGSGKtT~a~~La~---~~g~~~i~~   33 (180)
T d1akya1           2 SIRMVLIGPPGAGKGTQAPNLQE---RFHAAHLAT   33 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH---HHCCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH---HhCCceEec
Confidence            56899999999999998877754   347776665

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=95.07  E-value=0.0062  Score=47.71  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=19.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|++|.|++|||||+++.++..
T Consensus         1 ikivlvG~~~vGKSsLi~~l~~   22 (160)
T d1r8sa_           1 MRILMVGLDAAGKTTILYKLKL   22 (160)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3799999999999999998753

>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=95.04  E-value=0.0074  Score=49.58  Aligned_cols=31  Identities=10%  Similarity=0.139  Sum_probs=22.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ...+++|.|++||||||...-+   |..-||..+
T Consensus         2 ~Pm~I~i~GppGsGKsT~a~~L---a~~~~~~~i   32 (189)
T d1zaka1           2 DPLKVMISGAPASGKGTQCELI---KTKYQLAHI   32 (189)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHH---HHHHCCEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHH---HHHHCCcEE
Confidence            3568999999999999965433   444466654

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.04  E-value=0.013  Score=51.75  Aligned_cols=38  Identities=18%  Similarity=0.236  Sum_probs=34.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ..+.-..|+|+.|||||++++|++.-|.+.|-.|+||.
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyID   95 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFID   95 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEE
Confidence            56778889999999999999999999999998898883

>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=94.98  E-value=0.0063  Score=51.12  Aligned_cols=29  Identities=21%  Similarity=0.124  Sum_probs=25.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHh
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHE   93 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~   93 (342)
                      .++.-++|+|++|||||++..|++..|..
T Consensus        32 ~~G~~~li~G~pGsGKT~l~lq~~~~~~~   60 (251)
T d1szpa2          32 ETGSITELFGEFRTGKSQLCHTLAVTCQI   60 (251)
T ss_dssp             ESSSEEEEEESTTSSHHHHHHHHTTTTTS
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHhhh
Confidence            46788999999999999999999877643

>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=94.95  E-value=0.0098  Score=49.03  Aligned_cols=34  Identities=12%  Similarity=0.223  Sum_probs=26.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++...++|.|++||||||....+   |...||..|..
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~L---a~~~g~~~is~   39 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKL---VKDYSFVHLSA   39 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHH---HHHSSCEEEEH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHH---HHHhCCeEEeh
Confidence            45678999999999999987776   44568866654

>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=94.92  E-value=0.013  Score=52.60  Aligned_cols=36  Identities=17%  Similarity=0.228  Sum_probs=26.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+...++|+||+|||||.+..++. -.....++.+..
T Consensus        47 ~~~~~iLl~GPpG~GKT~lAkalA-~~~~~~~~~i~~   82 (309)
T d1ofha_          47 VTPKNILMIGPTGVGKTEIARRLA-KLANAPFIKVEA   82 (309)
T ss_dssp             CCCCCEEEECCTTSSHHHHHHHHH-HHHTCCEEEEEG
T ss_pred             CCCceEEEECCCCCCHHHHHHHHh-hccccchhcccc
Confidence            356789999999999998876544 444556666544

>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=94.88  E-value=0.01  Score=50.24  Aligned_cols=30  Identities=17%  Similarity=0.164  Sum_probs=26.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .++.-++|+|++|||||++..|.++.+..+
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~~~~   63 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMVQLP   63 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSC
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHhhch
Confidence            467789999999999999999999988654

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=94.87  E-value=0.0074  Score=48.43  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=22.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++..|++|.|.+|||||+++.+++.
T Consensus        13 ~k~~kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1          13 HQEHKVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHhc
Confidence            4678999999999999999998754

>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=94.84  E-value=0.012  Score=46.56  Aligned_cols=34  Identities=18%  Similarity=0.222  Sum_probs=22.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..-++|+|++||||||+...+.. .....|+.+..
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~-~l~~~~~~~~~   36 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQS-VLPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH-HSSSCEEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH-HcCCCeEEeec
Confidence            34578899999999987766533 23345555543

>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=94.84  E-value=0.0052  Score=49.59  Aligned_cols=26  Identities=23%  Similarity=0.243  Sum_probs=22.0

Q ss_pred             CCCCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          63 FDRPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        63 ~~~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ...+..|+++.|++|||||+++.+++
T Consensus        12 ~~~~~~kI~vvG~~~vGKSsLi~~l~   37 (176)
T d1fzqa_          12 APDQEVRILLLGLDNAGKTTLLKQLA   37 (176)
T ss_dssp             CCSSCEEEEEEESTTSSHHHHHHHHC
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHh
Confidence            34567899999999999999998764

>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=94.83  E-value=0.013  Score=49.87  Aligned_cols=35  Identities=14%  Similarity=0.178  Sum_probs=28.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..-++|.|+.|+||||+++-+.++..++|.=|.-|
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~li   43 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA   43 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            44577899999999999999999888777554443

>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=94.83  E-value=0.01  Score=52.41  Aligned_cols=29  Identities=17%  Similarity=0.336  Sum_probs=24.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      ...++|-|.+|||||++|.+.+++...++
T Consensus        24 ~g~~lV~g~aGSGKTt~l~~ri~~ll~~~   52 (318)
T d1pjra1          24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEK   52 (318)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEecCCccHHHHHHHHHHHHHHcC
Confidence            34588999999999999999888776543

>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=94.74  E-value=0.0075  Score=49.22  Aligned_cols=30  Identities=20%  Similarity=0.230  Sum_probs=21.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|.|++||||||....+..   ..|+..+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~---~~g~~~is~   31 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVE---KYGTPHIST   31 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH---HHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HHCCceeeH
Confidence            689999999999996554443   346665543

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.70  E-value=0.0058  Score=51.26  Aligned_cols=37  Identities=11%  Similarity=0.077  Sum_probs=29.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCC-eEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENN-YLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g-wiVl~v  101 (342)
                      .++.-++|.|++|+|||+++.|++..+..++ |.+++.
T Consensus        32 ~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~   69 (258)
T d2i1qa2          32 ESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEE   69 (258)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTT
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEe
Confidence            4677899999999999999999998887654 444443

>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=94.67  E-value=0.014  Score=47.85  Aligned_cols=31  Identities=16%  Similarity=0.255  Sum_probs=23.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++|.|++||||||....+..   .-||..|..
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~---~~g~~~i~~   32 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVE---KYGYTHLSA   32 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH---HHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH---HhCCceEcH
Confidence            4689999999999998876654   338776643

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.65  E-value=0.0087  Score=50.61  Aligned_cols=30  Identities=17%  Similarity=0.037  Sum_probs=26.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .++.-++|+|++|||||++..|+++.|...
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~   64 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLP   64 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSC
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            567799999999999999999999987654

>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=94.64  E-value=0.019  Score=53.36  Aligned_cols=44  Identities=23%  Similarity=0.295  Sum_probs=33.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccccc
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLRWF  108 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~~~  108 (342)
                      .+.--++++|+.||||||+|.-++.+.-.++--|+.|=++-++.
T Consensus       156 ~~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~  199 (401)
T d1p9ra_         156 RPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFD  199 (401)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSC
T ss_pred             hhhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccc
Confidence            45677999999999999999999998755444567775555553

>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=94.63  E-value=0.014  Score=50.91  Aligned_cols=39  Identities=36%  Similarity=0.469  Sum_probs=30.7

Q ss_pred             hhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          48 NCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        48 ~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +...++...+++   ......+++|.|.+|+|||++++.++-
T Consensus        16 ~~l~e~~~~l~~---~~~~~l~I~LvG~tg~GKSSliN~ilg   54 (257)
T d1h65a_          16 TKLLELLGNLKQ---EDVNSLTILVMGKGGVGKSSTVNSIIG   54 (257)
T ss_dssp             HHHHHHHHHHHH---TTCCEEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHhh---cCCCCcEEEEECCCCCcHHHHHHHHhC
Confidence            344567777776   335578999999999999999999873

>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=94.54  E-value=0.012  Score=47.76  Aligned_cols=30  Identities=23%  Similarity=0.269  Sum_probs=22.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++|.|++||||||.-..+...   -|+..+.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~---~g~~~i~~   31 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEK---LGIPQIST   31 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH---HTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---HCCceEch
Confidence            7899999999999966655543   37766654

>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=94.53  E-value=0.014  Score=53.61  Aligned_cols=36  Identities=11%  Similarity=0.074  Sum_probs=26.5

Q ss_pred             CCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          63 FDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        63 ~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..++.+.++|+||+|||||++...++..+   |+=++.|
T Consensus       150 ~~~~~~~~~~~g~~~~gk~~~~~~~~~~~---~~~~i~i  185 (362)
T d1svma_         150 NIPKKRYWLFKGPIDSGKTTLAAALLELC---GGKALNV  185 (362)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHH---CCEEECC
T ss_pred             CCCCcCeEEEECCCCCCHHHHHHHHHHHc---CCCEEEE
Confidence            34567799999999999999876655443   5556665

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.45  E-value=0.016  Score=47.91  Aligned_cols=32  Identities=13%  Similarity=0.117  Sum_probs=27.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++|.|.-||||||++..+..+-...|+=|+.+
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~   34 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATL   34 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            78999999999999999999988888755554

>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=94.44  E-value=0.011  Score=46.54  Aligned_cols=24  Identities=25%  Similarity=0.346  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..|++|.|.+|||||+++..++.
T Consensus         4 ke~kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           4 REMRILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHhC
Confidence            457899999999999999998653

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.31  E-value=0.0092  Score=47.82  Aligned_cols=25  Identities=24%  Similarity=0.349  Sum_probs=21.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++..|++|.|+.|||||++|.+.+.
T Consensus         2 ~k~~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           2 SKSRKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             CEEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcceEEEEECCCCcCHHHHHHHHHh
Confidence            3567999999999999999998864

>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=94.30  E-value=0.016  Score=48.00  Aligned_cols=35  Identities=14%  Similarity=0.088  Sum_probs=25.9

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +++-.|++|.|++||||||.-..+..   ..||..+.+
T Consensus         3 ~~r~mrIiliG~PGSGKtT~a~~La~---~~g~~~is~   37 (189)
T d2ak3a1           3 SARLLRAAIMGAPGSGKGTVSSRITK---HFELKHLSS   37 (189)
T ss_dssp             SSCCCEEEEECCTTSSHHHHHHHHHH---HBCCEEEEH
T ss_pred             CCcceeEEEECCCCCCHHHHHHHHHH---HHCCeEEcH
Confidence            35678999999999999998666554   456665433

>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=94.27  E-value=0.011  Score=51.54  Aligned_cols=28  Identities=11%  Similarity=0.178  Sum_probs=23.2

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      ...++|.|++|||||++|.+.+.+...+
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~rv~~ll~~   41 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNKIAHLIRG   41 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeeCCccHHHHHHHHHHHHHHh
Confidence            3458889999999999999988887543

>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=94.20  E-value=0.0087  Score=54.52  Aligned_cols=42  Identities=24%  Similarity=0.168  Sum_probs=34.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc-cccc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV-LRWF  108 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~-~~~~  108 (342)
                      ..|++|.|.-|+||||++..+..+....|.-|+++|++ ..|.
T Consensus         5 ~lrI~IEG~iGsGKSTl~~~L~~~l~~~g~~v~~~~EP~~~W~   47 (331)
T d1osna_           5 VLRIYLDGAYGIGKTTAAEEFLHHFAITPNRILLIGEPLSYWR   47 (331)
T ss_dssp             EEEEEEEESSSSCTTHHHHHHHHTTTTSGGGEEEECCCHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEeCchHhhh
Confidence            46899999999999999999999888887777777765 3443

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.17  E-value=0.013  Score=45.57  Aligned_cols=21  Identities=19%  Similarity=0.349  Sum_probs=19.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |++|.|++|+|||++|..++.
T Consensus         2 KI~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            789999999999999998664

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.11  E-value=0.012  Score=47.98  Aligned_cols=26  Identities=23%  Similarity=0.342  Sum_probs=22.9

Q ss_pred             CCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          64 DRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        64 ~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +++..+++|-|.+|||||+++.+.+.
T Consensus         2 ~p~~iKivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           2 SPQAIKCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             CCEEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CceeEEEEEECCCCCCHHHHHHHHHh
Confidence            35667999999999999999999875

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.03  E-value=0.025  Score=49.72  Aligned_cols=39  Identities=21%  Similarity=0.284  Sum_probs=32.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PW  103 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~  103 (342)
                      ......+|.|..|||||..-..++..|.++|.=|+.. |.
T Consensus       102 ~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt  141 (264)
T d1gm5a3         102 EKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPT  141 (264)
T ss_dssp             SSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSC
T ss_pred             cCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeeh
Confidence            4456778999999999999999999999888766554 53

>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=93.97  E-value=0.016  Score=46.90  Aligned_cols=28  Identities=18%  Similarity=0.350  Sum_probs=21.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      |++|.|++||||||....+..   ..||..+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~---~~~~~~i   29 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIME---KYGIPQI   29 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH---HHCCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCcee
Confidence            789999999999998766653   2355444

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.80  E-value=0.024  Score=52.29  Aligned_cols=39  Identities=21%  Similarity=0.158  Sum_probs=32.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CCcc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PWVL  105 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~~~  105 (342)
                      ...+++.|..|||||+++..++..+...|.-|+-+ |.++
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kge   89 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGD   89 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTH
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCChh
Confidence            45699999999999999999998888877766666 6653

>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=93.78  E-value=0.022  Score=45.04  Aligned_cols=27  Identities=15%  Similarity=0.372  Sum_probs=21.4

Q ss_pred             ceeecCCCCHHHH-HHHHHHHHhCCCcc
Q psy3261         290 VPIHVPELNDEEF-HNLLNLYESKKWLQ  316 (342)
Q Consensus       290 ~~i~v~~~s~~E~-~~ll~yy~~~~~l~  316 (342)
                      ..|...+.|.+|. ..++++..+.|++.
T Consensus       154 i~IDT~~~s~~e~v~~I~~~L~~~g~~~  181 (183)
T d1m8pa3         154 LVVDFSKQSVRSIVHEIILVLESQGFLE  181 (183)
T ss_dssp             EEECTTTSCHHHHHHHHHHHHHHTTTTC
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHcCCCC
Confidence            3577788998887 67779999999883

>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=93.69  E-value=0.019  Score=45.74  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=19.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|++|.|++|||||+++.+.+.
T Consensus         3 iKv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           3 IKMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            5899999999999999998775

>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=93.66  E-value=0.016  Score=47.54  Aligned_cols=38  Identities=24%  Similarity=0.275  Sum_probs=27.8

Q ss_pred             CCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          63 FDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        63 ~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      .+++..-++|.|.-||||||++..+..+.  +++.++..|
T Consensus         5 ~~~kp~~I~ieG~~GsGKTTl~~~L~~~l--~~~~~~~ep   42 (197)
T d2vp4a1           5 EGTQPFTVLIEGNIGSGKTTYLNHFEKYK--NDICLLTEP   42 (197)
T ss_dssp             TTCCCEEEEEECSTTSCHHHHHHTTGGGT--TTEEEECCT
T ss_pred             CCCCceEEEEECCCCCCHHHHHHHHHHHh--CCcEEEEEe
Confidence            34566789999999999999888765432  456666555

>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=93.57  E-value=0.035  Score=46.83  Aligned_cols=46  Identities=20%  Similarity=0.273  Sum_probs=34.2

Q ss_pred             HHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeE
Q psy3261          50 MLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYL   97 (342)
Q Consensus        50 t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi   97 (342)
                      .++.+..|+.+....++.+.++|+||++||||+...-+++..  .|-+
T Consensus        36 ~~~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l--~G~v   81 (205)
T d1tuea_          36 FITFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFI--QGAV   81 (205)
T ss_dssp             HHHHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHH--TCEE
T ss_pred             HHHHHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHh--CCEE
Confidence            445555565555556788999999999999999987777764  4644

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=93.55  E-value=0.03  Score=46.07  Aligned_cols=38  Identities=32%  Similarity=0.402  Sum_probs=33.6

Q ss_pred             CCeEEEEccC-CCcHHHHHHHHHHHHHhCCeEEEEe-CCc
Q psy3261          67 SPRFVLYGEH-GVGKSMALVYALQYAHENNYLLVHI-PWV  104 (342)
Q Consensus        67 ~~r~vL~G~~-GsGKS~~L~q~~~~A~~~gwiVl~v-P~~  104 (342)
                      +.||+++|.- |+|||++-+.+.....+.|.=|+.| |.+
T Consensus         1 ~~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~d~   40 (224)
T d1byia_           1 SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVA   40 (224)
T ss_dssp             CEEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECSEE
T ss_pred             CceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECccc
Confidence            3689999995 9999999999999999999999999 443

>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=93.52  E-value=0.023  Score=45.72  Aligned_cols=29  Identities=17%  Similarity=0.222  Sum_probs=21.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ..++|.|.+||||||+-..+..   .-||-.+
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~---~Lg~~~i   31 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELAR---ALGYEFV   31 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH---HHTCEEE
T ss_pred             CCEEEECCCCCCHHHHHHHHHH---HhCCCEE
Confidence            4588999999999998776643   3366554

>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=93.52  E-value=0.019  Score=52.25  Aligned_cols=37  Identities=24%  Similarity=0.148  Sum_probs=30.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ..|++|.|.-||||||++..+..+....+ -++++|++
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l~~~~-~v~~~~EP   42 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAASGGS-PTLYFPEP   42 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGGGCSS-CEEEECCC
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHhccCC-CeEEEeCc
Confidence            46999999999999999998888765444 56677766

>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=93.49  E-value=0.019  Score=45.58  Aligned_cols=22  Identities=23%  Similarity=0.285  Sum_probs=19.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..|++|.|++|||||+++.++.
T Consensus         2 ~~ki~ivG~~~~GKTsLi~~l~   23 (165)
T d1ksha_           2 ELRLLMLGLDNAGKTTILKKFN   23 (165)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHT
T ss_pred             cEEEEEECCCCCCHHHHHHHHc
Confidence            4689999999999999998753

>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=93.47  E-value=0.055  Score=45.29  Aligned_cols=91  Identities=10%  Similarity=0.072  Sum_probs=53.1

Q ss_pred             HHHHHHHHhccccCCCceEEEEEeCccccccCCCcCCCCCCCcccCCccchHHHHHHhhc-CCCCCeEEEEEeCCCCCCC
Q psy3261         188 VDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQ-SDWNNGAIVLALSPRANLP  266 (342)
Q Consensus       188 ~~~l~~EL~~~~~~~~~pVLvavD~~n~~~~~s~~y~~~~~~~I~~~~l~l~~~~~~~~~-~~~~~G~vv~AtS~~~~~~  266 (342)
                      +..+++|+...    ..+|++.||++..+++....          ...+.+...|+.+++ |+   --+|+||+...-  
T Consensus       103 l~~il~e~~~~----~~~iILfIDeih~l~~~g~~----------~g~~d~~~~Lkp~L~rg~---l~~IgatT~eey--  163 (195)
T d1jbka_         103 LKGVLNDLAKQ----EGNVILFIDELHTMVGAGKA----------DGAMDAGNMLKPALARGE---LHCVGATTLDEY--  163 (195)
T ss_dssp             HHHHHHHHHHS----TTTEEEEEETGGGGTT----------------CCCCHHHHHHHHHTTS---CCEEEEECHHHH--
T ss_pred             HHHHHHHHhcC----CCcEEEEcchHHHHhcCCCC----------CCcccHHHHHHHHHhCCC---ceEEecCCHHHH--
Confidence            55677788654    46799999999999876330          112567788888886 33   346777764320  


Q ss_pred             CCccCcchhHHhhhcCCCCCCCcceeecCCCCHHHHHHHH
Q psy3261         267 DRRESHLPLYMLKKAGFESIDPFVPIHVPELNDEEFHNLL  306 (342)
Q Consensus       267 ~~~~~~~p~~llg~~g~~~~dP~~~i~v~~~s~~E~~~ll  306 (342)
                      .. ...--..+.        .-|.+|.|...|.++...++
T Consensus       164 ~~-~~e~d~aL~--------rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         164 RQ-YIEKDAALE--------RRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HH-HTTTCHHHH--------TTEEEEECCCCCHHHHHTTC
T ss_pred             HH-HHHcCHHHH--------hcCCEeecCCCCHHHHHHHh
Confidence            00 000001111        22567999999999886553

>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=93.47  E-value=0.022  Score=46.80  Aligned_cols=23  Identities=30%  Similarity=0.353  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..++|.||.||||++++.+++..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHh
Confidence            35899999999999999988554

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=93.44  E-value=0.021  Score=45.03  Aligned_cols=21  Identities=29%  Similarity=0.278  Sum_probs=19.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .+++|.|++|+|||+++.++.
T Consensus         2 ~kI~lvG~~nvGKSsLin~l~   22 (161)
T d2gj8a1           2 MKVVIAGRPNAGKSSLLNALA   22 (161)
T ss_dssp             EEEEEEESTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            478999999999999998776

>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=93.43  E-value=0.022  Score=45.66  Aligned_cols=22  Identities=23%  Similarity=0.508  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|++|.|++|||||+++.+.+.
T Consensus         3 ~Ki~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           3 LKVIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHc
Confidence            3799999999999999998764

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=93.43  E-value=0.034  Score=47.84  Aligned_cols=24  Identities=25%  Similarity=0.185  Sum_probs=20.6

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..-.+|+|++|+|||+++.|++.
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHH
Confidence            356778999999999999999765

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.38  E-value=0.022  Score=46.06  Aligned_cols=26  Identities=4%  Similarity=0.245  Sum_probs=20.3

Q ss_pred             ceeecCCCCHHHH-HHHHHHHHhCCCc
Q psy3261         290 VPIHVPELNDEEF-HNLLNLYESKKWL  315 (342)
Q Consensus       290 ~~i~v~~~s~~E~-~~ll~yy~~~~~l  315 (342)
                      ..|...+.|.+|. ..++++..++|++
T Consensus       167 l~IdT~~~s~ee~~~~Il~~l~~~~~i  193 (195)
T d1x6va3         167 LVLKTDSCDVNDCVQQVVELLQERDIV  193 (195)
T ss_dssp             EEECTTTSCHHHHHHHHHHHHHHTTSS
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHCcCC
Confidence            3466778999984 5667999999887

>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=93.33  E-value=0.016  Score=49.34  Aligned_cols=34  Identities=26%  Similarity=0.307  Sum_probs=26.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      |-+-++|+|--||||||+|.+++.......|.||
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~~~~~riaVI   35 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVI   35 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSCCCCCEEEE
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhcCCCCcEEEE
Confidence            3456899999999999999999886444467665

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=93.29  E-value=0.023  Score=45.26  Aligned_cols=22  Identities=18%  Similarity=0.123  Sum_probs=19.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|++|.|++|||||+++.+.+.
T Consensus         3 ~ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           3 MELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            5899999999999999988753

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {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: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.24  E-value=0.028  Score=47.78  Aligned_cols=35  Identities=17%  Similarity=0.079  Sum_probs=24.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +..+++.+|.|+|||++....+.+...+|.-|++|
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv   92 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVI   92 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEE
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEE
Confidence            45689999999999987766665555555444444

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=93.21  E-value=0.024  Score=45.53  Aligned_cols=24  Identities=21%  Similarity=0.279  Sum_probs=21.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++..+++|.|++|||||+++.+++
T Consensus        10 ~k~~kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          10 NKEMRILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHTT
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHh
Confidence            667899999999999999998754

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.19  E-value=0.025  Score=45.90  Aligned_cols=21  Identities=24%  Similarity=0.567  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |++|.|.+|||||+++.+.+.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            789999999999999998764

>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=93.14  E-value=0.032  Score=45.65  Aligned_cols=26  Identities=19%  Similarity=0.125  Sum_probs=20.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      -++|.|.+||||||+..++..+-...
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~~~   29 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLNFI   29 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            47899999999999998887654433

>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=93.14  E-value=0.026  Score=45.15  Aligned_cols=22  Identities=36%  Similarity=0.522  Sum_probs=19.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -++++.|.+|||||+++.+.+.
T Consensus         7 ~Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           7 FKLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3789999999999999999875

>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=93.14  E-value=0.026  Score=45.26  Aligned_cols=22  Identities=36%  Similarity=0.449  Sum_probs=19.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|++|.|.+|||||+++.+.+.
T Consensus         6 ~Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           6 FKIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4799999999999999998764

>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=93.11  E-value=0.025  Score=46.04  Aligned_cols=23  Identities=30%  Similarity=0.288  Sum_probs=19.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .=++|.||.|||||++...+...
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            45789999999999998877643

>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=93.11  E-value=0.026  Score=45.21  Aligned_cols=22  Identities=41%  Similarity=0.538  Sum_probs=20.2

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|.|.+|||||++|.+.+.
T Consensus         6 ~Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           6 YRLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5899999999999999999875

>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=93.10  E-value=0.027  Score=45.32  Aligned_cols=22  Identities=32%  Similarity=0.599  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|+++.|++|||||+++.+.+.
T Consensus         4 ~KivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           4 FKYIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHhc
Confidence            3789999999999999998764

>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=93.09  E-value=0.027  Score=44.93  Aligned_cols=22  Identities=32%  Similarity=0.382  Sum_probs=19.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|.|.+|||||+++.+.+.
T Consensus         4 fKivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           4 FKVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3789999999999999998763

>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=93.02  E-value=0.028  Score=44.83  Aligned_cols=23  Identities=30%  Similarity=0.481  Sum_probs=20.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..|++|.|.+|||||+++.+++.
T Consensus         4 ~~Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           4 ELKVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHHh
Confidence            45899999999999999999875

>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=92.99  E-value=0.029  Score=44.48  Aligned_cols=22  Identities=18%  Similarity=0.274  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -+++|-|..|||||+++.+.+.
T Consensus         3 ~Kv~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           3 FKIIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3789999999999999999764

>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=92.97  E-value=0.029  Score=44.84  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=20.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..|++|-|.+|||||+++.+.+.
T Consensus         3 ~iKi~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           3 SIKLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEEECCCCcCHHHHHHHHHh
Confidence            45899999999999999999864

>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=92.96  E-value=0.029  Score=44.68  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=20.1

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .-+++|.|..|||||+++.+.+.
T Consensus         3 ~~Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           3 EYKVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHHh
Confidence            35899999999999999998764

>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=92.95  E-value=0.029  Score=44.74  Aligned_cols=22  Identities=36%  Similarity=0.537  Sum_probs=19.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|.|+.|||||+++.+.+.
T Consensus         4 ~Ki~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           4 YKLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4789999999999999999875

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=92.95  E-value=0.031  Score=44.71  Aligned_cols=28  Identities=21%  Similarity=0.227  Sum_probs=20.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      .++|.|.+||||||+..-+...   -||-.+
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~---l~~~~~   29 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKD---LDLVFL   29 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH---HTCEEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHH---hCCCEE
Confidence            4889999999999987665443   266544

>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=92.94  E-value=0.029  Score=44.91  Aligned_cols=23  Identities=35%  Similarity=0.616  Sum_probs=20.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|.|++|||||+++.+.+.
T Consensus         2 eiKi~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           2 EVKLAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHh
Confidence            35899999999999999998765

>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=92.92  E-value=0.029  Score=44.45  Aligned_cols=21  Identities=29%  Similarity=0.537  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |++|-|.+|||||+++.+.+.
T Consensus         2 Kv~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           2 KLVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            789999999999999999764

>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=92.90  E-value=0.028  Score=44.89  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=19.2

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|.|.+|||||+++.+.+.
T Consensus         3 ~Ki~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           3 YRVAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3789999999999999988754

>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=92.88  E-value=0.036  Score=42.65  Aligned_cols=35  Identities=20%  Similarity=0.167  Sum_probs=23.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe-CC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI-PW  103 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v-P~  103 (342)
                      ...+.+|.++.|||||+.+.+   ++.+.|+-|+++ |.
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~---~~~~~~~~vli~~P~   42 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPA---AYAAQGYKVLVLNPS   42 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHH---HHHTTTCCEEEEESC
T ss_pred             CCCEEEEEeCCCCCHHHHHHH---HHHHcCCcEEEEcCh
Confidence            346779999999999986644   344555555544 53

>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=92.86  E-value=0.036  Score=44.78  Aligned_cols=25  Identities=24%  Similarity=0.320  Sum_probs=22.1

Q ss_pred             CCCCCCeEEEEccCCCcHHHHHHHH
Q psy3261          63 FDRPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        63 ~~~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      ...+..+++|.|.+|||||+++.++
T Consensus        13 ~~~k~~KI~lvG~~~vGKTsLi~~l   37 (182)
T d1moza_          13 GSNKELRILILGLDGAGKTTILYRL   37 (182)
T ss_dssp             TCSSCEEEEEEEETTSSHHHHHHHT
T ss_pred             CCCceEEEEEECCCCCCHHHHHHHH
Confidence            4567899999999999999999875

>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=92.82  E-value=0.031  Score=44.71  Aligned_cols=22  Identities=23%  Similarity=0.339  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -++++.|.+|||||+++.+.+.
T Consensus         6 ~Ki~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           6 FKILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHc
Confidence            4799999999999999998764

>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=92.77  E-value=0.037  Score=45.29  Aligned_cols=23  Identities=22%  Similarity=0.424  Sum_probs=20.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -++++|.|++|||||+++..++.
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~   25 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTT   25 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999975

>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=92.75  E-value=0.031  Score=44.93  Aligned_cols=24  Identities=33%  Similarity=0.508  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..+++|.|.+|||||+++.+.+.
T Consensus         5 ~~~Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           5 ETHKLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CeEEEEEECCCCcCHHHHHHHHHh
Confidence            346899999999999999998764

>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=92.67  E-value=0.034  Score=45.80  Aligned_cols=22  Identities=41%  Similarity=0.433  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+||.||.|||||++..+++..
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            4899999999999998887765

>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=92.65  E-value=0.033  Score=44.85  Aligned_cols=22  Identities=23%  Similarity=0.484  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|.|..|||||+++.+.+.
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~   24 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSK   24 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4789999999999999988764

>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=92.61  E-value=0.048  Score=45.24  Aligned_cols=31  Identities=23%  Similarity=0.216  Sum_probs=26.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYL   97 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwi   97 (342)
                      +.=+++.|..||||||....+..+..+.|.-
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L~~~g~~   32 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETLEQLGIR   32 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhCCCC
Confidence            3457889999999999999999998888863

>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=92.60  E-value=0.035  Score=47.78  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=19.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      .++-.+.|.|+.||||||+|.-+
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i   51 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTMLNII   51 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCcchhhHhc
Confidence            46789999999999999988743

>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=92.60  E-value=0.066  Score=46.16  Aligned_cols=39  Identities=23%  Similarity=0.338  Sum_probs=27.4

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ...++++.+++ +.  .....++|+|++||||+. ++.++|..
T Consensus         8 ~~~~~~~~~~~-~a--~~~~pvlI~Ge~GtGK~~-~A~~ih~~   46 (247)
T d1ny5a2           8 KMKEILEKIKK-IS--CAECPVLITGESGVGKEV-VARLIHKL   46 (247)
T ss_dssp             HHHHHHHHHHH-HT--TCCSCEEEECSTTSSHHH-HHHHHHHH
T ss_pred             HHHHHHHHHHH-Hh--CCCCCEEEECCCCcCHHH-HHHHHHHh
Confidence            45567777777 22  345679999999999985 56666543

>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=92.52  E-value=0.1  Score=46.21  Aligned_cols=68  Identities=15%  Similarity=0.062  Sum_probs=36.7

Q ss_pred             EEccCCCcHHHHHHHHHHHHHh-----CCeEEEEeCCccc-------cccCC--cceeccCCCCCccccHHHHHHHHHHH
Q psy3261          72 LYGEHGVGKSMALVYALQYAHE-----NNYLLVHIPWVLR-------WFAYP--KEVSHSLTKEGMVDLNIDAAMWLRHF  137 (342)
Q Consensus        72 L~G~~GsGKS~~L~q~~~~A~~-----~gwiVl~vP~~~~-------~~~~~--~~~~~s~~~~~~~~qP~~a~~~L~~~  137 (342)
                      |.|..||||||+...++.+..+     ..-++|.+.+-..       +-+..  .......-.||.+|.+ ...+.|+.+
T Consensus        32 i~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~-ll~~~l~~l  110 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMK-LLQEVLNTI  110 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHH-HHHHHHHHH
T ss_pred             eECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHH-HHHHHHHHH
Confidence            7899999999988888776543     2344555533211       11110  1111111247888874 445556666


Q ss_pred             HHh
Q psy3261         138 QKQ  140 (342)
Q Consensus       138 ~~~  140 (342)
                      ++.
T Consensus       111 ~~~  113 (286)
T d1odfa_         111 FNN  113 (286)
T ss_dssp             TC-
T ss_pred             Hhh
Confidence            443

>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=92.50  E-value=0.043  Score=45.53  Aligned_cols=30  Identities=13%  Similarity=0.215  Sum_probs=21.4

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEE
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLV   99 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl   99 (342)
                      ..++.|+||+||||||.-..+..   +-||.-+
T Consensus         3 ~i~IaIdGp~GsGKgT~ak~La~---~lg~~~i   32 (223)
T d1q3ta_           3 TIQIAIDGPASSGKSTVAKIIAK---DFGFTYL   32 (223)
T ss_dssp             CCEEEEECSSCSSHHHHHHHHHH---HHCCEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH---HhCCcEE
Confidence            35677999999999987665544   3466633

>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=92.47  E-value=0.037  Score=44.43  Aligned_cols=22  Identities=32%  Similarity=0.483  Sum_probs=20.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|-|.+|||||+++.+.+.
T Consensus         7 ~KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           7 FKVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4899999999999999999875

>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=92.47  E-value=0.04  Score=45.47  Aligned_cols=25  Identities=24%  Similarity=0.306  Sum_probs=21.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+..++|.|+.|+|||++.+.++..
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHTT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            3568999999999999999887753

>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=92.34  E-value=0.039  Score=43.86  Aligned_cols=22  Identities=32%  Similarity=0.538  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|.|.+|+|||+++.+.+.
T Consensus         5 ~KivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           5 FKYIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3789999999999999998765

>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=92.28  E-value=0.033  Score=46.74  Aligned_cols=35  Identities=17%  Similarity=0.253  Sum_probs=28.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        25 ~~Gei~~l~G~NGsGKSTLl~~i~gl~~p~~G~I~~   60 (200)
T d1sgwa_          25 EKGNVVNFHGPNGIGKTTLLKTISTYLKPLKGEIIY   60 (200)
T ss_dssp             ETTCCEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcccccCCCEEEE
Confidence            4678899999999999999998866544 5577765

>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=92.28  E-value=0.035  Score=48.29  Aligned_cols=26  Identities=31%  Similarity=0.414  Sum_probs=22.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcc
Confidence            57889999999999999999876554

>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=92.26  E-value=0.037  Score=44.31  Aligned_cols=21  Identities=33%  Similarity=0.521  Sum_probs=19.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .|++|-|..|||||+++.+.+
T Consensus         6 ~KI~lvG~~~vGKTsll~~~~   26 (174)
T d2bmea1           6 FKFLVIGNAGTGKSCLLHQFI   26 (174)
T ss_dssp             EEEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHH
Confidence            479999999999999999876

>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=92.24  E-value=0.039  Score=45.26  Aligned_cols=22  Identities=36%  Similarity=0.511  Sum_probs=19.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|-|++|||||+++.+++.
T Consensus         7 ~KivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           7 FKLLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHhh
Confidence            4789999999999999999874

>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=92.24  E-value=0.053  Score=44.66  Aligned_cols=24  Identities=29%  Similarity=0.386  Sum_probs=20.4

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+..++|.|++|+|||++.+.++.
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHH
Confidence            356899999999999998887664

>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=92.21  E-value=0.031  Score=50.72  Aligned_cols=36  Identities=22%  Similarity=0.392  Sum_probs=25.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCc
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV  104 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~  104 (342)
                      ..|++|.|.-||||||++..+..+...++  |+++|.+
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~l~~~~--v~~~~EP   39 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVALGSRDD--IVYVPEP   39 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC----CC--EEEECCC
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHHhCCCC--eEEeccc
Confidence            46899999999999999998877665555  5566654

>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=92.18  E-value=0.045  Score=47.12  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=21.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++..+.|-|+.||||||+|.-+.-
T Consensus        24 ~~Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhc
Confidence            4678899999999999999886544

>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=92.12  E-value=0.037  Score=48.21  Aligned_cols=35  Identities=20%  Similarity=0.342  Sum_probs=26.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||++.-+.-.-. ..|=|.+
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl~ll~gl~~p~~G~I~i   74 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIASLITRFYDIDEGHILM   74 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHHHHHTTTTCCSEEEEEE
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcccCCCccEEEE
Confidence            4678999999999999999877765433 3455443

>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=92.07  E-value=0.044  Score=43.59  Aligned_cols=22  Identities=41%  Similarity=0.529  Sum_probs=19.7

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -+++|.|..|||||+++.+.+.
T Consensus         4 ~KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           4 YKLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4799999999999999998765

>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=92.04  E-value=0.043  Score=43.91  Aligned_cols=24  Identities=38%  Similarity=0.629  Sum_probs=21.0

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |.-+++|-|.+|||||++|.+.+.
T Consensus         3 pt~Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           3 PTYKLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCcCHHHHHHHHHh
Confidence            456899999999999999988765

>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=92.04  E-value=0.079  Score=44.30  Aligned_cols=35  Identities=17%  Similarity=0.045  Sum_probs=28.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      +.=++|.|..||||||....+..+-.+.|.=|+.+
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~   37 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   37 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            44577889999999999999999988888766554

>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=92.02  E-value=0.045  Score=43.77  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=20.8

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      |--|++|.|.+|||||+++.+.+.
T Consensus         3 ~~~KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           3 ALHKVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceeEEEEECCCCcCHHHHHHHHHh
Confidence            445899999999999999998764

>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=92.01  E-value=0.037  Score=48.30  Aligned_cols=25  Identities=20%  Similarity=0.235  Sum_probs=21.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++..+.|.|+.||||||+|.-+.-
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHh
Confidence            5788999999999999999875543

>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=91.97  E-value=0.049  Score=47.09  Aligned_cols=34  Identities=21%  Similarity=0.328  Sum_probs=25.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLL   98 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiV   98 (342)
                      .++.-+.|.|+.||||||+|..+.-.-. ..|=|.
T Consensus        30 ~~Ge~~~liGpsGaGKSTLl~~i~Gl~~p~sG~I~   64 (239)
T d1v43a3          30 KDGEFLVLLGPSGCGKTTTLRMIAGLEEPTEGRIY   64 (239)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSCCSEEEEE
T ss_pred             CCCCEEEEECCCCChHHHHHHHHHcCCCCCCCEEE
Confidence            4677899999999999999997765433 334443

>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=91.94  E-value=0.072  Score=46.95  Aligned_cols=37  Identities=19%  Similarity=0.305  Sum_probs=30.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~v  101 (342)
                      .++.|..|.|.+|+|||+++.+++..+. .+.-++||+
T Consensus        66 gkGQr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~  103 (276)
T d2jdid3          66 AKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFA  103 (276)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEE
T ss_pred             cCCCEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEE
Confidence            4688999999999999999999998854 344566666

>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=91.92  E-value=0.043  Score=44.40  Aligned_cols=21  Identities=29%  Similarity=0.442  Sum_probs=18.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .|++|-|.+|||||+++.+.+
T Consensus         6 ~Ki~ivG~~~vGKTsLi~~l~   26 (186)
T d2f7sa1           6 IKLLALGDSGVGKTTFLYRYT   26 (186)
T ss_dssp             EEEEEESCTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHh
Confidence            589999999999999998765

>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=91.87  E-value=0.04  Score=47.68  Aligned_cols=24  Identities=33%  Similarity=0.368  Sum_probs=19.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      .-+.|.||.||||||+|.-+.-.-
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC
Confidence            466788999999999998877643

>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=91.87  E-value=0.048  Score=43.81  Aligned_cols=22  Identities=41%  Similarity=0.493  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++++-|++|||||+++.+.+.
T Consensus         5 ~Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           5 FKVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4789999999999999988765

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=91.83  E-value=0.059  Score=49.24  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=22.0

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      ..-.+|+|++|||||+++.+++....
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~  188 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALI  188 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHH
Confidence            56899999999999999988776544

>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=91.81  E-value=0.048  Score=47.16  Aligned_cols=26  Identities=19%  Similarity=0.248  Sum_probs=21.4

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i~Gl   54 (240)
T d3dhwc1          29 PAGQIYGVIGASGAGKSTLIRCVNLL   54 (240)
T ss_dssp             CSSCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            45778999999999999998776543

>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=91.77  E-value=0.047  Score=43.60  Aligned_cols=20  Identities=35%  Similarity=0.394  Sum_probs=18.0

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +++|.|.+|||||+++.+..
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~   22 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFG   22 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHh
Confidence            68999999999999998764

>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=91.75  E-value=0.051  Score=48.03  Aligned_cols=26  Identities=23%  Similarity=0.346  Sum_probs=22.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .++..+.|.|+.||||||+|.-+.-.
T Consensus        60 ~~Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          60 EKGEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCC
Confidence            57889999999999999998877643

>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=91.64  E-value=0.044  Score=47.39  Aligned_cols=35  Identities=23%  Similarity=0.327  Sum_probs=26.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||++.-+.-... ..|=|.+
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl~ll~gl~~p~~G~I~i   62 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLI   62 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhcCCCCCCEEEE
Confidence            4688999999999999999887776543 3455544

>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=91.64  E-value=0.049  Score=43.71  Aligned_cols=21  Identities=48%  Similarity=0.515  Sum_probs=18.6

Q ss_pred             CeEEEEccCCCcHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      -+++|.|.+|||||+++.+..
T Consensus         4 ~Kv~lvG~~~vGKTsLi~~~~   24 (172)
T d2g3ya1           4 YRVVLIGEQGVGKSTLANIFA   24 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHH
Confidence            478999999999999998764

>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=91.59  E-value=0.041  Score=47.56  Aligned_cols=35  Identities=17%  Similarity=0.318  Sum_probs=25.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||++.-+.-.-. ..|=|.+
T Consensus        26 ~~Ge~vaivG~sGsGKSTLl~ll~gl~~p~~G~I~i   61 (242)
T d1mv5a_          26 QPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITI   61 (242)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSSCCSBSCEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHhhCCCCCEEEE
Confidence            4678999999999999988776654432 4566655

>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=91.56  E-value=0.054  Score=42.95  Aligned_cols=22  Identities=41%  Similarity=0.640  Sum_probs=19.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .|+++-|.+|||||+++.+.+.
T Consensus         3 ~Ki~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           3 MKILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3789999999999999988753

>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=91.55  E-value=0.052  Score=44.27  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ..+++|-|.+|||||+++.+.+.
T Consensus         3 ~iKvvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           3 TIKCVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCcCHHHHHHHHHh
Confidence            35899999999999999988765

>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=91.53  E-value=0.028  Score=47.22  Aligned_cols=34  Identities=21%  Similarity=0.272  Sum_probs=26.3

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIP  102 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP  102 (342)
                      ...++|.|.-||||||++..+..+.  +++-+..+|
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l--~~~~~~~e~   35 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLC--EDWEVVPEP   35 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGC--TTEEEECCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH--hcCCCeeee
Confidence            3578999999999999999877764  455555555

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.52  E-value=0.086  Score=43.35  Aligned_cols=37  Identities=16%  Similarity=0.160  Sum_probs=24.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHh-CCeEEEEeCC
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHE-NNYLLVHIPW  103 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~-~gwiVl~vP~  103 (342)
                      +..++|.+|.|||||++..-.+.++.. .+-+|+-+|.
T Consensus        40 ~~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~   77 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPL   77 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCEEEEcCCCCchhHHHHHHHHHHhhccCcceeeccc
Confidence            456899999999999876555555443 3444444454

>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=91.52  E-value=0.053  Score=44.05  Aligned_cols=25  Identities=24%  Similarity=0.287  Sum_probs=21.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +...|++|.|..|||||+++.+.+.
T Consensus         7 ~~~~Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1           7 ALMLKCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEEEECCCCCCHHHHHHHHhh
Confidence            3456899999999999999988764

>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=91.50  E-value=0.055  Score=43.49  Aligned_cols=24  Identities=33%  Similarity=0.523  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +..|++|.|.+|||||+++.+++.
T Consensus         6 ~~iKi~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           6 TTLKILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceeEEEEECCCCcCHHHHHHHHHh
Confidence            456899999999999999998764

>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=91.41  E-value=0.056  Score=43.78  Aligned_cols=22  Identities=23%  Similarity=0.321  Sum_probs=19.5

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+++|-|..|||||+++.+.+.
T Consensus         3 ~KivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           3 CKIVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            3789999999999999998765

>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=91.40  E-value=0.058  Score=43.00  Aligned_cols=22  Identities=36%  Similarity=0.514  Sum_probs=19.4

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -+++|.|++|||||+++.+.+.
T Consensus         7 fKi~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           7 FKVMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4799999999999999998764

>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=91.38  E-value=0.054  Score=43.14  Aligned_cols=20  Identities=25%  Similarity=0.361  Sum_probs=18.3

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++|.|++|+|||+++.++.
T Consensus         2 ~V~liG~~n~GKSsLi~~L~   21 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLV   21 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            57899999999999999886

>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=91.37  E-value=0.059  Score=43.66  Aligned_cols=25  Identities=28%  Similarity=0.333  Sum_probs=21.9

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|..|+++-|..|||||+++.+.+.
T Consensus         3 ~p~~ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           3 IPELRLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             CCEEEEEEECCTTTTHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHh
Confidence            3568999999999999999998764

>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=91.34  E-value=0.063  Score=43.81  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=19.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .-++|.||.|+|||+++.+++.
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            4689999999999999987764

>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=91.26  E-value=0.057  Score=43.99  Aligned_cols=23  Identities=30%  Similarity=0.384  Sum_probs=20.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .-+++.|.|.+|+|||+++..+.
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~   44 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLI   44 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHhc
Confidence            34689999999999999999987

>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=91.25  E-value=0.064  Score=44.09  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=17.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      ++-+.|.||+||||||.-..++.
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            34678889999999987665544

>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=91.23  E-value=0.075  Score=44.21  Aligned_cols=27  Identities=22%  Similarity=0.188  Sum_probs=21.4

Q ss_pred             EEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          71 VLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        71 vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -|||..||||||+...    ..+.|+-|+.-
T Consensus         7 gitG~igSGKStv~~~----l~~~G~~vida   33 (208)
T d1vhta_           7 ALTGGIGSGKSTVANA----FADLGINVIDA   33 (208)
T ss_dssp             EEECCTTSCHHHHHHH----HHHTTCEEEEH
T ss_pred             EEECCCcCCHHHHHHH----HHHCCCcEEEc
Confidence            3799999999997764    35779988853

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=91.17  E-value=0.049  Score=48.42  Aligned_cols=42  Identities=17%  Similarity=0.076  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          49 CMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        49 ~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      -+..+|+.|--    -.++-|..|.|++|+|||+++.+++..+..+
T Consensus        29 ~~~r~ID~l~P----igrGQr~~I~g~~g~GKT~l~~~i~~~~~~~   70 (289)
T d1xpua3          29 LTARVLDLASP----IGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN   70 (289)
T ss_dssp             HHHHHHHHHSC----CBTTCEEEEEECSSSSHHHHHHHHHHHHHHH
T ss_pred             ccceeeeeccc----ccCCCeeeEeCCCCCCHHHHHHHHHHHHhhc
Confidence            35556665533    3578999999999999999999999988654

>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=91.13  E-value=0.064  Score=46.33  Aligned_cols=25  Identities=24%  Similarity=0.401  Sum_probs=20.6

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++-.+-|.|+.||||||+|.-+.-
T Consensus        27 ~~Ge~~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          27 KDGEFMILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHT
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhc
Confidence            4577899999999999998875543

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.05  E-value=0.04  Score=48.11  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      --+|.|+.|||||++| +|+.|+.
T Consensus        26 lnvlvG~NgsGKS~iL-~Ai~~~l   48 (308)
T d1e69a_          26 VTAIVGPNGSGKSNII-DAIKWVF   48 (308)
T ss_dssp             EEEEECCTTTCSTHHH-HHHHHTS
T ss_pred             eEEEECCCCCcHHHHH-HHHHHHh
Confidence            4589999999999976 7887763

>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=91.03  E-value=0.044  Score=47.49  Aligned_cols=35  Identities=20%  Similarity=0.277  Sum_probs=26.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++..+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        29 ~~Ge~~~iiG~sGsGKSTll~~i~gl~~p~~G~I~~   64 (242)
T d1oxxk2          29 ENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYF   64 (242)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHHcCcCCCCceEEE
Confidence            4678999999999999999988776432 4455443

>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=90.98  E-value=0.13  Score=42.89  Aligned_cols=37  Identities=16%  Similarity=0.165  Sum_probs=27.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      ++.=+++.|.-||||||....+..+-. .+..++..|.
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L~-~~~~~~~~p~   38 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKLQ-PNCKLLKFPE   38 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHTT-TSEEEEESSC
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHHH-hCCEEEEECC
Confidence            456688999999999999888776644 4556666664

>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=90.92  E-value=0.059  Score=46.26  Aligned_cols=35  Identities=23%  Similarity=0.464  Sum_probs=26.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++.-+.|-|+.||||||+|.-+.-.-. ..|=|.+
T Consensus        24 ~~Ge~~~liGpsGaGKSTll~~l~Gl~~p~sG~I~~   59 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLFLELIAGFHVPDSGRILL   59 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhcCcCCCCCEEEE
Confidence            4677899999999999999988765432 3354444

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=90.74  E-value=0.075  Score=47.80  Aligned_cols=38  Identities=13%  Similarity=0.255  Sum_probs=27.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCCccc
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWVLR  106 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~~~~  106 (342)
                      ..+++.|+.||||||+|..++.+. ..+.-++.|=+..+
T Consensus       167 ~nili~G~tgSGKTT~l~al~~~i-~~~~rivtiEd~~E  204 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIMEFI-PKEERIISIEDTEE  204 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGS-CTTCCEEEEESSCC
T ss_pred             CCEEEEeeccccchHHHHHHhhhc-ccccceeeccchhh
Confidence            459999999999999998766554 34555666643333

>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=90.72  E-value=0.081  Score=44.26  Aligned_cols=24  Identities=21%  Similarity=0.332  Sum_probs=20.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +.=++|.||.|||||++...++.-
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhh
Confidence            455899999999999999988764

>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=90.67  E-value=0.064  Score=45.10  Aligned_cols=27  Identities=26%  Similarity=0.213  Sum_probs=22.9

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      ..+++.|.-||||||++.++..+....
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l~~~   29 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTYPEW   29 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCTTS
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhhc
Confidence            478999999999999999998875443

>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=90.51  E-value=0.17  Score=43.25  Aligned_cols=35  Identities=17%  Similarity=0.169  Sum_probs=27.6

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ..-+++.|+=|+||||+-+++.....+.|.=|+.|
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllv   54 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLT   54 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            34455569999999999999877777778777777

>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=90.44  E-value=0.076  Score=43.62  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=18.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++|.|++|||||++|.++..
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999998875

>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=90.42  E-value=0.043  Score=43.98  Aligned_cols=22  Identities=32%  Similarity=0.534  Sum_probs=9.8

Q ss_pred             CeEEEEccCCCcHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -|++|-|.+|||||+++.+.+.
T Consensus         7 ~Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           7 FKLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEEECCCCC-----------
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4789999999999999998864

>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=90.32  E-value=0.04  Score=44.21  Aligned_cols=21  Identities=33%  Similarity=0.562  Sum_probs=18.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      +++|.|..|||||+++.+.+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            789999999999999987654

>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=90.30  E-value=0.073  Score=43.10  Aligned_cols=20  Identities=30%  Similarity=0.336  Sum_probs=18.7

Q ss_pred             CeEEEEccCCCcHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~   87 (342)
                      .+++|-|..|||||++|.+.
T Consensus         3 iKivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           3 VKILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            58999999999999999988

>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=90.17  E-value=0.071  Score=42.74  Aligned_cols=24  Identities=21%  Similarity=0.223  Sum_probs=20.7

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..+++|-|..|+|||+++.|...-
T Consensus         2 e~KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           2 EVKLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhC
Confidence            358999999999999999997653

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=90.17  E-value=0.082  Score=43.17  Aligned_cols=25  Identities=20%  Similarity=0.347  Sum_probs=20.7

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+..++|.|++|+|||++.+.++..
T Consensus        14 ~g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc
Confidence            3568999999999999988776654

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

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: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=90.04  E-value=0.074  Score=46.03  Aligned_cols=38  Identities=18%  Similarity=0.175  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHH-HHHHHHHHHHhCCeEEEEe-C
Q psy3261          65 RPSPRFVLYGEHGVGKSM-ALVYALQYAHENNYLLVHI-P  102 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~-~L~q~~~~A~~~gwiVl~v-P  102 (342)
                      .+....+|.++.|||||+ .|..++..+..+|--|+++ |
T Consensus         7 ~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~P   46 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAP   46 (305)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEES
T ss_pred             hcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            356678899999999996 4556666666554333333 6

>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=89.99  E-value=0.089  Score=44.95  Aligned_cols=33  Identities=15%  Similarity=0.172  Sum_probs=25.8

Q ss_pred             CCCCCCHHHHHHhhcccccchhHHHHHHHHHHhc
Q psy3261         164 SEANIPLAALIEHGITRVKYASDVVDVLFTEIKK  197 (342)
Q Consensus       164 ~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~  197 (342)
                      .++|.-+.+.++.|.- +..+.+.+..+++||.+
T Consensus       191 ~EpgCaVk~av~~g~i-~~~Ry~~Y~~l~~el~~  223 (225)
T d1u0la2         191 DEPECGVKEAVENGEI-AESRYENYVKMFYELLG  223 (225)
T ss_dssp             SCSSCHHHHHHHHTSS-CHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHcCCC-CHHHHHHHHHHHHHHHh
Confidence            3567889999998865 45677888999999975

>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=89.60  E-value=0.051  Score=43.21  Aligned_cols=23  Identities=26%  Similarity=0.248  Sum_probs=20.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~   87 (342)
                      ....+++|.|.+++|||+++..+
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L   36 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTL   36 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTT
T ss_pred             ccCCEEEEECCCCCCHHHHHHHH
Confidence            35689999999999999999766

>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=89.58  E-value=0.11  Score=43.60  Aligned_cols=30  Identities=13%  Similarity=0.208  Sum_probs=22.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+-|||..||||||+...+..   ..|+.++..
T Consensus         3 iIgiTG~igSGKsTva~~l~e---~~g~~~i~~   32 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMS---NYSAVKYQL   32 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH---HSCEEECCT
T ss_pred             EEEEECCCCCCHHHHHHHHHH---hCCCeEEcc
Confidence            367999999999998776633   458777753

>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=89.45  E-value=0.12  Score=41.89  Aligned_cols=27  Identities=22%  Similarity=0.320  Sum_probs=20.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      +-|+|..||||||+...+    .+.|+-|+.
T Consensus         6 IgitG~~gSGKstva~~l----~~~g~~~~~   32 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALL----RSWGYPVLD   32 (191)
T ss_dssp             EEEEECTTSCHHHHHHHH----HHTTCCEEE
T ss_pred             EEEECCCCCCHHHHHHHH----HHCCCeEEE
Confidence            448999999999976544    356876664

>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=89.29  E-value=0.11  Score=42.93  Aligned_cols=27  Identities=26%  Similarity=0.206  Sum_probs=20.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEE
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVH  100 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~  100 (342)
                      +-|||..||||||+..    +..+.|+-|+.
T Consensus         5 IgITG~igSGKStv~~----~l~~~G~~vid   31 (205)
T d1jjva_           5 VGLTGGIGSGKTTIAN----LFTDLGVPLVD   31 (205)
T ss_dssp             EEEECSTTSCHHHHHH----HHHTTTCCEEE
T ss_pred             EEEECCCCCCHHHHHH----HHHHCCCeEEE
Confidence            3479999999999755    33567888775

>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=89.29  E-value=0.1  Score=41.59  Aligned_cols=20  Identities=25%  Similarity=0.366  Sum_probs=17.8

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++|.|.+|+|||+++..+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~   21 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLT   21 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            57899999999999998775

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=89.12  E-value=0.19  Score=45.03  Aligned_cols=36  Identities=14%  Similarity=0.102  Sum_probs=21.3

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEEEeCC
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQYAH-ENNYLLVHIPW  103 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl~vP~  103 (342)
                      ..++|+||+|||||.+...+..-+- .-..+.+..++
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~  160 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGE  160 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSC
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhH
Confidence            3456699999999876554443332 23455554433

>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=89.01  E-value=0.12  Score=41.46  Aligned_cols=24  Identities=25%  Similarity=0.319  Sum_probs=20.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +...|+.|.|..|+|||+++.-++
T Consensus         6 ~~~~kV~iiG~~~~GKSTLin~l~   29 (186)
T d1mkya2           6 TDAIKVAIVGRPNVGKSTLFNAIL   29 (186)
T ss_dssp             CSCEEEEEECSTTSSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
Confidence            346899999999999999998764

>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=88.93  E-value=0.11  Score=45.51  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=29.5

Q ss_pred             eEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          43 SILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        43 ~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .+.+-++++++++.++      .+..-+-+.|+.++|||++|.++..
T Consensus        14 ~l~~~~e~l~~l~~~~------~~v~vvsi~G~~~sGKS~llN~l~~   54 (277)
T d1f5na2          14 RLMANPEALKILSAIT------QPMVVVAIVGLYRTGKSYLMNKLAG   54 (277)
T ss_dssp             EEEECHHHHHHHHTCC------SBEEEEEEEEBTTSSHHHHHHHHTT
T ss_pred             eEEECHHHHHHHHcCC------CCEEEEEEECCCCCCHHHHHHHHcC
Confidence            3455666665544332      3566778899999999999999875

>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=88.92  E-value=0.12  Score=44.91  Aligned_cols=24  Identities=29%  Similarity=0.332  Sum_probs=20.2

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++-.+-|.|+.||||||++.-+.
T Consensus        26 ~~GEi~~iiG~sGsGKSTLl~~i~   49 (258)
T d1b0ua_          26 RAGDVISIIGSSGSGKSTFLRCIN   49 (258)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHT
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHH
Confidence            467889999999999998877654

>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=88.64  E-value=0.13  Score=42.42  Aligned_cols=21  Identities=24%  Similarity=0.216  Sum_probs=17.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      +-|+|+.||||||+...+...
T Consensus         5 IgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            458999999999988777665

>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=88.61  E-value=0.024  Score=45.29  Aligned_cols=22  Identities=36%  Similarity=0.456  Sum_probs=16.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+|+|+.|||||++|. |+.+|.
T Consensus        27 tvi~G~NGsGKStil~-Ai~~~L   48 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMA-AFVTAL   48 (222)
T ss_dssp             HHHHSCCSHHHHHHHH-HHHHHH
T ss_pred             EEEECCCCCCHHHHHH-HHHHHh
Confidence            4678999999999875 455554

>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=88.42  E-value=0.11  Score=47.92  Aligned_cols=23  Identities=26%  Similarity=0.242  Sum_probs=20.9

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ...++.|.|++|+|||++++.+.
T Consensus        55 ~~l~Iai~G~~n~GKSSLiNaL~   77 (400)
T d1tq4a_          55 SVLNVAVTGETGSGKSSFINTLR   77 (400)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHh
Confidence            46899999999999999999886

>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=88.40  E-value=0.081  Score=47.15  Aligned_cols=23  Identities=26%  Similarity=0.458  Sum_probs=19.1

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..++|.|++|||||+++.-+...
T Consensus        29 h~vLl~G~pG~GKT~lar~~~~i   51 (333)
T d1g8pa_          29 GGVLVFGDRGTGKSTAVRALAAL   51 (333)
T ss_dssp             CCEEEECCGGGCTTHHHHHHHHH
T ss_pred             CeEEEECCCCccHHHHHHHHHHh
Confidence            47999999999999997766543

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=88.38  E-value=0.41  Score=39.34  Aligned_cols=52  Identities=17%  Similarity=0.156  Sum_probs=32.9

Q ss_pred             eEEechhHHHHHHHHHhccCCCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEeCC
Q psy3261          43 SILIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPW  103 (342)
Q Consensus        43 ~~lvR~~t~el~~~l~~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~vP~  103 (342)
                      .+-+|+-=.+.++.+.+       ..+.+|.++.|+|||.+...++...  ++-+++-+|.
T Consensus        68 ~~~Lr~yQ~eav~~~~~-------~~~~ll~~~tG~GKT~~a~~~~~~~--~~~~Liv~p~  119 (206)
T d2fz4a1          68 EISLRDYQEKALERWLV-------DKRGCIVLPTGSGKTHVAMAAINEL--STPTLIVVPT  119 (206)
T ss_dssp             CCCCCHHHHHHHHHHTT-------TSEEEEEESSSTTHHHHHHHHHHHS--CSCEEEEESS
T ss_pred             CCCcCHHHHHHHHHHHh-------CCCcEEEeCCCCCceehHHhHHHHh--cCceeEEEcc
Confidence            34577755566665543       4577899999999998766555432  3444444453

>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=88.31  E-value=0.13  Score=41.24  Aligned_cols=23  Identities=22%  Similarity=0.212  Sum_probs=20.0

Q ss_pred             CeEEEEccCCCcHHHHHHHHHHH
Q psy3261          68 PRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        68 ~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .+++|-|..|+|||++|.+...-
T Consensus         3 ~Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           3 LKLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            57899999999999999987543

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=88.21  E-value=0.19  Score=42.96  Aligned_cols=33  Identities=21%  Similarity=0.355  Sum_probs=27.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++.++|+=|+||||+..++.+...++|+=|+-|
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllI   35 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVV   35 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEE
Confidence            566899999999999999888777888766665

>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=88.02  E-value=0.45  Score=39.17  Aligned_cols=30  Identities=10%  Similarity=0.016  Sum_probs=25.0

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      +....++++|++||||+++......+....
T Consensus        13 ~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~   42 (198)
T d2gnoa2          13 SEGISILINGEDLSYPREVSLELPEYVEKF   42 (198)
T ss_dssp             CSSEEEEEECSSSSHHHHHHHHHHHHHHTS
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            457899999999999999988888766433

>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=87.97  E-value=0.11  Score=43.55  Aligned_cols=30  Identities=20%  Similarity=0.077  Sum_probs=24.3

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhC
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHEN   94 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   94 (342)
                      .++.-+.|+|.+||||||+...+...-.+.
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~l~~~   51 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQLVRD   51 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            567789999999999999888877665443

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {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: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=87.94  E-value=0.56  Score=37.66  Aligned_cols=36  Identities=14%  Similarity=0.182  Sum_probs=22.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHH-HHHhCCe-EEEEeCCc
Q psy3261          69 RFVLYGEHGVGKSMALVYALQ-YAHENNY-LLVHIPWV  104 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~-~A~~~gw-iVl~vP~~  104 (342)
                      ..++.+|.|+|||.+..-++. ++.+++. +|+-+|..
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~   62 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTK   62 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSH
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCch
Confidence            367889999999986554443 3344444 44444643

>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=87.78  E-value=0.37  Score=42.67  Aligned_cols=32  Identities=28%  Similarity=0.358  Sum_probs=22.7

Q ss_pred             CCCCCCeEEEEccCCCcHHHHHHHHHHHHHhCC
Q psy3261          63 FDRPSPRFVLYGEHGVGKSMALVYALQYAHENN   95 (342)
Q Consensus        63 ~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~g   95 (342)
                      .+.+..-+++.||+|||||.+..++.. +....
T Consensus        48 ~~~p~~~~lf~Gp~GvGKT~lak~la~-~l~~~   79 (315)
T d1r6bx3          48 EHKPVGSFLFAGPTGVGKTEVTVQLSK-ALGIE   79 (315)
T ss_dssp             TTSCSEEEEEECSTTSSHHHHHHHHHH-HHTCE
T ss_pred             CCCCceEEEEECCCcchhHHHHHHHHh-hccCC
Confidence            344555799999999999888777544 44433

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=87.77  E-value=0.13  Score=45.26  Aligned_cols=37  Identities=16%  Similarity=0.256  Sum_probs=30.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      .+..|..|.|++|+|||+++.+++.....++-+++++
T Consensus        65 g~GQr~~Ifg~~g~GKt~l~~~~~~~~~~~~~v~V~~  101 (276)
T d1fx0a3          65 GRGQRELIIGDRQTGKTAVATDTILNQQGQNVICVYV  101 (276)
T ss_dssp             BTTCBCBEEESSSSSHHHHHHHHHHTCCTTTCEEEEE
T ss_pred             cCCceEeeccCCCCChHHHHHHHHhhhcccCceeeee
Confidence            3688999999999999999999877666666677775

>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=87.76  E-value=0.2  Score=42.72  Aligned_cols=30  Identities=17%  Similarity=0.031  Sum_probs=23.8

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHHH--hCCe
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYAH--ENNY   96 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A~--~~gw   96 (342)
                      .+-+||||+..+|||+.|.++..-..  +-|+
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~   72 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGS   72 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTC
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCC
Confidence            45689999999999999999876554  3454

>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=87.27  E-value=0.13  Score=43.79  Aligned_cols=24  Identities=33%  Similarity=0.418  Sum_probs=20.1

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      .++.-+-|-|+.||||||+|..+.
T Consensus        23 ~~Gei~~iiG~nGaGKSTLl~~l~   46 (231)
T d1l7vc_          23 RAGEILHLVGPNGAGKSTLLARMA   46 (231)
T ss_dssp             ETTCEEECBCCTTSSHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHh
Confidence            367788999999999999987654

>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=87.08  E-value=0.18  Score=43.28  Aligned_cols=35  Identities=17%  Similarity=0.289  Sum_probs=25.8

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++.-+-|-|+.||||||++.-+.-.-. ..|=|.+
T Consensus        30 ~~Gei~~liGpnGaGKSTl~~~i~Gl~~p~~G~I~~   65 (240)
T d1ji0a_          30 PRGQIVTLIGANGAGKTTTLSAIAGLVRAQKGKIIF   65 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCCCCCccEEEe
Confidence            4677889999999999999988766433 3344443

>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=87.06  E-value=0.17  Score=42.32  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=19.9

Q ss_pred             CCeEEEEccCCCcHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~   88 (342)
                      ..|++|-|..|+|||++|.|..
T Consensus         6 ~~KilllG~~~vGKTsll~~~~   27 (221)
T d1azta2           6 THRLLLLGAGESGKSTIVKQMR   27 (221)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHH
T ss_pred             cCEEEEECCCCCCHHHHHHHHh
Confidence            5689999999999999999874

>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=86.60  E-value=0.074  Score=41.54  Aligned_cols=20  Identities=45%  Similarity=0.582  Sum_probs=18.4

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      +++|.|.+|+|||+++..+.
T Consensus         2 kI~liG~~n~GKSSLin~l~   21 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLL   21 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            78999999999999999875

>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=86.24  E-value=0.2  Score=39.97  Aligned_cols=20  Identities=35%  Similarity=0.378  Sum_probs=17.8

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~   88 (342)
                      -++|.|.+|+|||+++..+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~   26 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLL   26 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            58999999999999998764

>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=86.21  E-value=0.2  Score=39.60  Aligned_cols=19  Identities=37%  Similarity=0.443  Sum_probs=17.6

Q ss_pred             EEEEccCCCcHHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYAL   88 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~   88 (342)
                      ++|.|.+|+|||+++..+.
T Consensus         8 I~iiG~~nvGKSSLin~L~   26 (179)
T d1egaa1           8 IAIVGRPNVGKSTLLNKLL   26 (179)
T ss_dssp             EEEECSSSSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6789999999999999986

>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=86.02  E-value=0.11  Score=44.47  Aligned_cols=123  Identities=18%  Similarity=0.114  Sum_probs=57.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHH-HhCCeEEEEeCCccccccCCcceeccC----CCCCc--cccHH-HHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYA-HENNYLLVHIPWVLRWFAYPKEVSHSL----TKEGM--VDLNI-DAAMWLRHF  137 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A-~~~gwiVl~vP~~~~~~~~~~~~~~s~----~~~~~--~~qP~-~a~~~L~~~  137 (342)
                      ++...+|.|+.|+|||++++.++--. ..-|=|--..-.+++-+....-|.++-    -.||+  |..+. ...++...|
T Consensus        96 ~~~~~vl~G~SGVGKSSLiN~L~~~~~~~t~~vs~~~~rGrHTTt~~~l~~~~gg~iiDTPG~r~~~l~~~~~~~l~~~F  175 (231)
T d1t9ha2          96 QDKTTVFAGQSGVGKSSLLNAISPELGLRTNEISEHLGRGKHTTRHVELIHTSGGLVADTPGFSSLEFTDIEEEELGYTF  175 (231)
T ss_dssp             TTSEEEEEESHHHHHHHHHHHHCC-------------------CCCCCEEEETTEEEESSCSCSSCCCTTCCHHHHGGGS
T ss_pred             ccceEEEECCCCccHHHHHHhhccHhHhhhcccccccCCCceeeeeEEEEecCCCEEEECCccccccccccCcccchhhh
Confidence            45678899999999999999876432 221222111112222222211111110    02332  22221 112222223


Q ss_pred             HHhCccccCCCCcccccceecCC-CCCCCCCCCHHHHHHhhcccccchhHHHHHHHHHHhcc
Q psy3261         138 QKQNTKWLEDPRLTTSQEYVWSP-REKSEANIPLAALIEHGITRVKYASDVVDVLFTEIKKL  198 (342)
Q Consensus       138 ~~~N~~~L~~~~l~~s~~~~~~~-~e~~~~g~tL~dlv~~gi~~~~~a~~~~~~l~~EL~~~  198 (342)
                      ... .+..+  +.+      |.. .....+|.-+.+-++.|.- +....+.+..+++|++.+
T Consensus       176 ~ei-~~~~~--~Ck------F~dC~H~~EpgCaV~~av~~g~i-~~~Ry~~Y~~l~~e~~~~  227 (231)
T d1t9ha2         176 PDI-REKSS--SCK------FRGCLHLKEPKCAVKQAVEDGEL-KQYRYDHYVEFMTEIKDR  227 (231)
T ss_dssp             HHH-HHHGG--GCS------STTCCSSSCSSCHHHHHHHHTSS-CHHHHHHHHHHHHHHHTT
T ss_pred             hhH-HHHhC--CCC------CCCCCCCCCCCchHHHHHHcCCC-CHHHHHHHHHHHHHHHHh
Confidence            221 01122  222      322 1123567889999988875 346778899999999875

>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=85.72  E-value=0.23  Score=42.88  Aligned_cols=35  Identities=14%  Similarity=0.261  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++.-+-|.|+.||||||++.-+.-.-. ..|-|.+
T Consensus        28 ~~Gei~~liG~nGaGKSTLl~~i~Gl~~p~~G~I~~   63 (254)
T d1g6ha_          28 NKGDVTLIIGPNGSGKSTLINVITGFLKADEGRVYF   63 (254)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHHCCCcCCCcEEEE
Confidence            4577889999999999999887765433 3355554

>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=84.91  E-value=0.28  Score=41.93  Aligned_cols=35  Identities=23%  Similarity=0.312  Sum_probs=25.7

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH-hCCeEEE
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH-ENNYLLV   99 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~gwiVl   99 (342)
                      .++.-+-|-|+.||||||+|.-+.-.-. .+|=|.+
T Consensus        26 ~~Gei~glvG~nGaGKSTLl~~l~G~~~p~~G~i~i   61 (238)
T d1vpla_          26 EEGEIFGLIGPNGAGKTTTLRIISTLIKPSSGIVTV   61 (238)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCCCCCCEEEE
Confidence            4567788999999999999987665433 3455554

>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=84.49  E-value=0.32  Score=41.09  Aligned_cols=24  Identities=25%  Similarity=0.162  Sum_probs=21.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      -.+|||+..+|||+.|.|+.....
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l~~i   60 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTALIAL   60 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCccccchhhhhhHHHHH
Confidence            589999999999999999877654

>d2akab1 c.37.1.8 (B:6-304) Dynamin G 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: G proteins
domain: Dynamin G domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=84.41  E-value=0.59  Score=40.32  Aligned_cols=40  Identities=25%  Similarity=0.350  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhc---cC--CCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          50 MLELVGYLKSM---TN--FDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        50 t~el~~~l~~~---~~--~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      -++|++.|+..   ..  ..-.-+++++.|..++|||++|.-++-
T Consensus         4 ~~~~~~~l~d~l~~lg~~~~~~~P~ivvvG~~SsGKSsliNaLlg   48 (299)
T d2akab1           4 LIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVG   48 (299)
T ss_dssp             HHHHHHHHHHHHTTSCCCTTCCCCEEEEEEBTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCeEEEEcCCCCCHHHHHHHHhC
Confidence            35667766531   22  123457899999999999999998874

>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=84.33  E-value=0.59  Score=40.46  Aligned_cols=36  Identities=11%  Similarity=0.012  Sum_probs=25.4

Q ss_pred             HHHHhccC-CCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          55 GYLKSMTN-FDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        55 ~~l~~~~~-~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      ..|..+.+ ..++.+-++|+|+.++|||+++.-+.+.
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~  127 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHH
Confidence            34444333 3467889999999999999997554443

>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=84.01  E-value=0.22  Score=39.83  Aligned_cols=19  Identities=37%  Similarity=0.300  Sum_probs=16.9

Q ss_pred             eEEEEccCCCcHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~   87 (342)
                      .+-|.|++++|||+++..+
T Consensus         3 ~VaiiG~~nvGKSSLin~L   21 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVV   21 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            5789999999999999865

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, 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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.77  E-value=0.48  Score=36.63  Aligned_cols=32  Identities=25%  Similarity=0.240  Sum_probs=27.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          70 FVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      -+++||=.||||+-|.+.++.+...|--|+-+
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~i   36 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIAQYKCLVI   36 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHcCCcEEEE
Confidence            47889999999999999999998887766665

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.10  E-value=0.22  Score=44.75  Aligned_cols=23  Identities=26%  Similarity=0.382  Sum_probs=18.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      --+|+|+.|||||++|- |++||.
T Consensus        27 l~~i~G~NGsGKS~ile-Ai~~~l   49 (427)
T d1w1wa_          27 FTSIIGPNGSGKSNMMD-AISFVL   49 (427)
T ss_dssp             EEEEECSTTSSHHHHHH-HHHHHT
T ss_pred             EEEEECCCCCCHHHHHH-HHHHHh
Confidence            35899999999999876 445653

>d1jwyb_ c.37.1.8 (B:) Dynamin G domain {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: G proteins
domain: Dynamin G domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=82.46  E-value=0.6  Score=40.51  Aligned_cols=40  Identities=23%  Similarity=0.337  Sum_probs=29.0

Q ss_pred             HHHHHHHHHhccC----CCCCCCeEEEEccCCCcHHHHHHHHHH
Q psy3261          50 MLELVGYLKSMTN----FDRPSPRFVLYGEHGVGKSMALVYALQ   89 (342)
Q Consensus        50 t~el~~~l~~~~~----~~~~~~r~vL~G~~GsGKS~~L~q~~~   89 (342)
                      .++|++.|.....    ..-.-+++++.|..++|||++|.-++-
T Consensus         3 l~~~~n~l~d~~~~~~~~~~~lP~ivVvG~~ssGKSSliNaLlG   46 (306)
T d1jwyb_           3 LIPVINKLQDVFNTLGSDPLDLPQIVVVGSQSSGKSSVLENIVG   46 (306)
T ss_dssp             HHHHHHHHHHHTTTSSSCTTCCCEEEEEECSSSSHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhCcCCCCCCeEEEEeCCCCCHHHHHHHHhC
Confidence            4567777754211    122346899999999999999998884

>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=82.14  E-value=0.41  Score=44.66  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=19.5

Q ss_pred             CCeEEEEccCCCcHHHHHHHHHHHH
Q psy3261          67 SPRFVLYGEHGVGKSMALVYALQYA   91 (342)
Q Consensus        67 ~~r~vL~G~~GsGKS~~L~q~~~~A   91 (342)
                      ...++|.||+|||||.+...+...+
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l   73 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLA   73 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHh
Confidence            4579999999999998777555443

>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=82.06  E-value=0.55  Score=40.38  Aligned_cols=33  Identities=21%  Similarity=0.339  Sum_probs=24.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHHHHhCCeEEEEe
Q psy3261          69 RFVLYGEHGVGKSMALVYALQYAHENNYLLVHI  101 (342)
Q Consensus        69 r~vL~G~~GsGKS~~L~q~~~~A~~~gwiVl~v  101 (342)
                      ++.++|+=|+||||+-.++.+...+.|.=|+-|
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlI   36 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIV   36 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            577899999999999998766444555544444

>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=81.92  E-value=0.8  Score=36.53  Aligned_cols=42  Identities=21%  Similarity=0.166  Sum_probs=28.3

Q ss_pred             hHHHHHHHHHhcc--CCCCCCCeEEEEccCCCcHHHHHHHHHHH
Q psy3261          49 CMLELVGYLKSMT--NFDRPSPRFVLYGEHGVGKSMALVYALQY   90 (342)
Q Consensus        49 ~t~el~~~l~~~~--~~~~~~~r~vL~G~~GsGKS~~L~q~~~~   90 (342)
                      .|.++...|-+..  ....++.-++|.|+=|+|||++...++..
T Consensus        13 ~t~~lg~~la~~l~~~~~~~g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          13 SMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             HHHHHHHHHHHHHHHHCCSSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCCeEEEEecCCCccHHHHHHHHHhh
Confidence            4555555554311  12345667999999999999998877654

>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=81.66  E-value=0.38  Score=42.29  Aligned_cols=28  Identities=14%  Similarity=0.247  Sum_probs=24.5

Q ss_pred             CCCCeEEEEccCCCcHHHHHHHHHHHHH
Q psy3261          65 RPSPRFVLYGEHGVGKSMALVYALQYAH   92 (342)
Q Consensus        65 ~~~~r~vL~G~~GsGKS~~L~q~~~~A~   92 (342)
                      .+.-|+.|.|++|+|||++|.+++....
T Consensus        66 g~GQr~~If~~~g~GKt~ll~~~~~~~~   93 (285)
T d2jdia3          66 GRGQRELIIGDRQTGKTSIAIDTIINQK   93 (285)
T ss_dssp             BTTCBCEEEESTTSSHHHHHHHHHHHTH
T ss_pred             cCCCEEEeecCCCCChHHHHHHHHHhHH
Confidence            4688999999999999999999887654

>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=81.14  E-value=0.32  Score=38.63  Aligned_cols=18  Identities=33%  Similarity=0.254  Sum_probs=16.3

Q ss_pred             EEEEccCCCcHHHHHHHH
Q psy3261          70 FVLYGEHGVGKSMALVYA   87 (342)
Q Consensus        70 ~vL~G~~GsGKS~~L~q~   87 (342)
                      +.|.|.+|+|||+++..+
T Consensus         4 VaivG~~nvGKSTLin~L   21 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAM   21 (180)
T ss_dssp             EEEECCGGGCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            678899999999999876

>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=80.52  E-value=0.92  Score=38.48  Aligned_cols=80  Identities=19%  Similarity=0.205  Sum_probs=46.5

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhCCe--EEEEe-CCcccccc-----CCcceeccCCCCCccccHHHHHHHHHHH
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHENNY--LLVHI-PWVLRWFA-----YPKEVSHSLTKEGMVDLNIDAAMWLRHF  137 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~gw--iVl~v-P~~~~~~~-----~~~~~~~s~~~~~~~~qP~~a~~~L~~~  137 (342)
                      ...-+++.|+=|+||||+-+.+.....+.|-  ++|-. |. .++..     -..........++++..-......++.+
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~Dp~-~~l~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTDPA-SNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQY   85 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECCTT-CCHHHHTTSCCCSSCEECTTSTTEEEEECCHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCCCC-CCHHHHhCCCCcccccccccccccchhccChhhHHHHH
Confidence            3456677899999999998887776666554  55555 32 22211     0111111112356666666666777777


Q ss_pred             HHhCccccC
Q psy3261         138 QKQNTKWLE  146 (342)
Q Consensus       138 ~~~N~~~L~  146 (342)
                      .....+.+.
T Consensus        86 ~~~~~~~~~   94 (296)
T d1ihua1          86 RARIVDPIK   94 (296)
T ss_dssp             HHHHHGGGT
T ss_pred             Hhhccchhh
Confidence            655555455

>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=80.50  E-value=0.54  Score=41.30  Aligned_cols=41  Identities=17%  Similarity=0.093  Sum_probs=27.3

Q ss_pred             CCCeEEEEccCCCcHHHHHHHHHHHHHhC--CeEEEEeCCccc
Q psy3261          66 PSPRFVLYGEHGVGKSMALVYALQYAHEN--NYLLVHIPWVLR  106 (342)
Q Consensus        66 ~~~r~vL~G~~GsGKS~~L~q~~~~A~~~--gwiVl~vP~~~~  106 (342)
                      +.+-+-|+|..||||||+...+.+.....  .++||...+=..
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsfyr   45 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFHR   45 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGBS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCCCc
Confidence            44567899999999999988888776654  566776654433